Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history
Type
ArticleAuthors
Patiranage, Dilan Sarange RajapakshaRey, Elodie

Emrani, Nazgol
Wellman, Gordon

Schmid, Karl

Schmöckel, Sandra M
Tester, Mark A.

Jung, Christian

KAUST Department
Biological and Environmental Science and Engineering (BESE) DivisionPlant Science
Center for Desert Agriculture
KAUST Grant Number
OSR-2016-CRG5- 466 2966-02Date
2022-07-08Permanent link to this record
http://hdl.handle.net/10754/667681
Metadata
Show full item recordAbstract
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 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.Citation
Patiranage, D. S. R., Rey, E., Emrani, N., Wellman, G., Schmid, K., Schmöckel, S. M., Tester, M., & Jung, C. (2022). Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.66873Sponsors
We 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.Publisher
eLife Sciences Publications, LtdJournal
eLifePubMed ID
35801689Additional Links
https://elifesciences.org/articles/66873Relations
Is Supplemented By:- [Dataset]
Rajapaksha Patiranage, Dilan Sarange et al. (2021), Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history [Data set]. https://doi.org/10.5061/dryad.zgmsbcc9m. DOI: 10.5061/dryad.zgmsbcc9m Handle: 100754/668590
ae974a485f413a2113503eed53cd6c53
10.7554/elife.66873
Scopus Count
Except where otherwise noted, this item's license is described as Archived with thanks to eLife under a Creative Commons license, details at: http://creativecommons.org/licenses/by/4.0/
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