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

Dilan Sarange Rajapaksha Patiranage; Elodie Rey; Nazgol Emrani; Gordon Wellman; Karl Schmid; Sandra M Schmöckel; Mark A. Tester; Christian Jung

doi:10.7554/elife.66873

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

Dilan Sarange Rajapaksha Patiranage, Elodie Rey, Nazgol Emrani, Gordon Wellman, Karl Schmid, Sandra M Schmöckel, Mark A. Tester, Christian Jung

Research output: Contribution to journal › Article › peer-review

22 Scopus citations

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.

Original language	English (US)
Journal	eLife
Volume	11
DOIs	https://doi.org/10.7554/elife.66873
State	Published - Jul 8 2022

Bibliographical note

KAUST Repository Item: Exported on 2022-09-14
Acknowledged KAUST grant number(s): OSR-2016-CRG5- 466 2966-02
Acknowledgements: 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.

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology
General Medicine
General Immunology and Microbiology
General Neuroscience

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10.7554/elife.66873

https://repository.kaust.edu.sa/bitstream/10754/667681/5/elife-66873-v1.pdf

Cite this

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

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.",

author = "Patiranage, {Dilan Sarange Rajapaksha} and Elodie Rey and Nazgol Emrani and Gordon Wellman and Karl Schmid and Schm{\"o}ckel, {Sandra M} and Tester, {Mark A.} and Christian Jung",

note = "KAUST Repository Item: Exported on 2022-09-14 Acknowledged KAUST grant number(s): OSR-2016-CRG5- 466 2966-02 Acknowledgements: 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.",

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AU - Patiranage, Dilan Sarange Rajapaksha

AU - Rey, Elodie

AU - Emrani, Nazgol

AU - Wellman, Gordon

AU - Schmid, Karl

AU - Schmöckel, Sandra M

AU - Tester, Mark A.

AU - Jung, Christian

N1 - KAUST Repository Item: Exported on 2022-09-14 Acknowledged KAUST grant number(s): OSR-2016-CRG5- 466 2966-02 Acknowledgements: 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.

PY - 2022/7/8

Y1 - 2022/7/8

N2 - 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.

AB - 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.

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JO - eLife

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ER -

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

Abstract

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