Genome-wide differences of alternative splicing between Oryza sativa ssp. indica and Oryza sativa ssp. japonica

Alternative splicing (AS) is the direct cause of different transcripts in eukaryotes and plays a vital role in biological processes such as plant growth and signal transduction. Reproductive development is the key process for rice production. Although numerous studies on AS in plants have been identified, AS of reproductive development stage between japonica and indica rice has not been conducted. In this research, we identified 6994 genes (19.2% of the total number of genes) corresponding to 14,517 AS events from the rice genome using the transcriptome data of 58 representative panicles of japonica rice and indica rice. Among the different types of AS, the frequency of exon skipping (SE) is the highest, accounting for more than 87%; the frequency of the alternative 3 ' splice site (A3SS) type is about twice that of the alternative 5 ' splice site (A5SS) type. GO enrichment analysis results showed that AS genes were mainly enriched in cellular and metabolic processes in the biological process classification. Moreover, 68 differentially AS events involved 56 genes. The expression of these five genes (OscTPI, OsLOL1, RBS1, PTB1 and OsPDIL1;1) was significantly different between the two subspecies. The analysis of AS events in panicles of japonica and indica rice provide new information regarding AS occurrence and function during these two subspecies differentiation in rice domestication and provide a theoretical basis for subsequent variety improvement.