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

Plant Science

Alexander E. Lipka¹  Erik J. Sacks¹  Sandeep A. Sakhale²  Lindsay V. Clark³  Shailesh Yadav⁴  Arvind Kumar⁵ 

[1] Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States;Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States;International Rice Research Institute (IRRI), Los Baños, Philippines;International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India;Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States;Seattle Children’s Research Institute, Seattle, WA, United States;International Rice Research Institute (IRRI), Los Baños, Philippines;Africa Rice Center (AfricaRice), Abidjan, Côte d’Ivoire;International Rice Research Institute (IRRI), Los Baños, Philippines;International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India;

关键词: dry direct-seeded rice (Dry-DSR);    genome wide association study (GWAS);    mixed linear model (MLM);    quantitative trait loci (QTL);    rice diversity panel 1 (RDP1);    single nucleotide polymorphism (SNP);    3,000 rice genome project (3k RGP);   

DOI  :  10.3389/fpls.2023.1172816

 received in 2023-02-23, accepted in 2023-05-23,  发布年份 2023

来源: Frontiers

【 摘 要 】

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.

【 授权许可】

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Copyright © 2023 Sakhale, Yadav, Clark, Lipka, Kumar and Sacks