| Rice feed more than half of the world’s population as the main crop.At present,on the premise of the quality of rice,breeding improved is the primary aim.Grain size of rice,as an important agronomic trait that determines the yield and quality of rice,closely related to rice yield and quality,has become key point of the research.Although some rice grain-size-related genes have been cloned,most studies only focus on the single gene function,and ignore the interaction between different gene function variations.Whole genome sequencing material totals of 1488 rice,include wild rice species and representative rice from around the world.187 cloned genes controlling rice grain size were extracted and correlated with rice grain size,length-to-width ratio,width,length,and thousand-grain weight.To screen for significant association sites,combined with genetic analysis of the population,select the genes selected in domestication and breeding of rice,analyze the linkage relationship and morphological effects of grain type genes,and clarify the complex regulation network of grain types.Analysis of the genetic basis of rice GL,GW,LWR,and TGW diversity from the perspective of genomic and gene interactions.Following is the main results:1.Populations structure analysis,such as structure,PCA,and NJ showed that representative rice and wild rice resources in the world were divided into indica,japonica and wild rice in 1488.Among them,the indica population contain 5 populations,and the japonica population contain 2 populations.and the Oryza rufipogon contains 1 population.2.The phenotypic analysis of rice grain size indicated that the rice grain size between of indica and japonica was significantly different.Varieties of different years also existed differences in the japonica and indica.3.GWAS revealed a total of 968 significant loci.These loci were distributed across 128 genes,of which 319 were significant loci identified for LWR and 65 loci were related to GW,542 loci associated with GL,42 QTLs detcted with TGW.4.The results of selection analysis displayed that the japonica and indica populations exist significant differences,and 93 genes were selected in both cultivated rice populations.There are 38 genes that regulate multiple traits,and the other 55 genes are selected in only one trait.5.The selected genes MRG702,GW5 and Brd1 are involved in the selected genes in BR regulatory network in both two populations.Effective combinations of different variant types of genes help to produce a plump rice seed.This study can quickly find the target gene,because of the shortening of the location range of significance loci by GWAS,find the selected genes by combining with the selected analysis,and make the combination of the selected gene’s genetic loci play a cooperative role to explore the correlation between genes,it can not only increase rice yield,but also improved breeding,and providing theoretical basis for subsequent breeding production. |
