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QTL mapping and identification of candidate genes for cold tolerance at the germination stage in wild rice

文献类型： 外文期刊

作者： Pan, Ying-Hua 1 ; Nong, Bao-Xuan 1 ; Chen, Lei 1 ; Yang, Xing-Hai 1 ; Xia, Xiu-Zhong 1 ; Zhang, Zong-Qiong 1 ; Qing, Dong-Jin 1 ; Gao, Ju 2 ; Huang, Cheng-Cui 1 ; Li, Dan-Ting 1 ; Deng, Guo-Fu 2 ;

作者机构： 1.Guangxi Acad Agr Sci, Rice Res Inst, Guangxi Key Lab Rice Genet & Breeding, Nanning 530007, Peoples R China

2.Guangxi Acad Agr Sci, Guangxi Crop Genet Improvement & Biotechnol Lab, Nanning 530007, Peoples R China

关键词： Cold tolerance; Germination; QTL; Resequencing; Wild rice

期刊名称：GENES & GENOMICS （ 影响因子：2.1； 五年影响因子：1.9 ）

ISSN： 1976-9571

年卷期： 2023 年 45 卷 7 期

页码：

收录情况： SCI

摘要： BackgroundCold damage stress significantly affects rice growth (germination and seedling) and causes serious losses in yield in temperate and high-altitude areas around the globe.ObjectiveThis study aimed to explore the cold tolerance (CT) locus of rice and create new cold-tolerant germplasm. We constructed a chromosome segment substitution line (CSSL) with strong CT and fine mapped quantitative trait loci (QTLs) associated with CT by performing the whole-genome resequencing of CSSL with phenotypes under cold treatment.MethodsA chromosome CSSL, including 271 lines from a cross between the cold-tolerant wild rice Y11 (Oryza rufipogon Griff.) and the cold-sensitive rice variety GH998, was developed to map QTLs conferring CT at the germination stage. The whole-genome resequencing was performed on CSSL for mapping QTLs of associated with CT at the germination stage.ResultsA high-density linkage map of the CSSLs was developed using the whole-genome resequencing of 1484 bins. The QTL analysis using 615,466 single-nucleotide polymorphisms (SNPs) led to the identification of 2 QTLs related to germination rate at low-temperature on chromosome 8 (qCTG-8) and chromosome 11 (qCTG-11). The qCTG-8 and qCTG-11 explained 14.55% and 14.31% of the total phenotypic variation, respectively. We narrowed down qCTG-8 and qCTG-11 to 195.5 and 78.83-kb regions, respectively. The expression patterns of important candidate genes in different tissues, and of RNA-sequencing (RNA-seq) in CSSLs, were identified based on gene sequences in qCTG-8 and qCTG-11 cold-induced expression analysis. LOC_Os08g01120 and LOC_Os08g01390 were identified as candidate genes in qCTG-8, and LOC_Os11g32880 was identified as a candidate gene in qCTG-11.ConclusionsThis study demonstrated a general method that could be used to identify useful loci and genes in wild rice and aid in the future cloning of candidate genes of qCTG-8 and qCTG-11. The CSSLs with strong CT were supported for breeding cold-tolerant rice varieties.

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