Genetics of adaptation in modern chicken

0301 basic medicine 570 Genome Adaptation, Biological Computational Biology Genetic Variation Molecular Sequence Annotation Genomics QH426-470 Polymorphism, Single Nucleotide 630 ddc: 03 medical and health sciences Gene Frequency Genetics and Breeding in Agricultural Sciences Genetics Animals Chickens Genetik och förädling inom lantbruksvetenskap Alleles Research Article
DOI: 10.1371/journal.pgen.1007989 Publication Date: 2019-04-29T17:56:19Z
ABSTRACT
We carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken (Gallus gallus domesticus). We uncovered >21 million high quality SNPs of which 34% are newly detected variants. This panel comprises >115,000 predicted amino-acid altering substitutions as well as 1,100 SNPs predicted to be stop-gain or -loss, several of which reach high frequencies. Signatures of selection were investigated both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during domestication and breed development. Contrasting wild and domestic chicken we confirmed selection at the BCO2 and TSHR loci and identified 34 putative sweeps co-localized with ALX1, KITLG, EPGR, IGF1, DLK1, JPT2, CRAMP1, and GLI3, among others. Analysis of enrichment between groups of wild vs. commercials and broilers vs. layers revealed a further panel of candidate genes including CORIN, SKIV2L2 implicated in pigmentation and LEPR, MEGF10 and SPEF2, suggestive of production-oriented selection. SNPs with marked allele frequency differences between wild and domestic chicken showed a highly significant deficiency in the proportion of amino-acid altering mutations (P<2.5×10-6). The results contribute to the understanding of major genetic changes that took place during the evolution of modern chickens and in poultry breeding.
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