Comparative analysis of the transcriptomes of two rice subspecies reveals differentially expressed genes associated with phenotypic differences and reproductive isolation

Abstract

Background: Rice has been used as a model plant to study adaptation, genome evolution and reproductive isolation among species and the genetics and evolution of complex traits. Two subspecies of cultivated rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. Results: To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica plants, and identified 97,005 transcribed fragments and 7702 novel transcriptionally active regions. We also identified 1857 (4.58% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. According to previous population genetic analyses, these DEGs may associate with the phenotypic differences between the two subspecies. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5′ flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs.Conclusion: This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs that may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.