The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds. Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds. The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle.

中文翻译：

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十三个印度牛品种的遗传多样性和有效种群规模

基于从 699 只动物获得的 777 k 单核苷酸多态性 (SNP) 基因型，样本量从 17 到 140 只动物，对从 8 个州取样的​​一组不同的 15 个印度土著品种和非描述性土著牛的遗传结构进行了检查每个品种。迄今为止，这是对印度牛品种遗传多样性的最大和最详细的评估。混合物分析显示，所分析的 109 只土著动物含有超过 1% 的 Bos taurus 混合物，它们是相对较新的来源。纯本土动物被定义为具有 99% 以上的 Bos indicus 血统。使用主成分分析、F 统计、纯合性运行、基因组关系矩阵评估品种内部和品种之间的遗传多样性，基于等位基因频率的最大似然聚类显示，与 Bos taurus 品种相比，本土品种的遗传多样性水平较低。品种间 SNP 等位基因频率的相关性表明 Bos indicus 品种之间的遗传变异非常低。此外，印度本土品种之间的等位基因频率差异不到 1.5%，而 Bos taurus 奶牛品种之间的差异约为 40%。有效种群规模 (Ne) 在驯化后的一段时间内增加，特别是 Ongole 牛，然后在最后 100 代中下降。尽管我们发现大多数已确定的纯合子在印度本土品种中都很短，表明最近没有近亲繁殖，高 FROH 系数和低 FIS 值表明人口规模较小。尽管如此，印度本土品种的 Ne 目前仍大于 Bos taurus 奶牛品种的 Ne。有效种群规模估计值的变化与从大量本地种群驯化后合并为种群规模更有限的品种相一致。印度本土牛品种令人惊讶的低遗传多样性可能是由于它们自驯化以来的 Ne 大，与 Bos taurus 奶牛的约 250 至 500 代相比，仅在 100 代前才开始下降。有效种群规模估计值的变化与从大量本地种群驯化后合并为种群规模更有限的品种相一致。印度本土牛品种令人惊讶的低遗传多样性可能是由于它们自驯化以来的 Ne 大，与 Bos taurus 奶牛的约 250 至 500 代相比，仅在 100 代前才开始下降。有效种群规模估计值的变化与从大量本地种群驯化后合并为种群规模更有限的品种相一致。印度本土牛品种令人惊讶的低遗传多样性可能是由于它们自驯化以来的 Ne 大，与 Bos taurus 奶牛的约 250 至 500 代相比，仅在 100 代前才开始下降。