Comprehensive Genomic Analysis and Selection Signature Detection in Endangered Beigang Pigs Whole-Genome sequencing Data. And this is the Dataset for research.

The Beigang pig, identified as one of the endangered breeds during Chinese indigenous pigs genetic resource survey, is notable for their remarkable roughage tolerance and high reproductive capacity, according to historical records. Morphologically, Beigang pig shares similarities with most indigenous pigs in Eastern China, particularly their large ears, which serves as a valuable reference for research the genetic mechanisms underlying large ears in pigs. However, there is currently a lack of clear understanding regarding the genetic structure and inbreeding levels of the Beigang pig population. This study utilized whole-genome sequencing data from 145 Beigang pigs and integrated genetic information from commercial pigs and indigenous pigs in Eastern China to conduct an comprehensive analysis of the Beigang pig’s genetic structure. Two selection signal detection methods, Runs of Homozygosity (ROH) and Fixation Index (<i>F</i>_ST), were employed to explores the differences in genome between Beigang pig and other pigs. Additionally, FarmGtex gene expression prediction were used to uncover the genetic mechanisms controlling ear size in Beigang pigs. The results indicated that the Beigang pig holds a unique status among Chinese indigenous pigs, exhibiting a high degree of genetic diversity and a low level of inbreeding within its population. Furthermore, this research identified five homozygous variant sites in the <i>WIF1</i> gene as important candidate loci potentially influencing ear size in Beigang pigs.