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 2.9 million polymorphic high confidence SNP loci. Highland and Lowland quinoa were clustered into two main groups, with F_ST divergence of 0.36 and fast LD decay of 6.5 and 49.8 Kb, respectively. A genome-wide association study uncovered 600 SNPs stably associated with 17 agronomic traits. Two candidate genes are associated with thousand seed weight, and a resistance gene analog is associated with downy mildew resistance. We also identified pleiotropically acting loci for four agronomic traits that are highly responding to photoperiod hence important for the adaptation to different environments. This work demonstrates the use of re-sequencing data of an orphan crop, which is partially domesticated to rapidly identify marker-trait association and provides the underpinning elements for genomics-enabled quinoa breeding.

This data set contains genotype and phenotype data reported in this publication. CSV file includes the phenotype data, and genotype data is provided in .vcf format. For additional information please see the ReadMe file. 

Phenotype data were collected from a field experiment in Kiel. 

Accession ID and names are given in the Table S1 

Abbreviations: 

DTB- Days to bolting

DTF - Days to Flowering

DTBtoDTF- Duration between bolting and flowering

DTM - Days to Maturity

PH- Plant height

PD -Panicle density

NoB- Nuber of branches

STL- Stem lying 

Saponin- Foam height (Saponin content)

Yield- Seed yield (g) per plant 

FC- Flower color (conditional mean)

SC- Stem color  (conditional mean)

GT- Growth type (conditional mean)

PSH- Panicle shape  (conditional mean)