Table_8_Genome-wide association studies identified OsTMF as a gene regulating rice seed germination under salt stress.xlsx

IntroductionSalt tolerance during seed germination is an important trait for direct seeding and low-cost rice production. Nevertheless, it is still not clear how seed germination under salt stress is regulated genetically.
MethodsIn this study, genome-wide association studies (GWAS) were performed to decipher the genetic basis of seed germination under salt stress using 541 rice varieties collected worldwide.
Results and discussionThree quantitative trait loci (QTLs) were identified including qGRG3-1 on chromosome 3, qGRG3-2 on chromosome 5, and qGRG4 on chromosome 4. Assessment of candidate genes in these loci for their responses to salt stress identified a TATA modulatory factor (OsTMF) in qGRG3-2. The expression of OsTMF was up-regulated in both roots and shoots after exposure to salt stress, and OsTMF knockout mutants exhibited delayed seed germination under salt stress. Haplotype analysis showed that rice varieties carrying OsTMF-Hap2 displayed elevated salt tolerance during seed germination. These results provide important knowledge and resources to improve rice seed germination under salt stress in the future.

引言 种子萌发期的耐盐性是水稻直播与低成本生产的重要性状。然而，盐胁迫下种子萌发的遗传调控机制仍未阐明。
方法 本研究利用全球范围内收集的541份水稻品种，通过全基因组关联分析（genome-wide association studies, GWAS）解析盐胁迫下水稻种子萌发的遗传基础。
结果与讨论 本研究共鉴定到3个数量性状位点（quantitative trait loci, QTLs），分别为3号染色体上的qGRG3-1、5号染色体上的qGRG3-2以及4号染色体上的qGRG4。对上述位点内的候选基因进行盐胁迫响应评估后，在qGRG3-2位点中发现了一个TATA调控因子（TATA modulatory factor, OsTMF）。盐胁迫处理后，OsTMF在水稻根与茎中的表达均显著上调；OsTMF敲除突变体在盐胁迫下的种子萌发进程显著延迟。单倍型分析显示，携带OsTMF-Hap2的水稻品种在种子萌发期表现出更高的耐盐性。本研究结果可为未来提升盐胁迫下水稻种子萌发能力提供重要的理论依据与遗传资源。