Data from: Genomic characterisation of the indigenous Irish Kerry cattle breed

Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH¬) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.

凯里牛（Kerry cattle）是一种濒危的地方传统畜禽品种，对爱尔兰而言具有重要文化价值。本研究利用全基因组单核苷酸多态性芯片（genome-wide SNP array）数据，评估了凯里牛种群内部的基因组多样性，以及凯里牛与其他欧洲肉牛品种间的基因组差异。通过构建带有祖先图谱的系统发育树分析品种间遗传分化与基因流模式，结果显示英国短角牛（British Shorthorn）曾向现代凯里牛的祖先种群发生过历史基因交流。主成分分析（PCA）与遗传聚类分析凸显了凯里牛相较于对照英国及欧洲肉牛品种的遗传独特性。遗传有效种群大小（Ne）建模结果显示，该种群的有效规模随时间呈现持续缩减的种群动态趋势，且当前凯里牛种群的估算有效规模或已低于可持续遗传保育的阈值。此外，全基因组纯合性（FROH）分析结果表明，1992至2012年的二十年间，基因组近交程度已显著升高。最后，选择信号分析揭示了凯里牛在适应爱尔兰西南部气候、地理环境与农业生态系统过程中，受到自然与人工选择作用的基因组区域。