Identification of Candidate Genes for Cold Tolerance at Seedling Stage by GWAS in Rice (Oryza sativa L.)

文献类型： 外文期刊

第一作者： Shi, Huimin

作者： Shi, Huimin;Song, Qingxin;Shi, Huimin;Zhang, Wenyu;Cao, Huimin;Xu, Jianlong;Zhai, Laiyuan;Xu, Jianlong;Xu, Jianlong

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关键词： rice; GWAS; cold tolerance; candidate genes; favorable haplotype

期刊名称：BIOLOGY-BASEL （ 影响因子：3.5； 五年影响因子：4.0 ）

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年卷期： 2024 年 13 卷 10 期

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收录情况： SCI

摘要： Simple Summary The adverse impact of cold temperatures on rice farming has resulted in a significant decrease in both the yield and quality of rice. Therefore, the identification of quantitative trait loci (QTLs) for cold tolerance (CT) holds immense theoretical and practical value for enhancing CT in rice breeding. In this study, we evaluated CT phenotypes at the seedling stage across 1992 rice germplasms and observed variations in CT among different subpopulations. We successfully identified high CT germplasms within both geng and xian subspecies. By conducting a genome-wide association study (GWAS), we dissected QTLs associated with CT and discovered favorable haplotypes linked to novel candidate genes at crucial QTLs. These findings offer valuable germplasms exhibiting high CT potential as well as favorable haplotypes that can be utilized for developing new varieties with enhanced CT through marker-assisted selection.Abstract Due to global climate change, cold temperatures have significantly impacted rice production, resulting in reduced yield and quality. In this study, we investigated two traits related to the cold tolerance (CT) of 1992 diverse rice accessions at the seedling stage. Geng accessions exhibited higher levels of CT compared to xian accessions, with the GJ-tmp subgroup displaying the strongest CT. However, extreme CT accessions were also identified within the xian subspecies. Through GWAS analysis based on the survival rate (SR) and leaf score of cold tolerance (SCT), a total of 29 QTLs associated with CT at the seedling stage were identified, among which four QTLs (qSR3.1a, qSR4.1a, qSR11.1x, and qSR12.1a) were found to be important. Furthermore, five candidate genes (LOC_Os03g44760, LOC_Os04g06900, LOC_Os04g07260, LOC_Os11g40610, and LOC_Os12g10710) along with their favorable haplotypes were identified through gene function annotation and haplotype analysis. Pyramiding multiple favorable haplotypes resulted in a significant improvement in CT performance. Subsequently, three selected accessions (CX534, B236, and IRIS_313-8565), carrying different superior alleles for CT, were selected and recommended for molecular breeding for CT using marker-assisted selection (MAS). The findings from this study provide valuable resources for enhancing rice's ability for CT while laying a foundation for the future cloning of novel genes involved in conferring CT.

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