ERP124671 PRJEB40957 ena-STUDY-KAUST-25-10-2020-13:05:13:122-212 296 accessions of Chenopodium quinoa Quinoa germplasm preserves useful and substantial genetic variation, yet it remains untapped due to a lack of implementation of modern breeding tools. We have integrated field and sequence data to characterize a large diversity panel of quinoa. Whole-genome sequencing of 310 accessions revealed 2.8 million polymorphic high confidence SNP loci. Highland and Lowland quinoa were clustered into two main groups, with FST divergence of 0.36. Diverged selection pressure was observed between two groups where lowland quinoa underwent strict selection. Fast LD decay was identified, ranging between 6.5 and 49.8 Kb, which is typical for crops with a short breeding history. A genome-wide association study uncovered 600 stably associated SNP loci with 17 agronomic traits. A SNP density of 2.39 SNPs/kb enabled the identification of candidate genes controlling these traits. We identified two candidate genes associated with thousand seed weight and a resistant gene analog associated with downy mildew resistance. We also identified pleiotropically acting loci for four agronomic traits that are highly influenced by the photoperiod hence important for the adaptation to different environments, e.g. long-day conditions in Europe and North America. This work demonstrates the use of re-sequence data of an orphan crop, which is partially domesticated to rapidly identify marker-trait association and provides the underpinning elements for genomic-enabled quinoa breeding. Quinoa re-sequencing Quinoa germplasm preserves useful and substantial genetic variation, yet it remains untapped due to a lack of implementation of modern breeding tools. We have integrated field and sequence data to characterize a large diversity panel of quinoa. Whole-genome sequencing of 310 accessions revealed 2.8 million polymorphic high confidence SNP loci. Highland and Lowland quinoa were clustered into two main groups, with FST divergence of 0.36. Diverged selection pressure was observed between two groups where lowland quinoa underwent strict selection. Fast LD decay was identified, ranging between 6.5 and 49.8 Kb, which is typical for crops with a short breeding history. A genome-wide association study uncovered 600 stably associated SNP loci with 17 agronomic traits. A SNP density of 2.39 SNPs/kb enabled the identification of candidate genes controlling these traits. We identified two candidate genes associated with thousand seed weight and a resistant gene analog associated with downy mildew resistance. We also identified pleiotropically acting loci for four agronomic traits that are highly influenced by the photoperiod hence important for the adaptation to different environments, e.g. long-day conditions in Europe and North America. This work demonstrates the use of re-sequence data of an orphan crop, which is partially domesticated to rapidly identify marker-trait association and provides the underpinning elements for genomic-enabled quinoa breeding. ENA-FIRST-PUBLIC 2022-01-05 ENA-LAST-UPDATE 2022-01-05