Lv Feng-Hua, Agha Saif, Kantanen Juha, Colli Licia, Stucki Sylvie, Kijas James W, Joost Stéphane, Li Meng-Hua, Ajmone Marsan Paolo
CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.
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.
Mol Biol Evol. 2014 Dec;31(12):3324-43. doi: 10.1093/molbev/msu264. Epub 2014 Sep 23.
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.
驯化之后，绵羊（Ovis aries）通过适应各种不同的环境和多样的生产系统，成为了全球重要的养殖动物。气候介导的选择压力塑造了表型变异，并在不同农业生态区饲养的品种基因组中留下了遗传“印记”。与众多仅使用群体遗传学数据寻找选择证据的研究不同，在此我们对环境数据与单核苷酸多态性（SNP）变异进行了综合共分析。通过检测来自32个适应不同区域气候的古老本地绵羊品种的49,034个SNP，我们鉴定出230个有选择证据的SNP，其可能归因于气候介导的压力。其中，189个（82%）在来自全球范围不同地理区域和气候的更大一组本地群体中，等位基因频率与气候变量之间显示出显著相关性（P≤0.05）。对与显著SNP共定位的基因进行基因本体分析，在能量代谢以及内分泌和自身免疫调节的生物学过程中，鉴定出17个与GTP酶调节剂和肽受体活性相关的候选基因。我们还观察到TBC1D12的核心单倍型TBC1D12-CH1存在高度连锁不平衡和显著的扩展单倍型纯合性。核心单倍型和等位基因OAR22_18929579-A的全球频率分布呈现出明显的地理模式，并且与气候变化存在显著（P≤0.05）相关性。我们的结果表明，对当地气候的适应塑造了一些变异的空间分布，这些变异可能是支撑绵羊适应性变异的候选因素。
