Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation 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, an understanding of the genomic regions and underly...
| Autores principales: | , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2023
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/132707 |
| _version_ | 1855524646318768128 |
|---|---|
| author | Sakhale, S.A. Shailesh, Y. Clark, L.V. Likpa, A. Kumar, A. Sacks, E. |
| author_browse | Clark, L.V. Kumar, A. Likpa, A. Sacks, E. Sakhale, S.A. Shailesh, Y. |
| author_facet | Sakhale, S.A. Shailesh, Y. Clark, L.V. Likpa, A. Kumar, A. Sacks, E. |
| author_sort | Sakhale, S.A. |
| 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, an understanding of the genomic regions and underlying genes that confer emergence in 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 of aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes that primarily regulate 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 | Journal Article |
| id | CGSpace132707 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1327072025-12-08T10:29:22Z Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation to dry-direct seeding in the field Sakhale, S.A. Shailesh, Y. Clark, L.V. Likpa, A. Kumar, A. Sacks, E. genomes climate resilience genes breeding rice 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, an understanding of the genomic regions and underlying genes that confer emergence in 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 of aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes that primarily regulate 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 2023-11-03T13:26:13Z 2023-11-03T13:26:13Z Journal Article https://hdl.handle.net/10568/132707 en Open Access application/pdf Frontiers Media Sakhale, S.A., Shailesh, Y., Clark, L.V., Likpa, A., Kumar, A. and Sacks, E. 2023. Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation to dry-direct seeding in the field. Frontiers in Plant Science 14:1172816. |
| spellingShingle | genomes climate resilience genes breeding rice Sakhale, S.A. Shailesh, Y. Clark, L.V. Likpa, A. Kumar, A. Sacks, E. Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation 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 for adaptation 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 for adaptation 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 for adaptation 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 for adaptation 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 for adaptation 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 for adaptation to dry direct seeding in the field |
| topic | genomes climate resilience genes breeding rice |
| url | https://hdl.handle.net/10568/132707 |
| work_keys_str_mv | AT sakhalesa genomewideassociationanalysisforemergenceofdeeplysownriceoryzasativarevealsnovelausspecificphytohormonecandidategenesforadaptationtodrydirectseedinginthefield AT shaileshy genomewideassociationanalysisforemergenceofdeeplysownriceoryzasativarevealsnovelausspecificphytohormonecandidategenesforadaptationtodrydirectseedinginthefield AT clarklv genomewideassociationanalysisforemergenceofdeeplysownriceoryzasativarevealsnovelausspecificphytohormonecandidategenesforadaptationtodrydirectseedinginthefield AT likpaa genomewideassociationanalysisforemergenceofdeeplysownriceoryzasativarevealsnovelausspecificphytohormonecandidategenesforadaptationtodrydirectseedinginthefield AT kumara genomewideassociationanalysisforemergenceofdeeplysownriceoryzasativarevealsnovelausspecificphytohormonecandidategenesforadaptationtodrydirectseedinginthefield AT sackse genomewideassociationanalysisforemergenceofdeeplysownriceoryzasativarevealsnovelausspecificphytohormonecandidategenesforadaptationtodrydirectseedinginthefield |