How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.

Animal and Grassland Research and Innovation Centre Teagasc Moorepark Fermoy Co Cork Ireland

CAAS ILRI Joint Laboratory on Livestock and Forage Genetic Resources Institute of Animal Science Chinese Academy of Agricultural Sciences Beijing China

CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Beijing China

Center for Tropical Livestock Genetics and Health The Roslin Institute University of Edinburgh Easter Bush Midlothian United Kingdom

College of Animal Science and Technology China Agricultural University Beijing China

College of Life Sciences University of Chinese Academy of Sciences Beijing China

Commonwealth Scientific and Industrial Research Organisation Agriculture and Food Queensland Bioscience Precinct St Lucia Brisbane QLD Australia

Department of Agriculture Payame Noor University Tehran Iran

Department of Animal Breeding and Genetics Justus Liebig University Giessen Giessen Germany

Department of Animal Science Faculty of Agriculture Shahid Bahonar University of Kerman Kerman Iran

Department of Animal Sciences Food and Nutrition Università Cattolica del Sacro Cuore Piacenza Italy

Department of Biological Sciences University of Alberta Edmonton AB Canada

Department of Virology State Veterinary Institute Jihlava Jihlava Czech Republic

Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica Università degli Studi di Bari Aldo 24 Moro Bari Italy

Faculty of Veterinary Medicine Utrecht University Utrecht The Netherlands

Fish and Wildlife Enforcement Branch Forensic Unit Government of Alberta Edmonton AB Canada

Institute of Animal Breeding and Genetics University of Veterinary Medicine Vienna Austria

Institute of Animal Husbandry and Veterinary Medicine Xinjiang Academy of Agricultural and Reclamation Sciences Shihezi China

Institute of Animal Science Ningxia Academy of Agriculture and Forestry Sciences Hui Autonomous Region Yinchuan Ningxia China

L K Ernst Federal Science Center for Animal Husbandry Moscow Region Podolsk Russian Federation

Livestock Genetics Program International Livestock Research Institute Addis Abeba Ethiopia

Livestock Genetics Program International Livestock Research Institute Nairobi Kenya

Production Systems Natural Resources Institute Finland Jokioinen Finland

School of Biosciences Cardiff University Cathays Park Cardiff United Kingdom

School of Life Sciences University of Nottingham University Park Nottingham United Kingdom

Small Ruminant Genomics International Center for Agricultural Research in the Dry Areas Addis Ababa Ethiopia

Sustainable Places Research Institute Cardiff University Cardiff United Kingdom

Xinjiang Academy of Agricultural and Reclamation Sciences State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding Shihezi China

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Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci