基于细胞质基因组核苷酸多样性的亚洲栽培稻起源与进化研究

Asian cultivated rice (Oryza sativa) is one of world's oldest and most important crop species. Understanding the origins and domestication of cultivated rice impacts our understanding of the resources utilization and rice breeding. In our previously research, the origin of rice and the genetic diversity of Chinese wild rice were well documented. It is believed that China is one of the domestication centers of rice. However, the number of domestication times and the exactly geographic origin of rice in China are still under debate. In this proposed project, the evolutionary history of cultivated rice was re-examined. We selected 507 accessions of cultivated rice and wild rice from the world to examine the nucleotide diversity of chloroplast and mitochondrial genomes. We will study the nucleotide polymorphism on the whole organelle genome level, identify the genetic differentiation between rice and wild rice, in search of the domestication loci and variations. Based on haplotype analysis, phylogenetic analysis and population structure analysis, we will confirm that two main subspecies of rice, indica and japonica, were multiple independent origin or single domestication origin. We will calculate the time of the divergence of indica and japonica by molecular dating. The ancestors of cultivated rice and geographic origin will be identified. Compared with distribution information of ancestors of cultivated rice and the genetic diversity data of Chinese wild rice, we will identify the exactly geographic origin and found the vital population of wild rice which should be the direct ancestor of cultivated rice. Overall, the outputs of this project will settle the disputes of origin and domestication of cultivated rice, provide deeply insights for evolution of cultivated rice and theoretical basis for Chinese wild rice conservation and utilization.

深入理解农作物的起源进化过程有利于在农作物野生近缘种中寻找新的种质资源，发掘驯化过程中丢失的优异基因。亚洲栽培稻作为世界上最重要的粮食作物，其起源进化过程以及籼、粳稻的驯化方式目前都存在较大的争议，准确的起源地以及祖先种仍不清楚。前人对亚洲栽培稻起源进化的研究集中于利用核基因组的重测序，而在细胞质全基因组水平上的研究尚未有报导。申请人前期对水稻起源进化、中国野生稻遗传多样性都进行了深入的研究，在此基础上选择507份来源广泛、代表性强的栽培稻与野生稻材料，进行叶绿体和线粒体基因组测序，通过细胞质基因组的核苷酸多样性分析与系统发育分析，寻找驯化位点，揭示亚洲栽培稻的进化过程以及籼粳分化的方式，明确分化开始的时间。结合亲缘地理学分析以及起源中心野生稻遗传多样性分析，确定亚洲栽培稻在中国精确的起源地、祖先种，寻找与亚洲栽培稻驯化有关的重要野生稻居群。为中国野生稻种质资源的保护与利用提供理论依据。

深入理解农作物的起源进化过程有利于在农作物野生近缘种中寻找新的种质资源，发掘驯化过程中丢失的优异基因。亚洲栽培稻作为世界上最重要的粮食作物，其起源进化过程以及籼、粳稻的驯化方式目前都存在较大的争议，准确的起源地以及祖先种仍不清楚。前人对亚洲栽培稻起源进化的研究集中于利用核基因组的重测序，而在细胞质全基因组水平上的研究尚未有报导。申请人前期对水稻起源进化、中国野生稻遗传多样性都进行了深入的研究，在此基础上选择507份来源广泛、代表性强的栽培稻与野生稻材料，进行叶绿体和线粒体基因组测序，通过细胞质基因组的核苷酸多样性分析与系统发育分析，寻找驯化位点，揭示亚洲栽培稻的进化过程以及籼粳分化的方式，明确分化开始的时间。结合亲缘地理学分析以及起源中心野生稻遗传多样性分析，确定亚洲栽培稻在中国精确的起源地、祖先种，寻找与亚洲栽培稻驯化有关的重要野生稻居群。为中国野生稻种质资源的保护与利用提供理论依据。