Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history
Rajapaksha Patiranage, Dilan Sarange et al. (2022), Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history, Dryad, Dataset, https://doi.org/10.5061/dryad.zgmsbcc9m
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 FST 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
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)
Competitive Research Grant of the King Abdullah University of Science and Technology, Saudi Arabia , Award: OSR-2016-CRG5- 466 2966-02