Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wroclaw, 51631, Poland.
Sci Rep. 2017 Jan 13;7:40688. doi: 10.1038/srep40688.
Since domestication, population bottlenecks, breed formation, and selective breeding have radically shaped the genealogy and genetics of Bos taurus. In turn, characterization of population structure among diverse bull (males of Bos taurus) genomes enables detailed assessment of genetic resources and origins. By analyzing 432 unrelated bull genomes from 13 breeds and 16 countries, we demonstrate genetic diversity and structural complexity among the European/Western cattle population. Importantly, we relaxed a strong assumption of discrete or admixed population, by adapting latent variable models for individual-specific allele frequencies that directly capture a wide range of complex structure from genome-wide genotypes. As measured by magnitude of differentiation, selection pressure on SNPs within genes is substantially greater than that on intergenic regions. Additionally, broad regions of chromosome 6 harboring largest genetic differentiation suggest positive selection underlying population structure. We carried out gene set analysis using SNP annotations to identify enriched functional categories such as energy-related processes and multiple development stages. Our population structure analysis of bull genomes can support genetic management strategies that capture structural complexity and promote sustainable genetic breadth.
自驯化以来，人口瓶颈、品种形成和选择性繁殖从根本上塑造了家牛的谱系和遗传学。反过来，对不同公牛（家牛雄性）基因组的种群结构进行特征描述，可以详细评估遗传资源和起源。通过分析来自 13 个国家的 432 头非相关公牛的基因组，我们展示了欧洲/西方牛种群的遗传多样性和结构复杂性。重要的是，我们通过适应个体特定等位基因频率的潜在变量模型来放松离散或混合种群的强烈假设，该模型可以直接从全基因组基因型中捕获广泛的复杂结构。根据分化程度衡量，基因内 SNPs 所受到的选择压力远大于基因间区域。此外，染色体 6 上包含最大遗传分化的广泛区域表明，种群结构下存在正选择。我们使用 SNP 注释进行了基因集分析，以确定富含功能类别，如与能量相关的过程和多个发育阶段。我们对公牛基因组的种群结构分析可以支持遗传管理策略，从而捕获结构复杂性并促进可持续的遗传广度。
