Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history
- Christian-Albrechts University of Kiel, Germany
- King Abdullah University of Science and Technology, Saudi Arabia
- University of Hohenheim, Germany
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 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.
Data availability
The raw sequencing data have been submitted to the NCBI Sequence Read Archive (SRA) under the BioProject PRJNA673789. Quinoa reference genome version 2 is available at CoGe database under genome id 53523. Phenotype data and ready-use genotype data (vcf file) are available at https://doi.org/10.5061/dryad.zgmsbcc9m. A detailed description of the germplasm, phenotyping methods, and phenotypes are available at https://quinoa.kaust.edu.sa/#/ (Stanschewski et al., 2021). Seeds are available from the public gene banks such as IPK Gatersleben (https://www.ipk-gatersleben.de/en/genebank/) and the U.S. National Plant Germplasm System (https://npgsweb.ars-grin.gov/gringlobal/search).Custom scripts used for SNP calling are available on GitHub: https://github.com/IBEXCluster/ IBEX-SNPcaller/blob/master/workflow.sh. Additional information of other custom scripts used for making plots are available at https://github.com/DilanSarange/quinoaDPgwas
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Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding historyDryad Digital Repository, doi:10.5061/dryad.zgmsbcc9m.
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Chenopodium quinoa diversity genome re-sequencingNCBI BioProject, PRJNA673789.
Article and author information
Author details
Funding
King Abdullah University of Science and Technology (OSR-2016-CRG5- 466 2966-02)
- Dilan Sarange Rajapaksha Patiranage
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Patiranage et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history
eLife 11:e66873.
https://doi.org/10.7554/eLife.66873
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