Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history

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 single nucleotide polymorphism (SNP) loci. Highland and Lowland quinoa were clustered into two main groups, with F ST divergence of 0.36 and linkage disequilibrium (LD) decay of 6.5 and 49.8 kb, respectively. A genome-wide association study using multi-year phenotyping trials uncovered 600 SNPs stably associated with 17 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 important for adaptation. 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. As human populations grow and climate change tightens its grip, developing nutritious crops which can thrive on poor soil and under difficult conditions will become a priority. Quinoa, a harvest currently overlooked by agricultural research, could be an interesting candidate in this effort. With its high nutritional value and its ability to tolerate drought, frost and high concentrations of salt in the soil, this hardy crop has been cultivated in the Andes for the last 5,000 to 7,000 years. Today its commercial production is mainly limited to Peru, Bolivia, and Ecuador. Pinpointing the genetic regions that control traits such as yields or flowering time would help agronomists to create new varieties better suited to life under northern latitudes and mechanical farming. To identify these genes, Patiranage et al. grew 310 varieties of quinoa from all over the world under the same conditions; the genomes of these plants were also examined in great detail. Analyses were then performed to link specific genetic variations with traits relevant to agriculture, helping to pinpoint changes in the genetic code linked to differences in how the plants grew, resisted disease, or produced seeds of varying quality. Candidate genes likely to control these traits were then put forward. The study by Patiranage et al. provides a genetic map where genes of agronomical impo