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

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cg.contributor.affiliationUniversity of Illinois
cg.contributor.affiliationAfrica Rice Center
cg.contributor.affiliationInternational Rice Research Institute
cg.identifier.doihttps://doi.org/10.22541/essoar.167407907.78496270/v1
dc.contributor.authorSakhale, Sandeep
dc.contributor.authorYadav, Shailesh
dc.contributor.authorClark, Lindsay
dc.contributor.authorLipka, Alexander
dc.contributor.authorKumar, Arvind
dc.contributor.authorSacks, Erik
dc.date.accessioned2024-12-19T12:53:12Zen
dc.date.available2024-12-19T12:53:12Zen
dc.identifier.urihttps://hdl.handle.net/10568/163938
dc.titleGenome-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 fielden
dcterms.abstractDry 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.en
dcterms.bibliographicCitationSakhale, 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.en
dcterms.issued2023-06-12
dcterms.languageen
dcterms.publisherAuthorea, Inc.
dcterms.typePreprint

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