Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)

Background Cultivated rice consists of two subspecies,IndicaandJaponica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1). Results The transcriptomes of the two subspecies of rice are highly divergent.Japonicahave significantly lower expression and genetic diversity relative toIndica, which is likely a consequence of a population bottleneck duringJaponicadomestication. We leveraged high-density genotypic data and transcript levels to identify cis-regulatory variants that may explain the genetic divergence between the subspecies. We identified significantly more eQTL that were specific to theIndicasubspecies compared toJaponica, suggesting that the observed differences in expression and genetic variability also extends to cis-regulatory variation. Conclusions Using RNA sequencing data for 91diverse rice accessions and high-density genotypic data, we show that the two species are highly divergent with respect to gene expression levels, as well as the genetic regulation of expression. The data generated by this study provide, to date, the largest collection of genome-wide transcriptional levels for rice, and provides a community resource to accelerate functional genomic studies in rice.