Genetic lineages analysis of black goat subpopulations in southern areas of China: Correlation of SNPs and methylation sites in their differentiated genes.

Black goats are widely distributed across southern China, exhibiting substantial phenotypic diversity across geographical regions. However, the genetic lineages distinct black goat populations across diverse geographical regions have remained critically under explored. In this study, whole-genome sequencing analysis was conducted on 66 black goats collected from 3 varieties in Hainan, Guangdong, Shandong, Guangxi, and Yunnan Provinces. Population structure analysis revealed significant genetic relationships: Hainan large-ear size black goats clustered closely with Nubian and Yunnan black goats, whereas Hainan small-ear size black goats demonstrated greater genetic affinity with Guangdong black goats. Furthermore, 8943 single nucleotide polymorphisms (SNPs) differentiating between small-ear black goats and large-ear or medium-ear black goats were selected to construct a low-density liquid-phase chip. The application of this chip to 263 Hainan black goats revealed significant genetic divergence between large-ear and small-ear subpopulations, suggesting two distinct ancestral origins for these phenotypic variants. These two subgroups had 10 significantly differentially expressed genes which were obtained through the joint analysis of θπ = 1.939 or θπ = 1.056 and fst = 0.227. It was found that 837 SNPs and 268 methylation sites for the 10 genes. Of them, 4 genes containing co-localized SNPs and methylation sites demonstrating a significant correlation. Notably, 2genes had only one methylation site that was significantly correlated with one SNP, and they were at the exact location. All these methylated and SNP-related sites might be key molecular markers for the identification of black goat subpopulations in southern China.