SREL Reprint #3510

Genetics of adaptation in modern chicken

Saber Qanbari1,2, Carl-Johan Rubin3, Khurram Maqbool4, Steffen Weigend5,6, Annett Weigend5,
Johannes Geibel1,6, Susanne Kerje3, Christine Wurmser7, Andrew Townsend Peterson8,
I. Lehr Brisbin, Jr.9, Ruedi Preisinger10, Ruedi Fries7, Henner Simianer1,6, and Leif Andersson3,4,11

1Animal Breeding and Genetics Group, Department of Animal Sciences,
University of Göttingen, Göttingen, Germany
2Department of Animal Biotechnology, Agricultural Biotechnology Research Institute of Iran (ABRII),
Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
3Science for Life Laboratory, Department of Medical Biochemistry and Microbiology,
Uppsala University, Uppsala, Sweden
4Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences,
Uppsala, Sweden
5Friedrich-Loeffler-Institut, Neustadt, Germany
6Center for Integrated Breeding Research, University of Göttingen, Göttingen, Germany
7Chair of Animal Breeding, Technical University Munich, Freising, Germany
8Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
9Savannah River Ecology Laboratory, Odum School of Ecology,
University of Georgia, Aiken, South Carolina, USA
10Lohmann Tierzucht GmbH, Cuxhaven, Germany
11Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, USA

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 aminoacid 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.

SREL Reprint #3510

Qanbari, S., C-J. Rubin, K. Maqbool, S. Weigend, A. Weigend, J. Geibel, S. Kerje, C. Wurmser, A. T. Peterson, I. L. Brisbin Jr., R. Preisinger, R. Fries, H. Simianer, and L. Andersson. 2019. Genetics of adaptation in modern chicken. PLoS Genetics 15(4): e1007989.

This information was provided by the University of Georgia's Savannah River Ecology Laboratory (srel.uga.edu).