Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India.
Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India.
Anim Biotechnol. 2022 Apr;33(2):297-311. doi: 10.1080/10495398.2020.1796696. Epub 2020 Jul 30.
Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock genetic resources. In this study, we presented a comprehensive genome-wide analysis of genetic diversity, ROH, inbreeding, linkage disequilibrium, effective population size and haplotype block structure in Tharparkar cattle of India. A total of 24 Tharparkar animals used in this study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs were retained, which were in HWE, MAF > 0.05 and genotyping rate >90%. The overall mean observed (H) and expected heterozygosity (H) were 0.339 ± 0.156 and 0.325 ± 0.129, respectively. The average minor allele frequency was 0.234 with a standard deviation of ± 0.131. We identified a total of 1832 ROH segments and the highest autosomal coverage of 13.87% was observed on chromosome 23. The genomic inbreeding coefficients estimates by F, F, F and F were 0.0589, 0.0215, 0.0532 and 0.0160 respectively. The overall mean linkage disequilibrium (LD) for a total of 133,532 pairwise SNPs measured by ' and was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations.
关于遗传多样性的知识对于家畜遗传资源的管理和可持续利用非常重要。在本研究中，我们对印度 Tharparkar 牛的遗传多样性、ROH、近交系数、连锁不平衡、有效种群大小和单倍型块结构进行了全面的全基因组分析。本研究共使用 24 头 Tharparkar 动物进行 Illumina BovineSNP50 芯片基因型分析。经过质量控制后，保留了 22825 个双等位基因 SNP，这些 SNP 处于 HWE、MAF > 0.05 和基因型率 >90%。总体观测杂合度（H）和期望杂合度（H）分别为 0.339±0.156 和 0.325±0.129。平均次要等位基因频率为 0.234，标准差为 ± 0.131。共鉴定出 1832 个 ROH 片段，在第 23 号染色体上观察到最高的常染色体覆盖率为 13.87%。由 F、F、F 和 F 估计的基因组近交系数分别为 0.0589、0.0215、0.0532 和 0.0160。总共 133532 对 SNP 的总平均连锁不平衡（LD）由 '和 ' 分别测量为 0.6452 和 0.1339。此外，我们观察到有效种群大小在过去几代中逐渐下降。
