Genome-wide association study in the pseudocereal quinoa reveals selection pattern typical for crops with a short breeding history
AuthorsPatiranage, Dilan S. R.
Schmöckel, Sandra M.
Tester, Mark A.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Desert Agriculture Initiative
The Salt Lab
Water Desalination and Reuse Research Center (WDRC)
KAUST Grant NumberOSR-2016-CRG5- 466 2966-02
Permanent link to this recordhttp://hdl.handle.net/10754/667681
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AbstractQuinoa 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.
CitationPatiranage, D. S. R., Rey, E., Emrani, N., Wellman, G., Schmid, K., Schmöckel, S. M., … Jung, C. (2020). Genome-wide association study in the pseudocereal quinoa reveals selection pattern typical for crops with a short breeding history. doi:10.1101/2020.12.03.410050
SponsorsWe thank David Jarvis for providing the updated version of the quinoa reference genome. We thank Monika Bruisch, Brigitte Neidhardt-Olf, Elisabeth Kokai-Kota, Verena Kowalewski, and Gabriele Fiene for technical assistance. The financial support of this work was provided by the Competitive Research Grant (Grant No. OSR-2016-CRG5- 466 2966-02) of the King Abdullah University of Science and Technology, Saudi Arabia and baseline funding from KAUST to Mark Tester.
PublisherCold Spring Harbor Laboratory
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