Selective Sweep With Significant Positive Selection Serves As The Driving Force For The Differentiation Of Japonica And Indica Rice Cultivars

Asian cultivated rice(Oryza sativa L.),including japonica and indica,is unarguable the most important crop in Asia as well as worldwide,and has been used as a major food source for more than half of the world’s population.However,a decisive conclusion of its origination and domestication processes are still lacking.Now,the hypothesis about the origin of these two subspecies is mainly composed of single origin theory and multiple origins theory.According to the single origin theory,although there are many differences between the two subspecies of indica and japonica,the wild rice,Oryza rufipogon,does not show these differences.Therefore,the cultivated rice domesticated from the wild rice,Oryza rufipogon,which was then followed by further differentiation.According to the multi-origin theory,these two subspecies were derived from different isolated of the wild rice,Oryza rufipogon,in different regions,so the differences between thses two subspecies have existed in their ancestors,respectively.The comprehensive and deeper survey of the genetic basis of domestication may contribute to improved domestication strategies of organisms and provide novel approaches in deciphering the process of domestication.Several genes closely related to the differentiation of these two subspecies or the domestication process of wild have been reported in the existing research.However,information on the mechanism underlying the differences in morphological,physiological,and biochemical features,as well as some other aspects between the two subspecies or wild rice and cultivated rice is limited.Moreover,the agronomic traits may be controlled by multiple genes,which were difficult to be identified.We collected a large number of rice accessions,which have been fully sequenced.Through systematic analysis,we revealed the origin and differentiation patterns of these two subspecies at the whole-genome scale,which may provide us new opportunities to get close to the answer of these questions.By compiling 296 whole-genome sequenced rice cultivars and 39 diverse wild rice,a total of 23,147,437 SNPs across all the 355 various rice samples were called and used to estimate diversity(π)among samples or divergence(Dxy)among groups.Furthermore,π/Dxy was applied as the genetic parameter to identify domesticated regions.For each window,when the,π values within japonica or indica individuals were both ≤0.0002,but the Dxy between japonica and indica was ≥0.002,we defined this region of this window as part of the domesticated region type Ⅰ(DR-1),which was with strong selective sweep signals within each subspecies.When the cultivar individuals had a low diversity(π values within the japonica and indica individuals were both≤0.0002,and Dxy between japonica and indica was also0.0002),whereas the π within the wild individuals was ≥0.001,we selected this window as part of domesticated region type Ⅱ(DR-Ⅱ)、DR-Ⅰ regions included 28 blocks which significantly differentiated between japonica and indica subspecies,while DR-Ⅱ regions were consisted of another 28 blocks which significantly differentiated between wild and cultivated rice.In-depth analysis suggested that both DR-Ⅰs and DR-Ⅱs could have originated from Indo-China Peninsula to southern China,and DR-Ⅱs might be introgressed from indica to japonica.Genes with significant positive selection and biased functions were also detected which could play important roles in rice domestication and differentiation processesIn summary,by compiling the sequences of a large number of rice accessions with high coverage,we systematically analyzed the domestication and differentiation process of indica and japonica at the whole-genome scale,and detected two types of domesticated regions with strong selective sweep signals,in which genes with significant positive selection and biased functions were also detected which may provide cluse for studying gene function and crop breeding.