Population structure, regions of homozygosity (ROH) and selection signal of two domesitic goat breeds revealed by whole-genome resequencing

Chinese indigenous goat breeds exhibit rich genetic diversity and a long history of domestication, endowing these native populations with superior traits in environmental adaptation, forage utilization, and disease resistance. The identification of selection signatures through comparative genomic analysis could facilitate the understanding of breed differentiation and enables the discovery of functionally important genes. Using whole-genome sequencing data (23.87× Average coverage), we assessed genetic variation, population stratification, runs of homozygosity (ROH), and selection signatures in two Chinese goat breeds: Inner Mongolia cashmere goats (IMCGs, n = 200) and Zhongwei goats (ZWGs, n = 200). The results showed that the two goat breeds exhibited distinct separation in the phylogenetic tree and the Principal component analysis (PCA) and the IMCG population exhibited a faster LD decay rate. A total of 11,484 and 7240 ROH fragments were detected in ZWGs and IMCGs respectively by homozygosity analysis of all chromosomes. Subsequently, the investigation of regions of homozygosity (ROH) was performed utilizing the PLINK software. In ZWGs and IMCGs, there were 5 and 14 genomic regions with high frequency of ROH island (ROHi) respectively, leading to the identification of 77 genes, containing 10 shared genes. Taking Fst (screening for population differentiation sites), π-Ratio (reflecting genetic diversity differences), and XP-CLR (detecting cross-population selection sweeps) as the core methods, cross-screening for strong selection signal regions; Tajima’s D is used to verify whether the candidate regions deviate from neutral evolution (to exclude genetic drift interference), and finally results to obtain 10 (ROHi) and 38 (Fst, π-Ratio, XP-CLR) shared candidate genes. Among these candidate genes are related to carcass and muscle development (CTNNA1, BIRC6, SIL1, BMPER, CACNA2D1, DGKB, MED13), fat deposition (BMPER, MAP3K3, PDGFD, FREBF2), growth and body size (DCHS2, GALNTL6, PDGFD, SHROOM3), cashmere (NBEA, TGFBR3, GALNTL6), reproduction (BRIC6, CDH23) and environmental adaptation (NBEA, CNGB3) of goats. Among them, PDGFD and TGFBR3 genes showed highly significant differentiation and haplotype patterns between the two groups. These results provide suggestive evidence that PDGFD and TGFBR3 genes may play an important role in the differentiation of goat body size and cashmere characteristics, which is worth further investigation. In summary, we conducted a genome-wide exploration of goats from two regions in China. Our analysis of the population structure, genetic diversity and selection signature of these two groups revealed several selection regions and candidate genes that could influence goat important traits and characteristics through various selection signal analysis methods. The findings of this study provide a basis for further conservation and utilization of goat resources and offer valuable materials for genetic improvement of goats.