Rapid identification of qtl for mesocotyl length in rice through combining QTL-seq and genome-wide association analysis

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dc.creatorWang, Yamei
dc.creatorLiu, Jindong
dc.creatorMeng, Yun
dc.creatorLiu, Hongyan
dc.creatorLiu, Chang
dc.creatorYe, Guoyou
dc.date2021-07-19
dc.date2024-12-19T12:53:37Z
dc.date2024-12-19T12:53:37Z
dc.date.accessioned2026-06-27T04:13:25Z
dc.descriptionMesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in direct-seeded rice. Thus, the identification of quantitative trait loci (QTL) associated with mesocotyl length (ML) could accelerate genetic improvement of rice for direct seeding cultivation. In this study, QTL sequencing (QTL-seq) applied to 12 F2 populations identified 14 QTL for ML, which were distributed on chromosomes 1, 3, 4, 5, 6, 7, and 9 based on the Δ(SNP-index) or G-value statistics. Besides, a genome-wide association study (GWAS) using two diverse panels identified five unique QTL on chromosomes 1, 8, 9, and 12 (2), respectively, explaining 5.3–14.6% of the phenotypic variations. Among these QTL, seven were in the regions harboring known genes or QTLs, whereas the other 10 were potentially novel. Six of the QTL were stable across two or more populations. Eight high-confidence candidate genes related to ML were identified for the stable loci based on annotation and expression analyses. Association analysis revealed that two PCR gel-based markers for the loci co-located by QTL-seq and GWAS, Indel-Chr1:18932318 and Indel-Chr7:15404166 for loci qML1.3 and qML7.2 respectively, were significantly associated with ML in a collection of 140 accessions and could be used as breeder-friendly markers in further breeding.
dc.identifierhttps://hdl.handle.net/10568/164224
dc.identifier.urihttp://hdl.handle.net/123456789/25643
dc.languageen
dc.publisherFrontiers Media
dc.rightsOpen Access
dc.sourceWang, Yamei; Liu, Jindong; Meng, Yun; Liu, Hongyan; Liu, Chang and Ye, Guoyou. 2021. Rapid identification of qtl for mesocotyl length in rice through combining QTL-seq and genome-wide association analysis. Front. Genet., Volume 12
dc.subjectgenetics
dc.subjectmedical sciences
dc.titleRapid identification of qtl for mesocotyl length in rice through combining QTL-seq and genome-wide association analysis
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)