Contributions to gene diversity and allelic richness were computed in a total of 2,260 domestic pig genotypes, sharing 53,626 autosomal SNPs, belonging to 98 pig subpopulations worldwide (41 Asian, 696 genotypes; 20 American, 262 genotypes; and 37 European, 686 genotypes), using 616 pig samples belonging to six different Cosmopolitan pig breeds as an outgroup, to ascertain if local pig subpopulation can be considered reservoirs of genetic diversity for the whole domestic pig species worldwide. Assessments were carried out for the whole dataset and separately for the American-European and Asian subsets. Effective population size was computed at the subpopulation level using molecular coancestry and linkage disequilibrium information to ensure that estimates of contributions to diversity were not affected by demographic issues. Most American and European pig subpopulations tended to have favorable contributions to both gene diversity and allelic richness. However, contributions to allelic richness were more consistent than those obtained for gene diversity, whether the computations are performed using either the whole dataset or the American-Asian subset, suggesting that allelic richness can be a key parameter to identify putative reservoirs for the species. The Asian pig subpopulations never contributed favorably to the allelic richness of the domestic pig metapopulation. Although these results can partially be explained by the highly divergent origins of the American-European and the Asian pig subpopulations, it cannot be discarded that the results obtained for the Asian subpopulations are biased due to a worse calling performance of the pig SNP arrays used for genotyping. The use of other potentially less biased sources of genotypic information is advisable to compare the Asian and American-European pig subpopulations genetic diversity.

中文翻译：

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通过对基因多样性和等位基因丰富度的贡献，将本地猪品种表征为全球家猪遗传变异的储存库


计算了总共 2,260 个家猪基因型对基因多样性和等位基因丰富度的贡献，共享 53,626 个常染色体 SNP，属于全球 98 个猪亚群（41 个亚洲，696 个基因型;20 个美洲，262 个基因型;和 37 个欧洲，686 个基因型），使用属于 6 个不同 Cosmopolitan 猪品种的 616 个猪样本作为外组，以确定当地猪亚群是否可以被视为全球整个家猪物种遗传多样性的储存库。 对整个数据集进行了评估，并分别对美洲-欧洲和亚洲子集进行了评估。使用分子同ances和连锁不平衡信息在亚群水平上计算有效种群规模，以确保对多样性贡献的估计不受人口问题的影响。大多数美国和欧洲猪亚群往往对基因多样性和等位基因丰富度都有有利的贡献。然而，无论是使用整个数据集还是美洲-亚洲子集进行计算，对等位基因丰富度的贡献都比对基因多样性的贡献更一致，这表明等位基因丰富度可以成为识别该物种的假定储库的关键参数。亚洲猪亚群从未对家猪元种群的等位基因丰富度做出有利贡献。尽管这些结果可以部分地用美洲-欧洲猪亚群和亚洲猪亚群的高度差异来解释，但不能忽视的是，由于用于基因分型的猪 SNP 阵列的检出性能较差，亚洲亚群获得的结果存在偏差。 建议使用其他可能偏差较小的基因型信息来源来比较亚洲和美洲-欧洲猪亚群的遗传多样性。