Genome-wide Differences In Alternative Splicing Between Subspecies Oryza Sativa And Oryza Rufipogon Griff

Oryza sativa L.is a plant of the family Poaceae,which provides food to one-half of the world's population.In the long-term domestication process of rice,some differentiation occurred in the morphological characteristics,physiology and biochemistry between Oryza rufipogon and Oryza sativa and between two subspecies of japonica and indica.Genetic differentiation related to agronomic traits has been an important part of rice research.Alternative splicing is the direct cause of the formation of different transcripts in organisms,and is of great significance for biological processes such as the growth,development,and signal transduction of animals and plants.This study took rufipogon and two subspecies of japonica and indica as research objects,selected 66 representative rice varieties,and used transcriptome sequencing technology to study the genome-wide difference of alternative splicing of O.rufipogon and O.sativa.Based on this,the alternative splicing events of O.rufipogon and O.sativa were analyzed using r MATS,and the differentially alternative spliced genes between O.rufipogon and O.sativa,and between japonica and indica of O.sativa were screened and GO enrichment At the same time,the key genes related to agronomic traits were annotated.The main findings are as follows:1.Based on the transcriptome data of rufipogon and two cultivated rice,after comparison with the reference genome after filtering,76.28% of rufipogon can be mapped to the reference genome,84.54% of japonica can be mapped to the reference genome,and 77.87% of indica can be mapped to the reference genome.2.Among the two major subspecies of O.sativa,japonica and indica,a total of 7301 genes have undergone alternative splicing events,with exon skipping as the main type.Among them,121 are differentially alternative splicing events,and 56 genes are related.During the differentiation process between rufipogon and japonica,a total of 6015 genes were spliced,40 of which were differentially spliced events and 38 related genes.A total of 6,123 genes were alternatively spliced between indica and rufipogon,of which 13 differentially alternative splicing events were related to 12 genes.3.GO enrichment analysis of differentially alternative splicing genes showed that the differentially alternative splicing genes were mainly related to metabolic processes,catalytic enzyme activity,substance binding,and cell components.4.Screen out 10 genes related to agronomic traits and stress response from 106 differentially alternative splicing genes and analyze their expression levels.The results of this study are of great significance for understanding the genetic differentiation between O.rufipogon and O.sativa and between two subspecies of O.sativa during the domestication of rice,and also provide a theoretical basis for subsequent varieties improvement.