Data from: Population structure and history of the Welsh sheep breeds determined by whole genome genotyping

Background: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project. Results: Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise FST between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825. Conclusions: Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK.背景：绵羊养殖是威尔士农业中最具经济重要性的板块之一，每年可为英国经济贡献约2.3亿英镑。数个世纪以来的表型选择培育出了多个本土绵羊品种，这些品种被认为已适应了威尔士多样且严苛的地貌环境。目前学界对这些品种的历史、遗传多样性及其与其他欧洲品种的亲缘关系仍知之甚少。本研究使用Illumina OvineSNP50基因分型芯片（Illumina OvineSNP50），对18个威尔士本土绵羊品种的353个个体进行基因分型，并解析了这些品种的遗传结构。随后将本研究获得的基因分型数据，与国际绵羊基因组联盟HapMap项目中收集的74个全球绵羊品种的数据集进行整合与比较。结果：针对威尔士与欧洲品种的基于模型的聚类分析显示二者存在共同祖先。该发现得到了多维尺度分析（MDS）的支持，该分析揭示了欧洲、非洲与亚洲品种的遗传分化。正如预期，商业化品种特克塞尔（Texel）与美利奴（Merino）与大多数欧洲品种存在广泛的共祖现象。威尔士本土品种与其他欧洲品种之间始终存在高水平的单倍型共享，但威尔士品种并未形成遗传同质的类群：品种间的成对FST平均值为0.107，波动范围为0.020至0.201。在18个本土品种中鉴定出4个亚群，其中大多数山地品种内部呈现高度遗传同质。基于连锁不平衡估计的近期有效种群大小范围为88至825。结论：威尔士绵羊品种具有高度遗传多样性，有效种群大小处于低至中等水平，且至少形成4个独特的遗传类群。本研究数据表明威尔士本土品种与欧洲品种拥有共同祖先。上述研究结果为未来开展全基因组关联研究奠定了基础，同时也是英国发展基因组辅助育种策略的第一步。