[Quantitative trait locus (QTL) mapping and candidate gene expression analysis of submergence tolerance of rice at...

Rice (Oryza sativa L.) is a major staple crop worldwide, and its germination (plumule) and seedling stages are susceptible to submergence stress, which leads to impaired germination and yield reduction. Identifying submergence tolerance genes is one of the most effective strategies to address this problem. To identify quantitative trait loci (QTLs) associated with submergence tolerance at the plumule and seedling stages in rice, we used an indica rice cultivar 'HZ', a japonica cultivar 'Nekken2', and 120 recombinant inbred lines (RILs) derived from the cross between them in this study. Traits including germination rate, plumule length, and root length at the plumule stage, as well as seedling survival rate, seedling length, and root length at the seedling stage, were measured after submergence stress. QTL mapping was performed on the basis of a previously constructed high-density genetic map. A total of 9 QTLs for submergence tolerance at the plumule stage and 12 QTLs at the seedling stage were detected, with the maximum LOD scores being 4.37 and 3.78, respectively. Three QTLs that were common to both the plumule and seedling stages were identified on chromosomes 3, 7, and 10. Candidate genes within the QTL intervals were screened and their expression was analyzed by RT-qPCR. The results showed that at the plumule stage, LOC_Os01g58970, LOC_Os01g61080, LOC_Os01g58580, LOC_Os02g44120, LOC_Os05g07420, LOC_Os06g40030, and LOC_Os09g25260 were differentially expressed between the two parents, suggesting their involvement in regulating submergence tolerance at the plumule stage. At the seedling stage, LOC_Os04g39110, LOC_Os07g06130, LOC_Os03g50980, LOC_Os02g43970, and LOC_Os09g11480 exhibited significantly different expression levels between the parents and were inferred to be key candidate genes governing submergence tolerance at the seedling stage. Notably, LOC_Os03g08860, LOC_Os07g40240, and LOC_Os10g40640 showed significant differential expression at both the plumule and seedling stages, which implied that these three genes played integrative roles in regulating early submergence tolerance in rice. These findings lay a foundation for fine mapping and cloning of submergence tolerance genes at the plumule and seedling stages and are of great significance for breeding submergence-tolerant rice varieties.