Genetic studies on cold tolerance at the reproductive stage in rice could lead to significant reductions in yield losses. However, knowledge about the genetic basis and adaptive differentiation, as well as the evolution and utilization of the underlying natural alleles, remains limited. Here, 580 rice accessions in two association panels were used to perform genome‐wide association study, and 156 loci associated with cold tolerance at the reproductive stage were identified. Os01g0923600 and Os01g0923800 were identified as promising candidate genes in qCTB1t, a major associated locus. Through population genetic analyses, 22 and 29 divergent regions controlling cold adaptive differentiation inter‐subspecies (Xian/Indica and Geng/Japonica) and intra‐Geng, respectively, were identified. Joint analyses of four cloned cold‐tolerance genes showed that they had different origins and utilizations under various climatic conditions. bZIP73 and OsAPX1 differentiating inter‐subspecies evolved directly from wild rice, whereas the novel mutations CTB4a and Ctb1 arose in Geng during adaptation to colder climates. The cold‐tolerant Geng accessions have undergone stronger selection under colder climate conditions than other accessions during the domestication and breeding processes. Additive effects of dominant allelic variants of four identified genes have been important in adaptation to cold in modern rice varieties. Therefore, this study provides valuable information for further gene discovery and pyramiding breeding to improve cold tolerance at the reproductive stage in rice.

中文翻译：

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天然等位基因在水稻生殖阶段对冷适应性的分化，进化和利用。

水稻生殖阶段耐寒性的遗传研究可能会大大减少产量损失。但是，关于遗传基础和适应性分化以及潜在自然等位基因的进化和利用的知识仍然有限。在这里，使用两个关联小组中的580个水稻种质来进行全基因组关联研究，并鉴定了156个与生殖阶段耐寒性相关的基因座。Os01g0923600和Os01g0923800被确定为qCTB1t（一个主要的相关基因座）中有希望的候选基因。通过种群遗传分析，控制冷适应性分化亚种的22和29个不同区域（西安/印度和Geng / Japonica）和Intra- Geng分别被确定。对四个克隆的耐寒基因的联合分析表明，它们在不同的气候条件下具有不同的起源和利用。bZIP73和OsAPX1分化间亚种直接从野生稻的演变，而新的突变CTB4a和CTB1在出现耿适应寒冷的气候中。耐寒耿在较冷的气候条件下，与其他种相比，在驯化和育种过程中对这些种进行了更强的选择。四个已鉴定基因的显性等位基因变异的加性效应对于适应现代水稻品种的寒冷十分重要。因此，这项研究为进一步的基因发现和金字塔育种提供了有价值的信息，以提高水稻生殖阶段的耐冷性。