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Evolution of cis- and trans-regulatory divergence in the chicken genome between two contrasting breeds analyzed using three tissue types at one-day-old

文献类型： 外文期刊

作者： Wang, Qiong 1 ; Jia, Yaxiong 3 ; Wang, Yuan 4 ; Jiang, Zhihua 5 ; Zhou, Xiang 6 ; Zhang, Zebin 1 ; Nie, Changsheng 1 ; Li 1 ;

作者机构： 1.China Agr Univ, Coll Anim Sci & Technol, Natl Engn Lab Anim Breeding, State Key Lab Anim Nutr,Dept Anim Genet & Breedin, Beijing, Peoples R China

2.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Key Lab Sustainable Utilizat Marine Fisheries Res, Minist Agr & Rural, Qingdao, Peoples R China

3.Chinese Acad Agr Sci, Inst Anim Sci, Beijing, Peoples R China

4.Qingdao Agr Univ, Dept Anim Sci & Technol, Qingdao, Peoples R China

5.Washington State Univ, Dept Anim Sci, Ctr Reprod Biol, Vet & Biomed Res Bldg, Pullman, WA 99164 USA

6.Huazhong Agr Univ, Coll Anim Sci & Vet Med, Wuhan, Peoples R China

关键词： Cis; Trans; Regulation; RNA-seq; Allele-specific expression

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2019 年 20 卷 1 期

页码：

收录情况： SCI

摘要： Background: Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population divergence in chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibit major differences in body size and reproductive traits, and used them to determine the degree of cis versus trans variation in the brain, liver, and muscle tissue of male and female 1-day-old specimens. Results: We provided an overview of how transcriptomes are regulated in hybrid progenies of two contrasting breeds based on allele specific expression analysis. Compared with cis-regulatory divergence, trans-acting genes were more extensive in the chicken genome. In addition, considerable compensatory cis- and trans-regulatory changes exist in the chicken genome. Most importantly, stronger purifying selection was observed on genes regulated by trans-variations than in genes regulated by the cis elements. Conclusions: We present a pipeline to explore allele-specific expression in hybrid progenies of inbred lines without a specific reference genome. Our research is the first study to describe the regulatory divergence between two contrasting breeds. The results suggest that artificial selection associated with domestication in chicken could have acted more on trans-regulatory divergence than on cis-regulatory divergence.

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