Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia.
BAIF Development Research Foundation, Pune, India.
Genet Sel Evol. 2021 Jun 1;53(1):47. doi: 10.1186/s12711-021-00640-3.
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 (N) 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 F coefficients and low F values point towards small population sizes. Nonetheless, the N 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 N since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle.
本研究基于 699 头个体的 777k 个单核苷酸多态性（SNP）基因型数据，对来自印度 8 个邦的 15 个多样化的本土品种和非描述性本土牛进行了遗传结构分析，每个品种的样本量为 17 到 140 头。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。
混合分析显示，分析的 109 头本土动物中有 1%以上是相对较近起源的牛。纯本土动物被定义为具有 99%以上印度野牛血统。通过主成分分析、F 统计量、纯合子运行、基因组关系矩阵和基于等位基因频率的最大似然聚类对品种内和品种间的遗传多样性进行评估，结果表明与牛品种相比，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，印度野牛品种之间的遗传变异非常低。此外，与牛品种之间约 40%的等位基因频率差异相比，印度本土品种之间的等位基因频率差异不到 1.5%。有效种群大小（N）在驯化后一段时间内增加，特别是对翁格尔牛，然后在过去 100 代中减少。虽然我们发现大多数印度本土品种中的纯合子运行较短，表明最近没有近交，但高 F 系数和低 F 值表明种群规模较小。尽管如此，印度本土品种的 N 目前仍大于牛品种。
有效种群大小估计的变化与从一个大的本地种群驯化后，种群规模缩小到具有更有限种群规模的品种相一致。印度本土牛品种之间令人惊讶的低遗传多样性可能是由于自驯化以来其 N 较大，而牛品种的 N 大约在 250 到 500 代之间，自驯化以来其 N 开始减少仅 100 代。
