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

View ORCID ProfileDilan S. R. Patiranage, Elodie Rey, Nazgol Emrani, Gordon Wellman, View ORCID ProfileKarl Schmid, Sandra M. Schmöckel, Mark Tester, Christian Jung
doi: https://doi.org/10.1101/2020.12.03.410050
Dilan S. R. Patiranage
1Plant Breeding Institute, Christian-Albrechts-University of Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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  • ORCID record for Dilan S. R. Patiranage
Elodie Rey
2King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
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Nazgol Emrani
1Plant Breeding Institute, Christian-Albrechts-University of Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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  • For correspondence: c.jung@plantbreeding.uni-kiel.de n.emrani@plantbreeding.uni-kiel.de
Gordon Wellman
2King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
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Karl Schmid
3Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany
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Sandra M. Schmöckel
4Department of Physiology of Yield Stability, University of Hohenheim, Fruwirthstr. 21, 70599
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Mark Tester
2King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
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Christian Jung
1Plant Breeding Institute, Christian-Albrechts-University of Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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  • For correspondence: c.jung@plantbreeding.uni-kiel.de n.emrani@plantbreeding.uni-kiel.de
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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 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.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted December 05, 2020.
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Genome-wide association study in the pseudocereal quinoa reveals selection pattern typical for crops with a short breeding history
Dilan S. R. Patiranage, Elodie Rey, Nazgol Emrani, Gordon Wellman, Karl Schmid, Sandra M. Schmöckel, Mark Tester, Christian Jung
bioRxiv 2020.12.03.410050; doi: https://doi.org/10.1101/2020.12.03.410050
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Genome-wide association study in the pseudocereal quinoa reveals selection pattern typical for crops with a short breeding history
Dilan S. R. Patiranage, Elodie Rey, Nazgol Emrani, Gordon Wellman, Karl Schmid, Sandra M. Schmöckel, Mark Tester, Christian Jung
bioRxiv 2020.12.03.410050; doi: https://doi.org/10.1101/2020.12.03.410050

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