Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history
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...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2022-07-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/66873 |
| _version_ | 1818017829733007360 |
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| author | Dilan SR Patiranage Elodie Rey Nazgol Emrani Gordon Wellman Karl Schmid Sandra M Schmöckel Mark Tester Christian Jung |
| author_facet | Dilan SR Patiranage Elodie Rey Nazgol Emrani Gordon Wellman Karl Schmid Sandra M Schmöckel Mark Tester Christian Jung |
| author_sort | Dilan SR Patiranage |
| collection | DOAJ |
| description | 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 single nucleotide polymorphism (SNP) loci. Highland and Lowland quinoa were clustered into two main groups, with FST divergence of 0.36 and linkage disequilibrium (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. |
| first_indexed | 2024-04-14T07:31:59Z |
| format | Article |
| id | doaj.art-5a314a79e0014b6f8f2493e1b66a4ce2 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-14T07:31:59Z |
| publishDate | 2022-07-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-5a314a79e0014b6f8f2493e1b66a4ce22022-12-22T02:05:49ZengeLife Sciences Publications LtdeLife2050-084X2022-07-011110.7554/eLife.66873Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding historyDilan SR Patiranage0https://orcid.org/0000-0001-6308-1838Elodie Rey1Nazgol Emrani2https://orcid.org/0000-0001-5673-3957Gordon Wellman3Karl Schmid4https://orcid.org/0000-0001-5129-895XSandra M Schmöckel5Mark Tester6https://orcid.org/0000-0002-5085-8801Christian Jung7https://orcid.org/0000-0001-8149-7976Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, GermanyKing Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi ArabiaPlant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, GermanyKing Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi ArabiaInstitute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, GermanyDepartment of Physiology of Yield Stability, University of Hohenheim, Stuttgart, GermanyKing Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi ArabiaPlant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, GermanyQuinoa 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 single nucleotide polymorphism (SNP) loci. Highland and Lowland quinoa were clustered into two main groups, with FST divergence of 0.36 and linkage disequilibrium (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.https://elifesciences.org/articles/66873Chenopodium quinoaadaptationdomesticationplant breedingre-sequencinggenetic variation |
| spellingShingle | Dilan SR Patiranage Elodie Rey Nazgol Emrani Gordon Wellman Karl Schmid Sandra M Schmöckel Mark Tester Christian Jung Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history eLife Chenopodium quinoa adaptation domestication plant breeding re-sequencing genetic variation |
| title | Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history |
| title_full | Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history |
| title_fullStr | Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history |
| title_full_unstemmed | Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history |
| title_short | Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history |
| title_sort | genome wide association study in quinoa reveals selection pattern typical for crops with a short breeding history |
| topic | Chenopodium quinoa adaptation domestication plant breeding re-sequencing genetic variation |
| url | https://elifesciences.org/articles/66873 |
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