Knowledge about genetic diversity and selection signatures are very essential for the management and sustainable utilization of sheep genetic resources in India. In this study, we performed a comprehensive genome-wide analysis of genetic diversity and selection signatures using SNP data. A total of 79 animals from three Indian sheep breeds: Changthangi (n = 29), Deccani (n = 24), and Garole (n = 26) genotyped with Illumina Ovine SNP50 BeadChip were included in this study. The average minor allele frequency was 0.284 with a standard deviation of 0.129. The overall mean observed (H_O) and expected heterozygosity (H_E) were 0.369±0.141 and 0.373±0.118, respectively. The proportion of polymorphic SNPs (P_N) ranged from 0.84 (Garole) to 0.93 (Changthangi). The average pairwise genetic distance (D) ranged from 0.301 (Garole) to 0.313 (Changthangi). We identified a total of 9244 ROH segments and the genomic inbreeding coefficients ranged from 0.0673 (Deccani) to 0.1779 (Garole). Two different statistical approaches (ROH and iHS) revealed selection signatures in 37 genomic regions mapping to 188 genes across 16 of the 26 autosomes in three sheep breeds. The selective sweeps provide new insights into the local adaptation and production potential of three Indian sheep breeds. Some notable candidate genes include the TRPM8 gene involved in cold adaptation, JADE2, PLEKHB2, SPP2, TSHR, and UBE2B genes associated with meat quality traits, and the PPP3CA gene associated with fecundity.

关于遗传多样性和选择标记的知识对于印度绵羊遗传资源的管理和可持续利用至关重要。在这项研究中，我们使用SNP数据对遗传多样性和选择标记进行了全基因组范围的全面分析。这项研究包括了用印度光绵羊SNP50 BeadChip进行基因分型的三种印度绵羊品种的总共79只动物：Changthangi（n = 29），Deccani（n = 24）和Garole（n = 26）。平均次要等位基因频率为0.284，标准差为0.129。观察到的总平均数（H _O）和预期的杂合度（H _E）分别为0.369±0.141和0.373±0.118。多态性SNP的比例（P _Ñ）介于0.84（Garole）至0.93（Changthangi）之间。平均成对遗传距离（D）介于0.301（Garole）至0.313（Changthangi）之间。我们共鉴定了9244个ROH区段，基因组近交系数的范围从0.0673（Deccani）到0.1779（Garole）。两种不同的统计方法（ROH和iHS）揭示了在37个基因组区域中的选择标记，这些标记映射到三个绵羊品种的26个常染色体中的16个常染色体上的188个基因。选择性扫除为三种印度绵羊品种的当地适应和生产潜力提供了新的见识。一些著名的候选基因包括与冷适应有关的TRPM8基因，与肉质性状相关的JADE2，PLEKHB2，SPP2，TSHR和UBE2B基因，以及PPP3CA 与生殖力有关的基因。