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_O) and expected heterozygosity (H_E) 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_ROH, F_HOM, F_GRM and F_UNI 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 D’ and r ² 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畜牧遗传资源的管理和可持续利用非常重要。在这项研究中，我们对印度 Tharparkar 牛的遗传多样性、ROH、近交、连锁不平衡、有效种群规模和单倍型块结构进行了全面的全基因组分析。本研究中使用的总共 24 只 Tharparkar 动物用 Illumina BovineSNP50 阵列进行了基因分型。经过质量控制，保留了22,825个双等位基因SNP，其中HWE，MAF> 0.05，基因分型率> 90％。观察到的总体平均值 (H _O ) 和预期杂合性 (H _E) 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，标准偏差为 ± 0.131。我们共鉴定出 1832 个 ROH 片段，在 23 号染色体上观察到最高的常染色体覆盖率 13.87%。 F _ROH、 F _HOM、 F _GRM和 F _UNI估计的基因组近交系数分别为 0.0589、0.0215、0.0532 和 0.0160。由D ' 和r ²测量的总共 133,532 个成对 SNP 的总体平均连锁不平衡 (LD)分别为 0.6452 和 0.1339。此外，我们观察到过去几代人的有效种群规模逐渐下降。