The low seedling rate of rice caused by submergence in the process of rice direct seeding has always been an important factor limiting the popularization of rice direct seeding technology. Improving the tolerance of rice to submergence stress will benefit the production of rice and the promotion of direct seeding technology. In this study, we determined the submergence coleoptile length (SCL), submergence shoot length (SSL), and submergence tolerance index (STI) of 166 different cultivated rice seedlings as the phenotypes. Through the genome-wide association analysis (GWAS) of SCL, SSL, and STI, we found multiple quantitative trait locus (QTL) locations, including nine reported QTL locations. To narrow down the candidate gene numbers, we combined data from GWAS, transcriptomic analysis, gene function annotation, and reported QTL locations, and 50 candidate genes for submergence stress were obtained. Some reported genes had been firstly found to play certain roles in submergence-mediated growth response. Combining with reported RNA-seq data and expression profile data, we focused on four adjacent genes (LOC_Os11g47550, LOC_Os11g47570, LOC_Os11g47590, and LOC_Os11g47610) located in qAG11. RNA-seq and expression profile suggested the expression of these genes in sensitive and tolerant types differs hundreds of times (146~510 fold). Based on the diverse germplasms, we determined the natural haplotype of these genes. The haplotype analysis of these four genes showed a large genetic difference between indica and japonica. These results help us to better understand the molecular mechanism of natural variations in submergence tolerance among diverse germplasms and provide materials and new genes for further selection of new submergence tolerance varieties.

水稻直播播种过程中因淹没造成水稻育苗率低一直是制约水稻直播播种技术普及的重要因素。提高水稻对淹没胁迫的耐受性将有利于水稻的生产和直接播种技术的推广。在这项研究中，我们确定了166种不同栽培稻幼苗的胚芽鞘长度（SCL），茎芽长度（SSL）和淹没耐受指数（STI）。通过SCL，SSL和STI的全基因组关联分析（GWAS），我们发现了多个数量性状基因座（QTL）位置，包括9个报告的QTL位置。为了缩小候选基因的数量，我们结合了来自GWAS，转录组分析，基因功能注释和报告的QTL位置的数据，获得了50个淹水胁迫候选基因。首先发现一些报道的基因在淹没介导的生长反应中起某些作用。结合报告的RNA-seq数据和表达谱数据，我们集中研究了四个相邻的基因（LOC_Os11g47550，LOC_Os11g47570，LOC_Os11g47590和LOC_Os11g47610）位于qAG11中。RNA-seq和表达谱表明，这些基因在敏感和耐性类型中的表达相差数百倍（146〜510倍）。基于不同的种质，我们确定了这些基因的自然单倍型。这四个基因的单倍型分析显示之间的大的遗传差异籼稻和粳稻。这些结果有助于我们更好地了解不同种质之间的耐淹性自然变化的分子机制，并为进一步选择新的耐淹性品种提供材料和新基因。