Study On Major Agronomic Traits And Preliminary Gene Mapping Of Plant Height In Recombinant Inbred Lines Of Rice Nipponbare/9311

Indica and japonica are two subspecies of cultivated rice.The use of heterosis among indica and japonica subspecies has always been the goal of hybrid rice breeding.As the first two rice varieties to complete the whole genome sequencing,Japonica rice Nipponbare and indica rice9311 have become model materials for research on the function of rice genes,genetic laws of important agronomic and economic traits,and molecular mechanism of heterosis among subspecies.A large number of studies have shown that the agronomic traits among indica and japonica subspecies exhibit obvious superparental advantage,but the relationship between genetic differences among subspecies and agronomic traits has not been studied in depth.In this study,Nipponbare and 9311recombinant inbred line F₁₈ population was used as research materials for carrying out the main agronomic traits and molecular genetic analysis to promote the analysis of the association between genes and agronomic traits in indica and japonica subspecies.The main results are as follows:1.The 963 plant groups for study showed a normal distribution in main agronomic traits such as plant height,panicle length,flag leaf length and tiller number;the absolute value of skewness and kurtosis were≤1and they showed continuous variation.They were controlled by micro-effect polygenes,which can be used for analysis of quantitative trait QTL mapping.There were differences in the variation of each trait,among which the variation of the scattered,leaf color and flag leaf width traits had small changes and were greatly affected by their genetic effects;traits such as flag leaf length,panicle length,plant height and tiller number larger and more susceptible to external environment influences.2.Correlation and regression analysis found that 10 pairs of trait combinations had significant or extremely significant difference relationships among the 21 pairs of trait combinations consisting of 7agronomic traits.And the remaining trait combinations showed different positive or negative correlations.There was a close linear relationship among trait combinations and the possibility of QTL linkage was high.3.Multivariate stepwise regression analysis yielded the optimal total equation:Plant height=91.23+1.38 Panicle length+0.08 Flag leaf length-2.35 Flag leaf width-0.05 Tiller number-1.8 Leaf color-3.13scattered.Scattered had the greatest effect and panicle length contributed the most to plant height.And other traits had no significant relationship with plant height traits.Linear partial correlation analysis with plant height as the control variable found that panicle length traits contributed the most to plant height and explained 19.84%total variation of plant height.The statistical backward elimination method was used to get the most optimal model of plant height and other traits,that is,plant height=84.95+1.43 panicle length-2.8 scattered.The coefficient of determination R²=0.2086 and explained the plant height traits with a total variation of 20.86%.K-means clustering method was used to divide the population into four categories.Different clusters has different distances to the final cluster center and indica and japonica blood biased vary.4.The whole genome sequencing analysis and quality control of Nipponbare/9311 offspring Dxj-12,Dxj-25,high-stalk gene pool and short-stalk gene pool showed that 52.59 Gbp effective data had been achieved,Q30 reached 80%,and the average sequencing depth was35.11X.The average alignment efficiency with Nipponbare genome was79.52%,the average coverage depth was 25.50X,the genome coverage was 93.46%.Among the SNP loci of the parents,the short-stalk parent Dxj-12 contained 32%japonica type loci and the high-stalk parent Dxj-25contained 21%japonica type loci.The intersection of SNP and InDel association analysis yielded a candidate region related to plant height traits located at a physical position of 11,100,000-15,450,000 bp on chromosome 8 with a total length of 4.35 Mb.A total of 676 genes were annotated in this region,including 388 nonsynonymous mutation genes and 132 frameshift mutation genes.This results laid the foundation for subsequent gene cloning and functional research.