The Genetic Diversity of Two Subpopulations of Shenxian Pigs as Revealed by Genome Resequencing

ABSTRACT Shenxian pigs can be divided into two main strains from their shape and appearance: Huangguazui and Wuhuatou. There are significant differences in the phenotypic characters between the two subpopulations. The Shenxian pig, as the only local pig breed listed in China Pig Breeds in Hebei Province, has the excellent traits of Chinese local pigs. In order to explore the genetic diversity and genetic distance of the different subpopulations of Shenxian pig, as well as understand their evolutionary process, whole genome resequencing and genetic structure analyses were performed for the two sub-population types of Shenxian pigs.The results showed that a total of 14,509,223 SNP sites were detected in the Huangguazui type and 13,660,201 SNP sites were detected in the Wuhuatou type. This study’s principal component analysis results showed that the genetic differentiation of the Shenxian pig population was serious, and there was obvious stratification in the population. The phylogenetic tree analysis results indicated that there was a certain genetic distance between the Huangguazui and Wuhuatou types.