1. Genetics and Genomics

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

  1. Dilan Sarange Rajapaksha Patiranage
  2. Elodie Rey
  3. Nazgol Emrani  Is a corresponding author
  4. Gordon Wellman
  5. Karl Schmid
  6. Sandra M Schmöckel
  7. Mark Tester
  8. Christian Jung  Is a corresponding author
  1. Christian-Albrechts University of Kiel, Germany
  2. King Abdullah University of Science and Technology, Saudi Arabia
  3. University of Hohenheim, Germany
https://doi.org/10.7554/eLife.66873
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Cite this article
  1. Dilan Sarange Rajapaksha Patiranage
  2. Elodie Rey
  3. Nazgol Emrani
  4. Gordon Wellman
  5. Karl Schmid
  6. Sandra M Schmöckel
  7. Mark Tester
  8. Christian Jung
(2022)
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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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

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Dilan Sarange Rajapaksha Patiranage

    Plant Breeding Institute, Christian-Albrechts University of Kiel, Kiel, Germany
    Competing interests
    The authors declare that no competing interests exist.

  2. Elodie Rey

    Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    Competing interests
    The authors declare that no competing interests exist.

  3. Nazgol Emrani

    Plant Breeding Institute, Christian-Albrechts University of Kiel, Kiel, Germany
    For correspondence
    n.emrani@plantbreeding.uni-kiel.de
    Competing interests
    The authors declare that no competing interests exist.

  4. Gordon Wellman

    Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    Competing interests
    The authors declare that no competing interests exist.

  5. Karl Schmid

    Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5129-895X

  6. Sandra M Schmöckel

    Department of Physiology of Yield Stability, University of Hohenheim, Stuttgart, Germany
    Competing interests
    The authors declare that no competing interests exist.

  7. Mark Tester

    Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5085-8801

  8. Christian Jung

    Plant Breeding Institute, Christian-Albrechts University of Kiel, Kiel, Germany
    For correspondence
    c.jung@plantbreeding.uni-kiel.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8149-7976

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.

Reviewing Editor

  1. Vincent Castric, Université de Lille, France

Version history

  1. Preprint posted: December 3, 2020 (view preprint)
  2. Received: January 25, 2021
  3. Accepted: July 7, 2022
  4. Accepted Manuscript published: July 8, 2022 (version 1)
  5. Version of Record published: August 18, 2022 (version 2)

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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  1. Dilan Sarange Rajapaksha Patiranage
  2. Elodie Rey
  3. Nazgol Emrani
  4. Gordon Wellman
  5. Karl Schmid
  6. Sandra M Schmöckel
  7. Mark Tester
  8. Christian Jung
(2022)
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

Share this article

https://doi.org/10.7554/eLife.66873

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