Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes that conferred adaption to dry-direct seeding in the field
Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, understanding the genomic regions and underlying ge...
| Autores principales: | , , , , , |
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| Formato: | Preprint |
| Lenguaje: | Inglés |
| Publicado: |
Authorea, Inc.
2023
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| Acceso en línea: | https://hdl.handle.net/10568/163938 |
| _version_ | 1855513558335356928 |
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| author | Sakhale, Sandeep Yadav, Shailesh Clark, Lindsay Lipka, Alexander Kumar, Arvind Sacks, Erik |
| author_browse | Clark, Lindsay Kumar, Arvind Lipka, Alexander Sacks, Erik Sakhale, Sandeep Yadav, Shailesh |
| author_facet | Sakhale, Sandeep Yadav, Shailesh Clark, Lindsay Lipka, Alexander Kumar, Arvind Sacks, Erik |
| author_sort | Sakhale, Sandeep |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, understanding the genomic regions and underlying genes that confer emergence for deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.9 million single nucleotide polymorphisms (SNPs) to identify associations with dry-DSR traits in the field and component traits in a controlled-environment experiment. Using genome-wide association study (GWAS) analyses, we identified 18 unique QTLs on chromosomes 1, 2, 4, 5, 6, 7, 9, 10, and 11, explaining phenotypic variance ranging from 2.6 to 17.8%. Three QTLs, namely, qSOE-1.1, qEMERG-AUS-1.2, and qEMERG-AUS-7.1, were co-located with previously reported QTLs for mesocotyl length. Among the identified QTLs, half were associated with the emergence in aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes, which primarily regulated phytohormone pathways such as cytokinin, auxin, gibberellic acid, and jasmonic acid. Prior studies indicated that these phytohormones play a critical role in mesocotyl length under deep-sowing. This study provides new insight into the importance of aus and indica as desirable genetic resources to mine favorable alleles for deep-sowing tolerance in rice. The candidate genes and marker-tagged desirable alleles identified in this study should benefit rice breeding programs directly. |
| format | Preprint |
| id | CGSpace163938 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Authorea, Inc. |
| publisherStr | Authorea, Inc. |
| record_format | dspace |
| spelling | CGSpace1639382024-12-22T05:44:44Z Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes that conferred adaption to dry-direct seeding in the field Sakhale, Sandeep Yadav, Shailesh Clark, Lindsay Lipka, Alexander Kumar, Arvind Sacks, Erik Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, understanding the genomic regions and underlying genes that confer emergence for deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.9 million single nucleotide polymorphisms (SNPs) to identify associations with dry-DSR traits in the field and component traits in a controlled-environment experiment. Using genome-wide association study (GWAS) analyses, we identified 18 unique QTLs on chromosomes 1, 2, 4, 5, 6, 7, 9, 10, and 11, explaining phenotypic variance ranging from 2.6 to 17.8%. Three QTLs, namely, qSOE-1.1, qEMERG-AUS-1.2, and qEMERG-AUS-7.1, were co-located with previously reported QTLs for mesocotyl length. Among the identified QTLs, half were associated with the emergence in aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes, which primarily regulated phytohormone pathways such as cytokinin, auxin, gibberellic acid, and jasmonic acid. Prior studies indicated that these phytohormones play a critical role in mesocotyl length under deep-sowing. This study provides new insight into the importance of aus and indica as desirable genetic resources to mine favorable alleles for deep-sowing tolerance in rice. The candidate genes and marker-tagged desirable alleles identified in this study should benefit rice breeding programs directly. 2023-06-12 2024-12-19T12:53:12Z 2024-12-19T12:53:12Z Preprint https://hdl.handle.net/10568/163938 en Authorea, Inc. Sakhale, Sandeep; Yadav, Shailesh; Clark, Lindsay; Lipka, Alexander; Kumar, Arvind and Sacks, Erik. 2023. Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes that conferred adaption to dry-direct seeding in the field. ESS Open Archive, [pre-print] 16 p. |
| spellingShingle | Sakhale, Sandeep Yadav, Shailesh Clark, Lindsay Lipka, Alexander Kumar, Arvind Sacks, Erik Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes that conferred adaption to dry-direct seeding in the field |
| title | Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes that conferred adaption to dry-direct seeding in the field |
| title_full | Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes that conferred adaption to dry-direct seeding in the field |
| title_fullStr | Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes that conferred adaption to dry-direct seeding in the field |
| title_full_unstemmed | Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes that conferred adaption to dry-direct seeding in the field |
| title_short | Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes that conferred adaption to dry-direct seeding in the field |
| title_sort | genome wide association analysis for emergence of deeply sown rice oryza sativa reveals novel aus specific phytohormone candidate genes that conferred adaption to dry direct seeding in the field |
| url | https://hdl.handle.net/10568/163938 |
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