Genetic selection shaped the gene expression patterns of mRNA and protein in rice subspecies

Eukaryotes gene expression of mRNA and protein is a basic cellular activity and regulated by multiple process, yet the expression patterns at these two levels and their genetic and evolutionary determinants remain undefined in plants. Here, using RNA-sequencing and TMT labeled LC-MS/MS analysis, we investigated the genome-wide variation of mRNA and protein expression in rice subspecies japonica C92, indica MH63 and their F1 hybrid. Different expression patterns of mRNA and protein between C92 and MH63 were linked to distinct functional categories. Genes with consistent divergence of mRNA and protein expression between subspecies tend to be regulated by cis effect and had higher sequence variation in nonsynonymous sites. Population differentiation (FST) analysis showed that genes with conserved expression of either mRNA or protein in C92 and MH63 were more likely to be under purify selection, while genes with consistent divergence in mRNA or protein expression were more likely to be under positive selection, especially in their nonsynonymous site have high frequency of positive selected genes that changed their protein sequence by nonsynonymous mutation. Furthermore, oxidative stress response genes were enriched in genes with consistent divergence of expression, and showed higher sequence variation in nonsynonymous sites and are more likely to be positive selected in evolution. These results suggested that cis-regulation with high nonsynonymous-variation was evolutionarily important feature to shape divergent expression patterns of mRNA and protein and may contribute to diversity in oxidative stress response between rice subspecies. Total RNA was isolated from the 14-day-old rice seedlings for three biological replicates RNA sequencing.