title: Adaptations to climate-mediated selective pressures in sheep.
abstract: Following domestication, sheep (Ovis aries) have become essential farmed animals across the world through adaptation to a diverse range of environments and varied production systems. Climate-mediated selective pressure has shaped phenotypic variation and has left genetic "footprints" in the genome of breeds raised in different agroecological zones. Unlike numerous studies that have searched for evidence of selection using only population genetics data, here, we conducted an integrated coanalysis of environmental data with single nucleotide polymorphism (SNP) variation. By examining 49,034 SNPs from 32 old, autochthonous sheep breeds that are adapted to a spectrum of different regional climates, we identified 230 SNPs with evidence for selection that is likely due to climate-mediated pressure. Among them, 189 (82%) showed significant correlation (P ≤ 0.05) between allele frequency and climatic variables in a larger set of native populations from a worldwide range of geographic areas and climates. Gene ontology analysis of genes colocated with significant SNPs identified 17 candidates related to GTPase regulator and peptide receptor activities in the biological processes of energy metabolism and endocrine and autoimmune regulation. We also observed high linkage disequilibrium and significant extended haplotype homozygosity for the core haplotype TBC1D12-CH1 of TBC1D12. The global frequency distribution of the core haplotype and allele OAR22_18929579-A showed an apparent geographic pattern and significant (P ≤ 0.05) correlations with climatic variation. Our results imply that adaptations to local climates have shaped the spatial distribution of some variants that are candidates to underpin adaptive variation in sheep.
authors.affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.
authors.forename: Feng-Hua
authors.initials: FH
authors.lastname: Lv
authors.affiliation: Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland Department of Animal Science, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
authors.forename: Saif
authors.initials: S
authors.lastname: Agha
authors.affiliation: Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland Department of Biology, University of Eastern Finland, Kuopio, Finland.
authors.forename: Juha
authors.initials: J
authors.lastname: Kantanen
authors.affiliation: Istituto di Zootecnica, Facoltà di Agraria, Università Cattolica del Sacro Cuore, Piacenza, Italy Biodiversity and Ancient DNA Research Center-BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy.
authors.forename: Licia
authors.initials: L
authors.lastname: Colli
authors.affiliation: Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Stucki
authors.affiliation: CSIRO Livestock Industries, St Lucia, Brisbane, Qld, Australia.
authors.forename: James W
authors.initials: JW
authors.lastname: Kijas
authors.affiliation: Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Joost
authors.affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China menghua.li@ioz.ac.cn.
authors.forename: Meng-Hua
authors.initials: MH
authors.lastname: Li
authors.affiliation: Istituto di Zootecnica, Facoltà di Agraria, Università Cattolica del Sacro Cuore, Piacenza, Italy Biodiversity and Ancient DNA Research Center-BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Ajmone Marsan
mesh_terms: D000064:Acclimatization / Q000235:genetics; D000818:Animals; D001947:Breeding; D002980:Climate; D019143:Evolution, Molecular; D005787:Gene Frequency; D063990:Gene Ontology; D005796:Genes; D006239:Haplotypes; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D034561:Sheep, Domestic / Q000235:genetics*; D013045:Species Specificity
keywords: GTPase regulator; TBC1D12; adaptation; climate-mediated selection; genome-wide scans; peptide receptor; sheep