Genetics of adaptation in modern chicken

• DOI: 10.1371/journal.pgen.1007989
• Publication Date: 2019-04-29T17:56:19Z
• Authors: Saber Qanbari; Carl-Johan Rubin; Khurram Maqbool; Steffen Weigend; Annett Weigend; Johannes Geibel; Susanne Kerje; Christine Wurmser; Andrew Townsend P...; I. Lehr Brisbin; Ruedi Preisinger; Ruedi Fries; Henner Simianer; Leif Andersson
• Keywords: Candidate gene

We carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations commercial broilers layers to perform a systematic screening adaptive changes in modern (Gallus gallus domesticus). uncovered >21 million high quality SNPs which 34% are newly detected variants. This panel comprises >115,000 predicted amino-acid altering substitutions as well 1,100 be stop-gain or -loss, several reach frequencies. Signatures selection were investigated both through analyses fixation differentiation reveal selective sweeps that may have had prominent roles during domestication breed development. Contrasting wild domestic we confirmed at the BCO2 TSHR loci identified 34 putative co-localized with ALX1, KITLG, EPGR, IGF1, DLK1, JPT2, CRAMP1, GLI3, among others. Analysis enrichment between groups vs. commercials revealed further candidate genes CORIN, SKIV2L2 implicated pigmentation LEPR, MEGF10 SPEF2, suggestive production-oriented selection. marked allele frequency differences showed highly significant deficiency proportion mutations (P<2.5×10−6). The results contribute understanding major genetic took place evolution chickens poultry breeding.