Increasing numbers of rice farmers are adopting methods of direct seeding in flooded paddy fields to save costs associated with labor and transplanting. Successful seedling establishment under anoxic conditions requires rapid coleoptile growth to access oxygen near the water surface. It is important to identify relevant genetic loci for coleoptile growth in rice. In this study, the coleoptile length (CL), coleoptile surface area (CSA), coleoptile volume (CV), and coleoptile diameter (CD) of a germplasm collection consisting of 200 cultivars growing in a low-oxygen environment for 6 days varied extensively. A genome-wide association study (GWAS) was performed using 161,657 high-quality single nucleotide polymorphisms (SNPs), which were obtained via genotyping by sequencing (GBS). A total of 96 target trait-associated loci were detected, of which 14 were detected repeatedly in both the wet and dry seasons. For these 14 loci, 384 genes were located within a 200-kb genomic region (± 100 kb from the peak SNP). In addition, 12,084 differentially expressed genes (DEGs) were identified using transcriptome expression profiling. Based on the GWAS and expression profiling, we further narrowed the candidate genes down to 111. Among the 111 candidate DEGs, Os02g0285300, Os02g0639300, Os04g0671300, Os06g0702600, Os06g0707300, and Os12g0145700 were the most promising candidates associated with anaerobic germination. In addition, we performed a detailed analysis of OsTPP7 sequences from 29 samples in our panel containing 200 diverse germplasms. A total of 11 mutation sites were identified, and four haplotypes were obtained. We found that 7 varieties with the OsTPP7-1 haplotype had higher phenotypic values. This work broadens our understanding of the genetic control of germination tolerance of anaerobic conditions. This study also provides a material basis for breeding superior direct-seeded rice varieties.

越来越多的稻农正在采用在淹水稻田中直接播种的方法，以节省劳动力和移栽成本。在缺氧条件下成功的幼苗建立需要胚芽鞘快速生长以获取水面附近的氧气。确定水稻胚芽鞘生长的相关遗传位点非常重要。在本研究中，由 200 个在低氧环境中生长 6 天的品种组成的种质资源，其胚芽鞘长度 (CL)、胚芽鞘表面积 (CSA)、胚芽鞘体积 (CV) 和胚芽鞘直径 (CD) 差异很大。使用通过测序基因分型 (GBS) 获得的 161,657 个高质量单核苷酸多态性 (SNP) 进行全基因组关联研究 (GWAS)。共检测到96个目标性状相关位点，其中14个在雨季和旱季重复检测到。对于这 14 个基因座，384 个基因位于 200 kb 基因组区域内（距峰值 SNP ± 100 kb）。此外，利用转录组表达谱鉴定了 12,084 个差异表达基因 (DEG)。基于GWAS和表达谱，我们进一步将候选基因缩小到111个。在111个候选DEG中，Os02g0285300、Os02g0639300、Os04g0671300、Os06g0702600、Os06g0707300和Os12g0145700是与厌氧菌相关的最有希望的候选基因信息。此外，我们对来自包含 200 种不同种质的 29 个样本的OsTPP7序列进行了详细分析。共鉴定出11个突变位点，获得4个单倍型。我们发现具有 OsTPP7-1 单倍型的 7 个品种具有较高的表型值。这项工作拓宽了我们对厌氧条件下发芽耐受性的遗传控制的理解。该研究也为选育优良直播水稻品种提供了物质基础。