Genome-wide Association Study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions

Vista sencilla de ítem
dc.creatorLiu, Hongyan
dc.creatorZhan, Junhui
dc.creatorLi, Jiaolong
dc.creatorLu, Xiang
dc.creatorLiu, Jindong
dc.creatorWang, Yamei
dc.creatorZhao, Quanzhi
dc.creatorYe, Guoyou
dc.date2019-12-31
dc.date2024-12-19T12:54:05Z
dc.date2024-12-19T12:54:05Z
dc.date.accessioned2026-06-27T04:12:10Z
dc.descriptionMesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significantly associated with mesocotyl length under various culture conditions, including sand, water and soil. The mesocotyl length ranges from 0 to 4.88 cm, 0 to 3.99 cm and 0 to 4.51 cm in sand, water and soil covering, respectively. A total of 2,338,336 SNPs were discovered by re-sequencing of 208 rice accessions. Genome-wide association study (GWAS) based on mixed linear model (MLM) was conducted and 16 unique loci were identified on chromosomes 1, 2 (2), 3, 4, 5 (2), 6 (2), 7, 8, 9 (2) and 12 (3), respectively, explaining phenotypic variations ranging from 6.3 to 15.9%. Among these loci, 12 were stable across two or more environments. Ten out of the sixteen loci coincided with known genes or quantitative trait locus (QTL), whereas the other six were potentially novel loci. Furthermore, five high-confidence candidate genes related to mesocotyl elongation were identified on chromosomes 1, 3, 5, 9 and 12. Moreover, qRT-PCR analysis showed that all the five genes showed significant expression difference between short-mesocotyl accessions and long-mesocotyl accessions. This study provides new insights into the genetic architecture of rice mesocotyl, the associated SNPs and germplasms with long mesocotyl could be useful in the breeding of mechanized dry direct-seeded rice.
dc.identifierhttps://hdl.handle.net/10568/164582
dc.identifier.urihttp://hdl.handle.net/123456789/24934
dc.languageen
dc.publisherMDPI
dc.rightsOpen Access
dc.sourceLiu, Hongyan, Zhan, Junhui, Li, Jiaolong, Lu, Xiang, Liu, Jindong, Wang, Yamei, Zhao, Quanzhi and Ye, Guoyou. 2019. Genome-wide Association Study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions. Genes, Volume 11 no. 1 p. 49
dc.subjectgenetics genetics(clinical)
dc.titleGenome-wide Association Study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions
dc.typeJournal Article

Archivos

Colecciones

Instituto Internacional de Investigación del Arroz (IRRI)