SRX5611570 GSM3693430 SRP189992 SRS4559247 GSM3693430 Bisulfite-Seq GENOMIC Reduced Representation The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples. The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature's protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C's EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer's protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads). The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads. RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample Illumina HiSeq 3000 gds 303693430 GSM3693430 GEO Accession GSM3693430 SRX5611571 GSM3693431 SRP189992 SRS4559248 GSM3693431 Bisulfite-Seq GENOMIC Reduced Representation The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples. The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature's protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C's EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer's protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads). The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads. RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample Illumina HiSeq 3000 gds 303693431 GSM3693431 GEO Accession GSM3693431 SRX5611572 GSM3693432 SRP189992 SRS4559249 GSM3693432 Bisulfite-Seq GENOMIC Reduced Representation The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples. The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature's protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C's EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer's protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads). The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads. RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample Illumina HiSeq 3000 gds 303693432 GSM3693432 GEO Accession GSM3693432 SRX5611573 GSM3693433 SRP189992 SRS4559250 GSM3693433 Bisulfite-Seq GENOMIC Reduced Representation The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples. The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature's protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C's EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer's protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads). The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads. RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample Illumina HiSeq 3000 gds 303693433 GSM3693433 GEO Accession GSM3693433 SRX5611574 GSM3693434 SRP189992 SRS4559251 GSM3693434 Bisulfite-Seq GENOMIC Reduced Representation The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples. The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature's protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C's EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer's protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads). The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads. RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample Illumina HiSeq 3000 gds 303693434 GSM3693434 GEO Accession GSM3693434 SRX5611575 GSM3693435 SRP189992 SRS4559252 GSM3693435 Bisulfite-Seq GENOMIC Reduced Representation The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples. The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature's protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C's EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer's protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads). The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads. RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample Illumina HiSeq 3000 gds 303693435 GSM3693435 GEO Accession GSM3693435 SRX5611576 GSM3693436 SRP189992 SRS4559253 GSM3693436 Bisulfite-Seq GENOMIC Reduced Representation The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples. The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature's protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C's EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer's protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads). The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads. RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample Illumina HiSeq 3000 gds 303693436 GSM3693436 GEO Accession GSM3693436 SRX5611577 GSM3693437 SRP189992 SRS4559254 GSM3693437 Bisulfite-Seq GENOMIC Reduced Representation The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples. The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature's protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C's EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer's protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads). The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads. RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample Illumina HiSeq 3000 gds 303693437 GSM3693437 GEO Accession GSM3693437 SRX5611578 GSM3693438 SRP189992 SRS4559255 GSM3693438 Bisulfite-Seq GENOMIC Reduced Representation The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples. The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature's protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C's EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer's protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads). The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads. RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample Illumina HiSeq 3000 gds 303693438 GSM3693438 GEO Accession GSM3693438 SRX5611579 GSM3693439 SRP189992 SRS4559256 GSM3693439 Bisulfite-Seq GENOMIC Reduced Representation The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples. The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature's protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C's EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer's protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads). The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads. RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample Illumina HiSeq 3000 gds 303693439 GSM3693439 GEO Accession GSM3693439 SRX5611580 GSM3693440 SRP189992 SRS4559257 GSM3693440 Bisulfite-Seq GENOMIC Reduced Representation The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples. The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature's protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C's EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer's protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads). The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads. RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample Illumina HiSeq 3000 gds 303693440 GSM3693440 GEO Accession GSM3693440 SRX5611581 GSM3693441 SRP189992 SRS4559258 GSM3693441 Bisulfite-Seq GENOMIC Reduced Representation The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples. The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature's protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C's EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer's protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads). The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads. RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample Illumina HiSeq 3000 gds 303693441 GSM3693441 GEO Accession GSM3693441