Department of Genetics and Genomics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK.
Heredity (Edinb). 2011 Feb;106(2):261-9. doi: 10.1038/hdy.2010.80. Epub 2010 Jun 16.
Recently developed Bayesian genotypic clustering methods for analysing genetic data offer a powerful tool to evaluate the genetic structure of domestic farm animal breeds. The unit of study with these approaches is the individual instead of the population. We aimed to empirically evaluate various individual-based population genetic statistical methods for characterization of genetic diversity and structure of livestock breeds. Eighteen British pig populations, comprising 819 individuals, were genotyped at 46 microsatellite markers. Three Bayesian genotypic clustering approaches, principle component analysis (PCA) and phylogenetic reconstruction were applied to individual multilocus genotypes to infer the genetic structure and diversity of the British pig breeds. Comparisons of the three Bayesian genotypic clustering methods (STRUCTURE, BAPS and STRUCTURAMA) revealed some broad similarities but also some notable differences. Overall, the methods agreed that majority of the British pig breeds are independent genetic units with little evidence of admixture. The three Bayesian genotypic clustering methods provided complementary, biologically credible clustering solutions but at different levels of resolution. BAPS detected finer genetic differentiation and in some cases, populations within breeds. Consequently, it estimated a greater number of underlying genetic populations (K, in the notation of Bayesian clustering methods). Two of the Bayesian methods (STRUCTURE and BAPS) and phylogenetic reconstruction provided similar success in assignment of individuals, supporting the use of these methods for breed assignment.
最近开发的用于分析遗传数据的贝叶斯基因型聚类方法为评估家畜品种的遗传结构提供了有力的工具。这些方法的研究单位是个体而不是群体。我们旨在通过实证评估各种基于个体的群体遗传统计方法，以描述家畜品种的遗传多样性和结构。对 18 个英国猪群体的 819 个个体进行了 46 个微卫星标记的基因型分析。应用三种贝叶斯基因型聚类方法（主成分分析（PCA）和系统发育重建）对个体的多位点基因型进行分析，以推断英国猪品种的遗传结构和多样性。三种贝叶斯基因型聚类方法（STRUCTURE、BAPS 和 STRUCTURAMA）的比较显示出一些广泛的相似之处，但也存在一些明显的差异。总体而言，这些方法都认为大多数英国猪品种是独立的遗传单位，几乎没有混合的证据。三种贝叶斯基因型聚类方法提供了互补的、具有生物学可信度的聚类解决方案，但分辨率不同。BAPS 检测到更细微的遗传分化，在某些情况下，还检测到品种内的群体。因此，它估计了更多潜在的遗传群体（贝叶斯聚类方法中的 K）。两种贝叶斯方法（STRUCTURE 和 BAPS）和系统发育重建在个体分配方面都取得了相似的成功，支持使用这些方法进行品种分配。
