Data from: Merino and Merino-derived sheep breeds: a genome-wide intercontinental study
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Background: Merino and Merino-derived sheep breeds have been widely distributed across the world, both as purebred and admixed populations. They represent an economically and historically important genetic resource which over time has been used as the basis for the development of new breeds. In order to examine the genetic influence of Merino in the context of a global collection of domestic sheep breeds, we analyzed genotype data that were obtained with the OvineSNP50 BeadChip (Illumina) for 671 individuals from 37 populations, including a subset of breeds from the Sheep HapMap dataset. Results: Based on a multi-dimensional scaling analysis, we highlighted four main clusters in this dataset, which corresponded to wild sheep, mouflon, primitive North European breeds and modern sheep (including Merino), respectively. The neighbor-network analysis further differentiated North-European and Mediterranean domestic breeds, with subclusters of Merino and Merino-derived breeds, other Spanish breeds and other Italian breeds. Model-based clustering, migration analysis and haplotype sharing indicated that genetic exchange occurred between archaic populations and also that a more recent Merino-mediated gene flow to several Merino-derived populations around the world took place. The close relationship between Spanish Merino and other Spanish breeds was consistent with an Iberian origin for the Merino breed, with possible earlier contributions from other Mediterranean stocks. The Merino populations from Australia, New Zealand and China were clearly separated from their European ancestors. We observed a genetic substructuring in the Spanish Merino population, which reflects recent herd management practices. Conclusions: Our data suggest that intensive gene flow, founder effects and geographic isolation are the main factors that determined the genetic makeup of current Merino and Merino-derived breeds. To explain how the current Merino and Merino-derived breeds were obtained, we propose a scenario that includes several consecutive migrations of sheep populations that may serve as working hypotheses for subsequent studies.
背景：美利奴（Merino）及其衍生绵羊品种已作为纯种与混血种群广泛分布于全球范围，二者是兼具经济与历史价值的重要遗传资源，长期以来被用作培育新品种的基础。为探究美利奴在全球家养绵羊品种体系中的遗传影响力，本研究对来自37个种群的671个个体的基因型数据展开分析，这些数据由绵羊50K单核苷酸多态性分型芯片（OvineSNP50 BeadChip, Illumina）检测获得，其中包含部分来自绵羊单倍型图谱（Sheep HapMap）数据集的品种子集。 结果：基于多维尺度分析（multi-dimensional scaling analysis），本研究在该数据集中明确划分出四大类群，分别对应野生绵羊、摩弗伦羊、北欧原始品种以及现代绵羊（含美利奴）。邻接网络分析（neighbor-network analysis）进一步区分了北欧与地中海家养品种，并呈现出美利奴及美利奴衍生品种、其他西班牙品种以及其他意大利品种的亚类群。基于模型的聚类分析（model-based clustering）、迁移分析及单倍型共享（haplotype sharing）结果显示，古代种群间存在遗传交流，同时也发生了近代以美利奴为介导的基因流（gene flow），即基因流向全球范围内的多个美利奴衍生种群。西班牙美利奴与其他西班牙绵羊品种间的紧密亲缘关系，与美利奴品种起源于伊比利亚半岛的结论相符，且可能更早受到其他地中海种群的遗传贡献。澳大利亚、新西兰与中国的美利奴种群与欧洲祖先群体明显分化。本研究还观察到西班牙美利奴种群存在遗传亚结构，这反映了近期的种群管理实践。 结论：本研究数据表明，高强度基因流、奠基者效应与地理隔离是塑造当前美利奴及美利奴衍生品种遗传构成的核心因素。为阐释当前美利奴及美利奴衍生品种的形成过程，本研究提出包含绵羊种群连续迁徙的假说，可作为后续研究的工作假设。
