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

ABSTRACT: 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.

ORGANISM(S): Oryza sativa Japonica Group Oryza sativa Indica Group x Oryza sativa Japonica Group Oryza sativa Indica Group

PROVIDER: GSE142770 | GEO | 2023/12/27

REPOSITORIES: GEO

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Project description:Plumage color plays a prominent role in reproductive isolation and thus understanding the genetic basis of pigmentation patterns can provide critical insight into speciation. Subspecies of the dark-eyed junco (Junco hyemalis) show marked differences in melanic plumage coloration known to have evolved rapidly since the Last Glacial Maximum just 18,000 years ago. To understand this rapid radiation we studied the pigment composition and the genetic basis of coloration in two divergent subspecies, the slate-colored and Oregon juncos. We used HPLC and light microscopy to investigate pigment deposition patterns in feathers from four body areas. RNA-seq data generated under common garden experimental conditions were then used to compare the relative roles of differential gene expression in growing feathers and sequence divergence in loci expressed during feather development. Junco feathers were found to differ in eumelanin and pheomelanin content and distribution, producing a range of black, gray and brown colors. Transcriptomic data revealed marked regulatory differences among subspecies and among body-parts within subspecies in known melanin-pathway genes (including PMEL, TYR, TYRP1, OCA2, MLANA), but also in several novel or poorly known loci (EDAR, VPS33B, HPS1). Within subspecies, lighter feathers expressed less melanin synthesis genes, more ASIP, and showed differential expression of Wnt signaling genes. Feathers from different body regions also showed differential expression of Hox genes. The two subspecies differed in expression of ASIP and three other genes (MFSD12, KCNJ13, HAND2) previously associated with color development. Sequence variation in the expressed genes was not related to color differences between junco subspecies. Our findings suggest that differential expression of a few genes can account for marked differences in plumage color and pattern, a mechanism that can account for the rapid diversification of juncos. Several novel candidate pigmentation genes found in juncos may contribute to the expression of melanic coloration in other vertebrates.

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

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