Landscape and evolution of cis- and trans-regulatory divergence in chicken genome between two contrasted breeds analyzed in three tissues at one day age
Abstract Background: Gene expression variation is an important mechanism underlying phenotypic variation, and can occur via cis- and trans-regulation. In order to understand the role of cis- and trans-regulatory variation on population divergence of chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, with major differences in body size and reproductive traits, and used them to identify the degree of cis versus trans variation in brain, liver and muscle of both male and female samples at 1 day age. Results: We provided a landscape about how the transcriptomes are regulated in the hybrid progenies of two contrasted breeds by allele specific expression analysis. Our results showed that compared with the cis-regulatory divergence, trans-acted genes existed more extensively in the chicken genome. Furthermore, a widespread tendency of compensatory regulation exists in chicken genome. Most importantly, we found the evidence of stronger purifying selection on genes regulated by trans variations than the cis elements. Conclusions: We demonstrated a pipeline to explore the allele-specific expression in the hybrid progenies of inbred lines without specific reference genome. Our research performed the first study to describe the regulatory divergence between two contrasted breeds. The results suggested that artificial selection associated with domestication in chicken may have more often acted on trans-regulatory divergence than cis.