Data from: Genetic diversity and population structure in South African, French and Argentinian Angora Goats from genome-wide SNP data

The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations.阿根廷（AR）、法国（FR）与南非（SA）的安哥拉山羊种群在地理与遗传层面均保持独立。鉴于各国采用了各具特色的选育与繁育策略，有必要从遗传维度对这些种群开展特征解析工作。本研究借助标准化50K山羊单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片，对来自三个不同地理区域的安哥拉山羊的遗传变异情况进行了分析，共完成104只山羊的基因分型，其中阿根廷种群30只、法国种群26只、南非种群48只。研究人员计算了各群体所有常染色体上的杂合度值与近交系数，以期望杂合度（Expected Heterozygosity, HE）衡量的遗传多样性范围为0.371（南非种群）至0.397（阿根廷种群），其中南非山羊是唯一群体平均近交系数为正值（0.009）的种群。在合并三个数据集并完成标准质量控制（Quality Control, QC）与连锁不平衡（Linkage Disequilibrium, LD）修剪后，共保留15105个SNP位点用于后续分析。本研究采用主成分分析与聚类分析可视化呈现了种群内部及种群间的个体亲缘关系，结果显示所有南非安哥拉山羊均与其他种群相互分离，形成了界限清晰的独特聚类群，而法国与阿根廷山羊群体中则检出异常个体；同时观察到阿根廷与法国种群间存在显著的遗传混合现象，且这两个群体均表现出与南非山羊拥有部分共同祖先的特征。研究人员还计算了三个种群每条染色体上相邻位点的平均连锁不平衡值，结果显示各群体在较短物理间隔内均呈现出最高的连锁不平衡水平。经估算，安哥拉山羊品种在10个世代前的有效种群大小（Ne）为149，整体呈现下降趋势。本研究结果证实，地理隔离与差异化选育策略是导致各山羊种群间遗传分化的核心原因。