Origin And Evolution Of Oryza Sativa Revealed By Nucleotide Polymorphisms

Rice (Oryza sativa) is an important food crop, widely grown in the world. It is also regarded as one of the model organisms in biological research and be used in the growth, development, genetics and plant research. Thanking for the efforts of biologists and archaeologists, we know that O. sativa was domesticated from its wild relatives in South Asia or China about ten thousand years ago, but some important issues about the origin and evolution of O. sativa are still in dispute. These disputes include that whether the ancestor of O. sativa is O. rufipogon or O. nivara, was O. sativa originated in South Asia or China and were the subspecies of O. sativa (indica and japonica) domesticated single or multiple times.Research of O. sativa origin and evolution involved in archeology, history, linguistics, anthropology, biology, climatology, and other social and natural sciences. However, using different research methods, it would come to totally different conclusions sometimes. With the development of biologic technology, research methods of O. sativa origin and evolution gradually evolved from morphological observation and genetic analysis into the isozyme analysis in biochemical level, then to AFLP, RAPD, RFLP, SSR, ISSR and SINE in molecular level. However, different markers and different materials used in the research might result in different answers.Because of the rapid development of sequencing technology, analysis of O. sativa origin and evolution in gene level by directly comparing the sequences of O. sativa and its wild relative species become possible. In this study, rich and representative materials of O. sativa and its wild relatives with high diversity, widely range and different phenotypes were collected and nucleotide polymorphisms of multiple loci were compared to analyze the origin and evolution of O. sativa. The main results are as follows:Ten organelle DNA fragments (including six chloroplast fragments and four mitochondrial fragments) were sequenced for Chinese mini-core collections of O. sativa and O. rufipogon. The nucleotide polymorphisms analysis showed that organelle DNA diversity of O. sativa was much less than O. rufipogon; genetic diversity of O. rufipogon was closely related to their geographic distribution; O. rufipogon from Southern China contained highest organelle DNA diversity and Southern China was the center of genetic diversity of O. rufipogon. Divergence of indica and japonica occurred about0.1million years ago, much earlier than the start of O. sativa domestication. In addition, genetic differentiation and phylogenetic analysis indicated that indica and japonica evolved from different O. rufipogon groups, while indica might be domesticated from tropical O. rufipogon, japonica was domesticated from O. rufipogon in higher latitudes. Southern China was the origin center of O. sativa in China.Chloroplast, mitochondrial and nuclear genes were sequenced for100accessions of O. sativa and111accessions of O. rufipogon from China. By comparing nucleotide polymorphisms of O. sativa and O. rufipogon, we found that the gene diversity of O. sativa was less than O. rufipogon in both organelle and nuclear DNA. The result indicated that genetic bottleneck had occurred during domestication. Phylogenetic and population structure analysis showed that the domestication process of O. sativa was complex, and may be accompanied by a number of independent domestication with a large-scale gene flow from japonica to indica. Geographic analysis showed that O. sativa was domesticated from O. rufipogon in the Pearl River Basin near the Tropic of Cancer in China.Eight loci were sequenced for225accessions of O. sativa from13countries in Asia,216accessions of O. rufipogon from13countries in Asia and65accessions of O. nivara from9countries in Asia. Nucleotide polymorphisms were detected and compared to reveal origin and evolution of O. sativa. Genetic diversity analysis showed that polymorphisms diversity was quite different among different loci of different O. nivara samples and gene diversity of O. nivara was higher than O. sativa in most loci. Phylogenetic and haplotype analysis showed that both O. nivara and O. rufipogon were the ancestors of O. sativa, O. sativa was domesticated multiple times, and japonica and indica were domesticated from China and South Asia, respectively. Moreover, japonica might further be domesticated to be temperate japonica in China, when it spreaded to Southeast Asia, it crossed with local O. rufipogon and generated tropical japonica, and when it spreaded to South Asia, it crossed with local O. nivara and become aromatic. Indica crossed with O. nivara in South Asia and generated aus.Hdl, the major gene included in the photoperiod control of O. sativa, was sequenced for Chinese mini-core collections of O. sativa and O. rufipogon. Combined with the sequence of the60foreign accessions, nucleotide polymorphisms of Hdl were analysis for all materials. The results showed that Hdl contained high nucleotide polymorphism diversity. But nucleotide polymorphisms were quite different in different gene regions and the first exon had highest nucleotide polymorphism diversity. Twenty four SSR primers were used to construct the population structure of cultivated O. sativa from China, and the result showed that all Chinese cultivated O. sativa can be divided into three groups. Association analysis found that Indel of Hdl coding region caused the variation of O. sativa flowering time. Phylogenetic analysis indicated that Hdl gene had been domesticated from at least three different ancestor groups.