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

Citation

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

Abstract

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.

Methods

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. 

Usage Notes

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)

Funding

Competitive Research Grant of the King Abdullah University of Science and Technology, Saudi Arabia , Award: OSR-2016-CRG5- 466 2966-02