Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3'-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.

Animal Biotechnological Research Center Xinjiang Academy of Animal Science Urumqi China

Animal Breeding Division National Animal Science Institute Nepal Agriculture Research Council Kathmandu Nepal

Animal Production and Health Laboratory Joint FAO IAEA Division International Atomic Energy Agency Vienna Austria

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

College of Animal Science and Technology China Agricultural University Beijing China

College of Animal Science and Technology Yunnan Agricultural University Kunming China

College of Animal Science Inner Mongolia Agricultural University Hohhot China

College of Life and Geographic Sciences Kashi University Kashi China

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

CTLGH and SRUC The Roslin Institute Building Easter Bush Campus Edinburgh Scotland

Department of Agriculture Payame Noor University Tehran Iran

Department of Animal Breeding and Genetics Faculty of Veterinary Medicine and Animal Science Swedish University of Agricultural Sciences Uppsala Sweden

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

Department of Animal Genetics Center for Research in Agricultural Genomics CSIC IRTA UAB UB Campus de la Universitat Autònoma de Barcelona Bellaterra Spain

Department of Animal Production Faculty of Agriculture Cairo University 12613 Giza Egypt

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

Department of Animal Science Faculty of Agriculture University of Zagreb Zagreb Croatia

Department of Animal Sciences Universitat Autònoma de Barcelona Bellaterra Spain

Department of Biological Sciences University of Alberta Edmonton Alberta Canada

Department of Microbial Cellular and Molecular Biology Addis Ababa University Addis Ababa Ethiopia

Department of Preclinical Sciences and Pathology Faculty of Veterinary Medicine Norwegian University of Life Sciences Ås Norway

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

Embrapa Recursos Genéticos e Biotecnologia Parque Estação Biológica PqEB Brasília DF Brazil

Faculty of Natural Resources and Environmental Sciences Agricultural University of Iceland Borgarnes Iceland

Faculty of Veterinary Medicine Utrecht University Utrecht the Netherlands

Grass Feeding Livestock Engineering Technology Research Center Ningxia Academy of Agriculture and Forestry Sciences Yinchuan China

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

Institute of Sheep and Goat Science Nanjing Agricultural University Nanjing China

LiveGene Program International Livestock Research Institute Addis Ababa Ethiopia

Livestock Genetics Program International Livestock Research Institute Nairobi Kenya

Novogene Bioinformatics Institute Beijing China

Production Systems Natural Resources Institute Finland Jokioinen Finland

School of Biosciences Cardiff University Cathays Park Cardiff Wales United Kingdom

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

Shandong Binzhou Academy of Animal Science and Veterinary Medicine Binzhou China

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

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

Sustainable Places Research Institute Cardiff University Wales United Kingdom

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

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