Whole-genome resequencing analysis of Pengxian Yellow Chicken to identify genome-wide SNPs and signatures of selection
- 91 Downloads
Chinese indigenous chickens have experienced strong selective pressure in genes or genomic regions controlling critical agricultural traits. To exploit the genetic features that may be useful in agriculture and are caused by artificial selection, we performed whole-genome sequencing of six Pengxian Yellow Chickens and downloaded the sequence data of five Red Jungle fowls from the NCBI. Through selective sweep analysis, we detected several regions with strong selection signals, containing 497 protein-coding genes. These genes were involved in developmental processes, metabolic processes, the response to external stimuli and other biological processes including digestion (ABCG5, ABCG8 and ADRB1), muscle development and growth (SMPD3, NELL1, and BICC1) and reduced immune function (CD86 and MTA3). Interestingly, we identified several genes with extremely strong selection signals associated with the loss of visual capability of domestic chickens relative to their wild ancestors. Amongst them, we propose that CTNND2 is involved in the evolutionary changes of domestic chickens toward reduced visual ability through the diopter system. VAT1 was also likely to contribute to these processes through its regulation of mitochondrial fusion. In summary, these data illustrate the patterns of genetic changes in Pengxian yellow chickens during domestication and provide valuable genetic resources that facilitate the utilization of chickens in agricultural production.
KeywordsPengxian Yellow Chicken Whole genome Resequencing Selection SNP
This work was supported by Sichuan Science and Technology Program (2016NYZ0050), and Technology Planning Project of Chengdu (2015-NY01-00036-NC).
Conceptualization, HY and QZ; methodology, HY and YW; software, HY and DL; formal analysis, HY and DL; resources, QZ; writing—original draft preparation, HY; writing—review and editing, HY and QZ; supervision, QZ; project administration, YW; funding acquisition, QZ and HY.
Compliance with ethical standards
Conflict of interest
All the authors report no conflicts of interest in this work.
All experimental operations were approved by the Animal Ethics Committee of Sichuan Agricultural University (approval number: 20171410401). Relevant guidelines and regulations were followed for all methods.
- Omar S, Qureshi YZ, Nakamura Kyoko, Attridge Kesley, Manzotti Claire, Schmidt Emily M, Baker Jennifer, Jeffery Louisa E, Kaur Satdip, Briggs Zoe, Hou Tie Z, Futter Clare E, Anderson Graham, Walker Lucy SK, Sansom David M (2011) Trans-endocytosis of CD80 and CD86: a molecular basis for the cell extrinsic function of CTLA-4. Science 332(6029):600–603CrossRefGoogle Scholar
- Parisi MA, Doherty D, Eckert ML, Shaw DW, Ozyurek H, Aysun S, Giray O, Al SA, Al SS, Dohayan N, Bakhsh E, Indridason OS, Dobyns WB, Bennett CL, Chance PF, Glass IA (2006) AHI1 mutations cause both retinal dystrophy and renal cystic disease in Joubert syndrome. J Med Genet 43(4):334–339CrossRefGoogle Scholar
- Wu CX (2001) The utilization of inheritance resource and local fowls breeders in the poultry producing. China Poult 23(23):3–4Google Scholar