SRX3648646 GSM2978514 SRP132196 SRS2913213 GSM2978514 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978514 GSM2978514 GEO Accession GSM2978514 SRX3648647 GSM2978515 SRP132196 SRS2913214 GSM2978515 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978515 GSM2978515 GEO Accession GSM2978515 SRX3648648 GSM2978516 SRP132196 SRS2913215 GSM2978516 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978516 GSM2978516 GEO Accession GSM2978516 SRX3648649 GSM2978517 SRP132196 SRS2913216 GSM2978517 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978517 GSM2978517 GEO Accession GSM2978517 SRX3648650 GSM2978518 SRP132196 SRS2913217 GSM2978518 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978518 GSM2978518 GEO Accession GSM2978518 SRX3648651 GSM2978519 SRP132196 SRS2913218 GSM2978519 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978519 GSM2978519 GEO Accession GSM2978519 SRX3648652 GSM2978520 SRP132196 SRS2913219 GSM2978520 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978520 GSM2978520 GEO Accession GSM2978520 SRX3648653 GSM2978521 SRP132196 SRS2913220 GSM2978521 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978521 GSM2978521 GEO Accession GSM2978521 SRX3648654 GSM2978522 SRP132196 SRS2913221 GSM2978522 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978522 GSM2978522 GEO Accession GSM2978522 SRX3648655 GSM2978523 SRP132196 SRS2913222 GSM2978523 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978523 GSM2978523 GEO Accession GSM2978523 SRX3648656 GSM2978524 SRP132196 SRS2913223 GSM2978524 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978524 GSM2978524 GEO Accession GSM2978524 SRX3648657 GSM2978525 SRP132196 SRS2913224 GSM2978525 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978525 GSM2978525 GEO Accession GSM2978525 SRX3648658 GSM2978526 SRP132196 SRS2913225 GSM2978526 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978526 GSM2978526 GEO Accession GSM2978526 SRX3648659 GSM2978527 SRP132196 SRS2913226 GSM2978527 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978527 GSM2978527 GEO Accession GSM2978527 SRX3648660 GSM2978528 SRP132196 SRS2913227 GSM2978528 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978528 GSM2978528 GEO Accession GSM2978528 SRX3648661 GSM2978529 SRP132196 SRS2913228 GSM2978529 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978529 GSM2978529 GEO Accession GSM2978529 SRX3648662 GSM2978530 SRP132196 SRS2913229 GSM2978530 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978530 GSM2978530 GEO Accession GSM2978530 SRX3648663 GSM2978531 SRP132196 SRS2913230 GSM2978531 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978531 GSM2978531 GEO Accession GSM2978531 SRX3648664 GSM2978532 SRP132196 SRS2913231 GSM2978532 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978532 GSM2978532 GEO Accession GSM2978532 SRX3648665 GSM2978533 SRP132196 SRS2913232 GSM2978533 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978533 GSM2978533 GEO Accession GSM2978533 SRX3648666 GSM2978534 SRP132196 SRS2913233 GSM2978534 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978534 GSM2978534 GEO Accession GSM2978534 SRX3648667 GSM2978535 SRP132196 SRS2913234 GSM2978535 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978535 GSM2978535 GEO Accession GSM2978535 SRX3648668 GSM2978536 SRP132196 SRS2913235 GSM2978536 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978536 GSM2978536 GEO Accession GSM2978536 SRX3648669 GSM2978537 SRP132196 SRS2913236 GSM2978537 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978537 GSM2978537 GEO Accession GSM2978537 SRX3648670 GSM2978538 SRP132196 SRS2913237 GSM2978538 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978538 GSM2978538 GEO Accession GSM2978538 SRX3648671 GSM2978539 SRP132196 SRS2913238 GSM2978539 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978539 GSM2978539 GEO Accession GSM2978539 SRX3648672 GSM2978540 SRP132196 SRS2913239 GSM2978540 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978540 GSM2978540 GEO Accession GSM2978540 SRX3648673 GSM2978541 SRP132196 SRS2913240 GSM2978541 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978541 GSM2978541 GEO Accession GSM2978541 SRX3648674 GSM2978542 SRP132196 SRS2913241 GSM2978542 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978542 GSM2978542 GEO Accession GSM2978542 SRX3648675 GSM2978543 SRP132196 SRS2913242 GSM2978543 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978543 GSM2978543 GEO Accession GSM2978543 SRX3648676 GSM2978544 SRP132196 SRS2913243 GSM2978544 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978544 GSM2978544 GEO Accession GSM2978544 SRX3648677 GSM2978545 SRP132196 SRS2913244 GSM2978545 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978545 GSM2978545 GEO Accession GSM2978545 SRX3648678 GSM2978546 SRP132196 SRS2913245 GSM2978546 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978546 GSM2978546 GEO Accession GSM2978546 SRX3648679 GSM2978547 SRP132196 SRS2913246 GSM2978547 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978547 GSM2978547 GEO Accession GSM2978547 SRX3648680 GSM2978548 SRP132196 SRS2913247 GSM2978548 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978548 GSM2978548 GEO Accession GSM2978548 SRX3648681 GSM2978549 SRP132196 SRS2913248 GSM2978549 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978549 GSM2978549 GEO Accession GSM2978549 SRX3648682 GSM2978550 SRP132196 SRS2913249 GSM2978550 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978550 GSM2978550 GEO Accession GSM2978550 SRX3648683 GSM2978551 SRP132196 SRS2913250 GSM2978551 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978551 GSM2978551 GEO Accession GSM2978551 SRX3648684 GSM2978552 SRP132196 SRS2913251 GSM2978552 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978552 GSM2978552 GEO Accession GSM2978552 SRX3648685 GSM2978553 SRP132196 SRS2913252 GSM2978553 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978553 GSM2978553 GEO Accession GSM2978553 SRX3648686 GSM2978554 SRP132196 SRS2913253 GSM2978554 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978554 GSM2978554 GEO Accession GSM2978554 SRX3648687 GSM2978555 SRP132196 SRS2913254 GSM2978555 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978555 GSM2978555 GEO Accession GSM2978555 SRX3648688 GSM2978556 SRP132196 SRS2913255 GSM2978556 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978556 GSM2978556 GEO Accession GSM2978556 SRX3648689 GSM2978557 SRP132196 SRS2913273 GSM2978557 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978557 GSM2978557 GEO Accession GSM2978557 SRX3648690 GSM2978558 SRP132196 SRS2913256 GSM2978558 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978558 GSM2978558 GEO Accession GSM2978558 SRX3648691 GSM2978559 SRP132196 SRS2913257 GSM2978559 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978559 GSM2978559 GEO Accession GSM2978559 SRX3648692 GSM2978560 SRP132196 SRS2913258 GSM2978560 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978560 GSM2978560 GEO Accession GSM2978560 SRX3648693 GSM2978561 SRP132196 SRS2913259 GSM2978561 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978561 GSM2978561 GEO Accession GSM2978561 SRX3648694 GSM2978562 SRP132196 SRS2913260 GSM2978562 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978562 GSM2978562 GEO Accession GSM2978562 SRX3648695 GSM2978563 SRP132196 SRS2913261 GSM2978563 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978563 GSM2978563 GEO Accession GSM2978563 SRX3648696 GSM2978564 SRP132196 SRS2913262 GSM2978564 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978564 GSM2978564 GEO Accession GSM2978564 SRX3648697 GSM2978565 SRP132196 SRS2913263 GSM2978565 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978565 GSM2978565 GEO Accession GSM2978565 SRX3648698 GSM2978566 SRP132196 SRS2913264 GSM2978566 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978566 GSM2978566 GEO Accession GSM2978566 SRX3648699 GSM2978567 SRP132196 SRS2913265 GSM2978567 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978567 GSM2978567 GEO Accession GSM2978567 SRX3648700 GSM2978568 SRP132196 SRS2913266 GSM2978568 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978568 GSM2978568 GEO Accession GSM2978568 SRX3648701 GSM2978569 SRP132196 SRS2913267 GSM2978569 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978569 GSM2978569 GEO Accession GSM2978569 SRX3648702 GSM2978570 SRP132196 SRS2913268 GSM2978570 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978570 GSM2978570 GEO Accession GSM2978570 SRX3648703 GSM2978571 SRP132196 SRS2913269 GSM2978571 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978571 GSM2978571 GEO Accession GSM2978571 SRX3648704 GSM2978572 SRP132196 SRS2913270 GSM2978572 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978572 GSM2978572 GEO Accession GSM2978572 SRX3648705 GSM2978573 SRP132196 SRS2913271 GSM2978573 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978573 GSM2978573 GEO Accession GSM2978573 SRX3648706 GSM2978574 SRP132196 SRS2913272 GSM2978574 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978574 GSM2978574 GEO Accession GSM2978574 SRX3648707 GSM2978575 SRP132196 SRS2913274 GSM2978575 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978575 GSM2978575 GEO Accession GSM2978575 SRX3648708 GSM2978576 SRP132196 SRS2913275 GSM2978576 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978576 GSM2978576 GEO Accession GSM2978576 SRX3648709 GSM2978577 SRP132196 SRS2913276 GSM2978577 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978577 GSM2978577 GEO Accession GSM2978577 SRX3648710 GSM2978578 SRP132196 SRS2913277 GSM2978578 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978578 GSM2978578 GEO Accession GSM2978578 SRX3648711 GSM2978579 SRP132196 SRS2913278 GSM2978579 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978579 GSM2978579 GEO Accession GSM2978579 SRX3648712 GSM2978580 SRP132196 SRS2913279 GSM2978580 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978580 GSM2978580 GEO Accession GSM2978580 SRX3648713 GSM2978581 SRP132196 SRS2913280 GSM2978581 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978581 GSM2978581 GEO Accession GSM2978581 SRX3648714 GSM2978582 SRP132196 SRS2913281 GSM2978582 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978582 GSM2978582 GEO Accession GSM2978582 SRX3648715 GSM2978583 SRP132196 SRS2913282 GSM2978583 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978583 GSM2978583 GEO Accession GSM2978583 SRX3648716 GSM2978584 SRP132196 SRS2913283 GSM2978584 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978584 GSM2978584 GEO Accession GSM2978584 SRX3648717 GSM2978585 SRP132196 SRS2913284 GSM2978585 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978585 GSM2978585 GEO Accession GSM2978585 SRX3648718 GSM2978586 SRP132196 SRS2913285 GSM2978586 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978586 GSM2978586 GEO Accession GSM2978586 SRX3648719 GSM2978587 SRP132196 SRS2913286 GSM2978587 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978587 GSM2978587 GEO Accession GSM2978587 SRX3648720 GSM2978588 SRP132196 SRS2913287 GSM2978588 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978588 GSM2978588 GEO Accession GSM2978588 SRX3648721 GSM2978589 SRP132196 SRS2913288 GSM2978589 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978589 GSM2978589 GEO Accession GSM2978589 SRX3648722 GSM2978590 SRP132196 SRS2913289 GSM2978590 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978590 GSM2978590 GEO Accession GSM2978590 SRX3648723 GSM2978591 SRP132196 SRS2913290 GSM2978591 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978591 GSM2978591 GEO Accession GSM2978591 SRX3648724 GSM2978592 SRP132196 SRS2913291 GSM2978592 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978592 GSM2978592 GEO Accession GSM2978592 SRX3648725 GSM2978593 SRP132196 SRS2913292 GSM2978593 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978593 GSM2978593 GEO Accession GSM2978593 SRX3648726 GSM2978594 SRP132196 SRS2913293 GSM2978594 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978594 GSM2978594 GEO Accession GSM2978594 SRX3648727 GSM2978595 SRP132196 SRS2913294 GSM2978595 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978595 GSM2978595 GEO Accession GSM2978595 SRX3648728 GSM2978596 SRP132196 SRS2913295 GSM2978596 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978596 GSM2978596 GEO Accession GSM2978596 SRX3648729 GSM2978597 SRP132196 SRS2913296 GSM2978597 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978597 GSM2978597 GEO Accession GSM2978597 SRX3648730 GSM2978598 SRP132196 SRS2913297 GSM2978598 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978598 GSM2978598 GEO Accession GSM2978598 SRX3648731 GSM2978599 SRP132196 SRS2913298 GSM2978599 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978599 GSM2978599 GEO Accession GSM2978599 SRX3648732 GSM2978600 SRP132196 SRS2913321 GSM2978600 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978600 GSM2978600 GEO Accession GSM2978600 SRX3648733 GSM2978601 SRP132196 SRS2913299 GSM2978601 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978601 GSM2978601 GEO Accession GSM2978601 SRX3648734 GSM2978602 SRP132196 SRS2913300 GSM2978602 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978602 GSM2978602 GEO Accession GSM2978602 SRX3648735 GSM2978603 SRP132196 SRS2913301 GSM2978603 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978603 GSM2978603 GEO Accession GSM2978603 SRX3648736 GSM2978604 SRP132196 SRS2913302 GSM2978604 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978604 GSM2978604 GEO Accession GSM2978604 SRX3648737 GSM2978605 SRP132196 SRS2913303 GSM2978605 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978605 GSM2978605 GEO Accession GSM2978605 SRX3648738 GSM2978606 SRP132196 SRS2913304 GSM2978606 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978606 GSM2978606 GEO Accession GSM2978606 SRX3648739 GSM2978607 SRP132196 SRS2913305 GSM2978607 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978607 GSM2978607 GEO Accession GSM2978607 SRX3648740 GSM2978608 SRP132196 SRS2913306 GSM2978608 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978608 GSM2978608 GEO Accession GSM2978608 SRX3648741 GSM2978609 SRP132196 SRS2913307 GSM2978609 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978609 GSM2978609 GEO Accession GSM2978609 SRX3648742 GSM2978610 SRP132196 SRS2913308 GSM2978610 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978610 GSM2978610 GEO Accession GSM2978610 SRX3648743 GSM2978611 SRP132196 SRS2913309 GSM2978611 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978611 GSM2978611 GEO Accession GSM2978611 SRX3648744 GSM2978612 SRP132196 SRS2913310 GSM2978612 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978612 GSM2978612 GEO Accession GSM2978612 SRX3648745 GSM2978613 SRP132196 SRS2913311 GSM2978613 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978613 GSM2978613 GEO Accession GSM2978613 SRX3648746 GSM2978614 SRP132196 SRS2913312 GSM2978614 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978614 GSM2978614 GEO Accession GSM2978614 SRX3648747 GSM2978615 SRP132196 SRS2913313 GSM2978615 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978615 GSM2978615 GEO Accession GSM2978615 SRX3648748 GSM2978616 SRP132196 SRS2913314 GSM2978616 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978616 GSM2978616 GEO Accession GSM2978616 SRX3648749 GSM2978617 SRP132196 SRS2913315 GSM2978617 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978617 GSM2978617 GEO Accession GSM2978617 SRX3648750 GSM2978618 SRP132196 SRS2913316 GSM2978618 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978618 GSM2978618 GEO Accession GSM2978618 SRX3648751 GSM2978619 SRP132196 SRS2913317 GSM2978619 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978619 GSM2978619 GEO Accession GSM2978619 SRX3648752 GSM2978620 SRP132196 SRS2913318 GSM2978620 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978620 GSM2978620 GEO Accession GSM2978620 SRX3648753 GSM2978621 SRP132196 SRS2913319 GSM2978621 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978621 GSM2978621 GEO Accession GSM2978621 SRX3648754 GSM2978622 SRP132196 SRS2913320 GSM2978622 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978622 GSM2978622 GEO Accession GSM2978622 SRX3648755 GSM2978623 SRP132196 SRS2913332 GSM2978623 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978623 GSM2978623 GEO Accession GSM2978623 SRX3648756 GSM2978624 SRP132196 SRS2913322 GSM2978624 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978624 GSM2978624 GEO Accession GSM2978624 SRX3648757 GSM2978625 SRP132196 SRS2913323 GSM2978625 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978625 GSM2978625 GEO Accession GSM2978625 SRX3648758 GSM2978626 SRP132196 SRS2913324 GSM2978626 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978626 GSM2978626 GEO Accession GSM2978626 SRX3648759 GSM2978627 SRP132196 SRS2913325 GSM2978627 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978627 GSM2978627 GEO Accession GSM2978627 SRX3648760 GSM2978628 SRP132196 SRS2913326 GSM2978628 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978628 GSM2978628 GEO Accession GSM2978628 SRX3648761 GSM2978629 SRP132196 SRS2913327 GSM2978629 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978629 GSM2978629 GEO Accession GSM2978629 SRX3648762 GSM2978630 SRP132196 SRS2913343 GSM2978630 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978630 GSM2978630 GEO Accession GSM2978630 SRX3648763 GSM2978631 SRP132196 SRS2913328 GSM2978631 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978631 GSM2978631 GEO Accession GSM2978631 SRX3648764 GSM2978632 SRP132196 SRS2913329 GSM2978632 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978632 GSM2978632 GEO Accession GSM2978632 SRX3648765 GSM2978633 SRP132196 SRS2913330 GSM2978633 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978633 GSM2978633 GEO Accession GSM2978633 SRX3648766 GSM2978634 SRP132196 SRS2913331 GSM2978634 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978634 GSM2978634 GEO Accession GSM2978634 SRX3648767 GSM2978635 SRP132196 SRS2913333 GSM2978635 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978635 GSM2978635 GEO Accession GSM2978635 SRX3648768 GSM2978636 SRP132196 SRS2913334 GSM2978636 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978636 GSM2978636 GEO Accession GSM2978636 SRX3648769 GSM2978637 SRP132196 SRS2913335 GSM2978637 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978637 GSM2978637 GEO Accession GSM2978637 SRX3648770 GSM2978638 SRP132196 SRS2913336 GSM2978638 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978638 GSM2978638 GEO Accession GSM2978638 SRX3648771 GSM2978639 SRP132196 SRS2913337 GSM2978639 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978639 GSM2978639 GEO Accession GSM2978639 SRX3648772 GSM2978640 SRP132196 SRS2913338 GSM2978640 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978640 GSM2978640 GEO Accession GSM2978640 SRX3648773 GSM2978641 SRP132196 SRS2913339 GSM2978641 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978641 GSM2978641 GEO Accession GSM2978641 SRX3648774 GSM2978642 SRP132196 SRS2913340 GSM2978642 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 2000 gds 302978642 GSM2978642 GEO Accession GSM2978642 SRX3648775 GSM2978643 SRP132196 SRS2913341 GSM2978643 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978643 GSM2978643 GEO Accession GSM2978643 SRX3648776 GSM2978644 SRP132196 SRS2913342 GSM2978644 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978644 GSM2978644 GEO Accession GSM2978644 SRX3648777 GSM2978645 SRP132196 SRS2913344 GSM2978645 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978645 GSM2978645 GEO Accession GSM2978645 SRX3648778 GSM2978646 SRP132196 SRS2913345 GSM2978646 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978646 GSM2978646 GEO Accession GSM2978646 SRX3648779 GSM2978647 SRP132196 SRS2913346 GSM2978647 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978647 GSM2978647 GEO Accession GSM2978647 SRX3648780 GSM2978648 SRP132196 SRS2913347 GSM2978648 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978648 GSM2978648 GEO Accession GSM2978648 SRX3648781 GSM2978649 SRP132196 SRS2913348 GSM2978649 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978649 GSM2978649 GEO Accession GSM2978649 SRX3648782 GSM2978650 SRP132196 SRS2913349 GSM2978650 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978650 GSM2978650 GEO Accession GSM2978650 SRX3648783 GSM2978651 SRP132196 SRS2913350 GSM2978651 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978651 GSM2978651 GEO Accession GSM2978651 SRX3648784 GSM2978652 SRP132196 SRS2913351 GSM2978652 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978652 GSM2978652 GEO Accession GSM2978652 SRX3648785 GSM2978653 SRP132196 SRS2913352 GSM2978653 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978653 GSM2978653 GEO Accession GSM2978653 SRX3648786 GSM2978654 SRP132196 SRS2913353 GSM2978654 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978654 GSM2978654 GEO Accession GSM2978654 SRX3648787 GSM2978655 SRP132196 SRS2913354 GSM2978655 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978655 GSM2978655 GEO Accession GSM2978655 SRX3648788 GSM2978656 SRP132196 SRS2913355 GSM2978656 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978656 GSM2978656 GEO Accession GSM2978656 SRX3648789 GSM2978657 SRP132196 SRS2913356 GSM2978657 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978657 GSM2978657 GEO Accession GSM2978657 SRX3648790 GSM2978658 SRP132196 SRS2913357 GSM2978658 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978658 GSM2978658 GEO Accession GSM2978658 SRX3648791 GSM2978659 SRP132196 SRS2913358 GSM2978659 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978659 GSM2978659 GEO Accession GSM2978659 SRX3648792 GSM2978660 SRP132196 SRS2913359 GSM2978660 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978660 GSM2978660 GEO Accession GSM2978660 SRX3648793 GSM2978661 SRP132196 SRS2913360 GSM2978661 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978661 GSM2978661 GEO Accession GSM2978661 SRX3648794 GSM2978662 SRP132196 SRS2913361 GSM2978662 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978662 GSM2978662 GEO Accession GSM2978662 SRX3648795 GSM2978663 SRP132196 SRS2913362 GSM2978663 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978663 GSM2978663 GEO Accession GSM2978663 SRX3648796 GSM2978664 SRP132196 SRS2913363 GSM2978664 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978664 GSM2978664 GEO Accession GSM2978664 SRX3648797 GSM2978665 SRP132196 SRS2913364 GSM2978665 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978665 GSM2978665 GEO Accession GSM2978665 SRX3648798 GSM2978666 SRP132196 SRS2913365 GSM2978666 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978666 GSM2978666 GEO Accession GSM2978666 SRX3648799 GSM2978667 SRP132196 SRS2913366 GSM2978667 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978667 GSM2978667 GEO Accession GSM2978667 SRX3648800 GSM2978668 SRP132196 SRS2913367 GSM2978668 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978668 GSM2978668 GEO Accession GSM2978668 SRX3648801 GSM2978669 SRP132196 SRS2913368 GSM2978669 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978669 GSM2978669 GEO Accession GSM2978669 SRX3648802 GSM2978670 SRP132196 SRS2913369 GSM2978670 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978670 GSM2978670 GEO Accession GSM2978670 SRX3648803 GSM2978671 SRP132196 SRS2913370 GSM2978671 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978671 GSM2978671 GEO Accession GSM2978671 SRX3648804 GSM2978672 SRP132196 SRS2913371 GSM2978672 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978672 GSM2978672 GEO Accession GSM2978672 SRX3648805 GSM2978673 SRP132196 SRS2913372 GSM2978673 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978673 GSM2978673 GEO Accession GSM2978673 SRX3648806 GSM2978674 SRP132196 SRS2913373 GSM2978674 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978674 GSM2978674 GEO Accession GSM2978674 SRX3648807 GSM2978675 SRP132196 SRS2913374 GSM2978675 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978675 GSM2978675 GEO Accession GSM2978675 SRX3648808 GSM2978676 SRP132196 SRS2913375 GSM2978676 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978676 GSM2978676 GEO Accession GSM2978676 SRX3648809 GSM2978677 SRP132196 SRS2913376 GSM2978677 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978677 GSM2978677 GEO Accession GSM2978677 SRX3648810 GSM2978678 SRP132196 SRS2913377 GSM2978678 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978678 GSM2978678 GEO Accession GSM2978678 SRX3648811 GSM2978679 SRP132196 SRS2913378 GSM2978679 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978679 GSM2978679 GEO Accession GSM2978679 SRX3648812 GSM2978680 SRP132196 SRS2913379 GSM2978680 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978680 GSM2978680 GEO Accession GSM2978680 SRX3648813 GSM2978681 SRP132196 SRS2913380 GSM2978681 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978681 GSM2978681 GEO Accession GSM2978681 SRX3648814 GSM2978682 SRP132196 SRS2913381 GSM2978682 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978682 GSM2978682 GEO Accession GSM2978682 SRX3648815 GSM2978683 SRP132196 SRS2913382 GSM2978683 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978683 GSM2978683 GEO Accession GSM2978683 SRX3648816 GSM2978684 SRP132196 SRS2913383 GSM2978684 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978684 GSM2978684 GEO Accession GSM2978684 SRX3648817 GSM2978685 SRP132196 SRS2913384 GSM2978685 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978685 GSM2978685 GEO Accession GSM2978685 SRX3648818 GSM2978686 SRP132196 SRS2913385 GSM2978686 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978686 GSM2978686 GEO Accession GSM2978686 SRX3648819 GSM2978687 SRP132196 SRS2913386 GSM2978687 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978687 GSM2978687 GEO Accession GSM2978687 SRX3648820 GSM2978688 SRP132196 SRS2913387 GSM2978688 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978688 GSM2978688 GEO Accession GSM2978688 SRX3648821 GSM2978689 SRP132196 SRS2913388 GSM2978689 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978689 GSM2978689 GEO Accession GSM2978689 SRX3648822 GSM2978690 SRP132196 SRS2913389 GSM2978690 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978690 GSM2978690 GEO Accession GSM2978690 SRX3648823 GSM2978691 SRP132196 SRS2913390 GSM2978691 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978691 GSM2978691 GEO Accession GSM2978691 SRX3648824 GSM2978692 SRP132196 SRS2913391 GSM2978692 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978692 GSM2978692 GEO Accession GSM2978692 SRX3648825 GSM2978693 SRP132196 SRS2913392 GSM2978693 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978693 GSM2978693 GEO Accession GSM2978693 SRX3648826 GSM2978694 SRP132196 SRS2913393 GSM2978694 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978694 GSM2978694 GEO Accession GSM2978694 SRX3648827 GSM2978695 SRP132196 SRS2913395 GSM2978695 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978695 GSM2978695 GEO Accession GSM2978695 SRX3648828 GSM2978696 SRP132196 SRS2913394 GSM2978696 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978696 GSM2978696 GEO Accession GSM2978696 SRX3648829 GSM2978697 SRP132196 SRS2913396 GSM2978697 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978697 GSM2978697 GEO Accession GSM2978697 SRX3648830 GSM2978698 SRP132196 SRS2913397 GSM2978698 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978698 GSM2978698 GEO Accession GSM2978698 SRX3648831 GSM2978699 SRP132196 SRS2913398 GSM2978699 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978699 GSM2978699 GEO Accession GSM2978699 SRX3648832 GSM2978700 SRP132196 SRS2913399 GSM2978700 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978700 GSM2978700 GEO Accession GSM2978700 SRX3648833 GSM2978701 SRP132196 SRS2913400 GSM2978701 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978701 GSM2978701 GEO Accession GSM2978701 SRX3648834 GSM2978702 SRP132196 SRS2913401 GSM2978702 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978702 GSM2978702 GEO Accession GSM2978702 SRX3648835 GSM2978703 SRP132196 SRS2913403 GSM2978703 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978703 GSM2978703 GEO Accession GSM2978703 SRX3648836 GSM2978704 SRP132196 SRS2913402 GSM2978704 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978704 GSM2978704 GEO Accession GSM2978704 SRX3648837 GSM2978705 SRP132196 SRS2913405 GSM2978705 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978705 GSM2978705 GEO Accession GSM2978705 SRX3648838 GSM2978706 SRP132196 SRS2913404 GSM2978706 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978706 GSM2978706 GEO Accession GSM2978706 SRX3648839 GSM2978707 SRP132196 SRS2913406 GSM2978707 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978707 GSM2978707 GEO Accession GSM2978707 SRX3648840 GSM2978708 SRP132196 SRS2913407 GSM2978708 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978708 GSM2978708 GEO Accession GSM2978708 SRX3648841 GSM2978709 SRP132196 SRS2913409 GSM2978709 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978709 GSM2978709 GEO Accession GSM2978709 SRX3648842 GSM2978710 SRP132196 SRS2913408 GSM2978710 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978710 GSM2978710 GEO Accession GSM2978710 SRX3648843 GSM2978711 SRP132196 SRS2913410 GSM2978711 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978711 GSM2978711 GEO Accession GSM2978711 SRX3648844 GSM2978712 SRP132196 SRS2913411 GSM2978712 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978712 GSM2978712 GEO Accession GSM2978712 SRX3648845 GSM2978713 SRP132196 SRS2913412 GSM2978713 OTHER GENOMIC other Genomic DNA was isolated from whole blood using the NRBC Blood DNA Kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer's instruction. In this study, the red jungle fowl genome (Gallus_Gallus 4.0, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002315.2_Gallus_gallus-4.0) was chosen as the reference genome to perform enzyme digestion prediction with in-house related software. The fragments predictably digested by the enzyme that was selected for genome digestion should be in line with below rules, including a low proportion of that locating repetitive sequences, a uniform distribution across the genome to the greatest extent, a preferable identity between the fragment length and the experiment system and the digested fragments number predicted meeting the expectation (i.e., 100,000 SLAF). We herein selected restriction enzyme HaeIII to digest QYP DNA samples, predictably giving rise to 113,202 SLAF, with the length ranging from 364-444 bp. After digested by HaeIII, the genomic DNA fragments (SLAF) from each sample was added with A-tailing at 3' end, further ligated with Dual-index adaptor, and then amplified by PCR. After that, SLAF from each sample was purified and then mixed for further target fragment selection via gel electrophoresis and extraction, thereby obtaining the SLAF library for high-sequencing. Ultimately, SLAF libraries from each sample were sequenced on Illumina HiSeq 2500 platform, according to Illumina instructions (operated by Biomarker Biological Technology Co., Ltd., Beijing, China). We herein developed a total of 622,443 SLAF markers, including 424,810 polymorphic ones, and their corresponding average sequencing depth reached 10.03 ×. Illumina HiSeq 4000 gds 302978713 GSM2978713 GEO Accession GSM2978713