Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China.
Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China.
BMC Plant Biol. 2022 Nov 14;22(1):526. doi: 10.1186/s12870-022-03924-y.
Rice is the world's second largest food crop and accelerated global climate change due to the intensification of human activities has a huge impact on rice. Research on the evolution of different rice ecotypes is essential for enhancing the adaptation of rice to the unpredictable environments.
The sequencing data of 868 cultivated and 140 wild rice accessions were used to study the domestication history and signatures of adaptation in the distinct rice ecotypes genome. The different populations had formed distinct rice ecotypes by phylogenetic analyses and were domesticated independently in the two subspecies of rice, especially deepwater and upland rice. The domestication history of distinct rice ecotypes was confirmed and the four predicted admixture events mainly involved gene flow between wild rice and cultivated rice. Importantly, we identified numerous selective sweeps that have occurred during the domestication of different rice ecotypes and one candidate gene (LOC_Os11g21804) for deepwater based on transcriptomic evidence. In addition, many regions of genomic differentiation between the different rice ecotypes were identified. Furthermore, the main reason for the increase in genetic diversity in the ecotypes of xian (indica) rice was the high proportion of alternative allele frequency in new mutations. Genome-wide association analysis revealed 28 QTLs associated with flood tolerance which contained 12 related cloned genes, and 20 candidate genes within 13 deepwater QTLs were identified by transcriptomic and haplotype analyses.
These results enhanced our understanding of domestication history in different rice ecotypes and provided valuable insights for genetic improvement and breeding of rice in the current changing environments.
水稻是世界上第二大粮食作物，由于人类活动的加剧，全球气候变化对水稻产生了巨大影响。研究不同水稻生态型的进化对于提高水稻适应不可预测环境的能力至关重要。
利用 868 份栽培稻和 140 份野生稻的测序数据，研究了不同水稻生态型基因组的驯化历史和适应特征。通过系统发育分析和群体遗传分析，不同群体形成了不同的水稻生态型，这些生态型在水稻的两个亚种中独立驯化，特别是深水稻和陆稻。确认了不同水稻生态型的驯化历史，并预测了四个主要涉及野生稻和栽培稻基因流的混合事件。重要的是，我们基于转录组证据鉴定了许多在不同水稻生态型驯化过程中发生的选择清除，并发现了一个深水稻候选基因（LOC_Os11g21804）。此外，还鉴定了不同水稻生态型之间基因组分化的许多区域。此外，籼稻生态型遗传多样性增加的主要原因是新突变中替代等位基因频率的比例较高。全基因组关联分析揭示了 28 个与耐淹水相关的 QTL，其中包含 12 个相关克隆基因，通过转录组和单倍型分析鉴定了 20 个候选基因在 13 个深水 QTL 中。
这些结果增强了我们对不同水稻生态型驯化历史的认识，为当前变化环境下水稻的遗传改良和育种提供了有价值的见解。
