Identification of candidate genes for hypoxia tolerance in rice by genome-wide association analysis and transcriptome sequencing

Direct-seeded rice has gained increasing popularity due to its advantage of lower labor costs. Flooding/hypoxia is an important abiotic stress with severe negative impacts on the germination and emergence of direct-seeded rice. Hence, improving the hypoxic germination tolerance of rice is an important way to promote the further development of direct-seeded rice. In this study, 276 rice germplasms were used as materials to analyze the correlation traits of hypoxia tolerance in rice by genome-wide association analysis(GWAS). In addition, transcriptome sequencing was performed on the strong and weak hypoxic tolerance varieties under flooding and normal conditions. By comparing the results of GWAS and transcriptome sequencing, the candidate genes were further screened and analyzed.As a result, a total of 86 genes related to hypoxic germination tolerance were detected by GWAS, and 51 genes were mapped by GWAS and transcriptome sequencing. Combined with gene functional annotation and haplotype analysis, five important candidate genes related to hypoxia tolerance were screened, including LOC_Os01g07420, LOC_Os02g01890, LOC_Os03g45720, LOC_Os04g56920, and LOC_Os11g41680. The findings may provide an important foundation for mining and cloning of genes for hypoxic germination tolerance in rice with biotechnological improvement.

直播稻（direct-seeded rice）因用工成本更低的显著优势，愈发受到青睐。淹水/低氧胁迫是一类重要的非生物胁迫，对直播稻的萌发与出苗具有严重的负面影响。因此，提升水稻的耐低氧萌发能力，是推动直播稻产业进一步发展的重要途径。本研究以276份水稻种质资源为试验材料，通过全基因组关联分析（genome-wide association analysis, GWAS）解析水稻耐低氧相关性状。此外，本研究针对淹水与正常培养条件下耐低氧性强弱各异的水稻品种开展转录组测序。通过整合GWAS与转录组测序的分析结果，进一步筛选并分析候选基因。最终，GWAS共检测到86个与耐低氧萌发相关的基因，其中51个同时被GWAS与转录组测序定位。结合基因功能注释与单倍型分析，本研究筛选得到5个与耐低氧胁迫相关的重要候选基因，分别为LOC_Os01g07420、LOC_Os02g01890、LOC_Os03g45720、LOC_Os04g56920及LOC_Os11g41680。本研究结果可为借助生物技术改良手段挖掘、克隆水稻耐低氧萌发相关基因提供重要理论基础。