Genetic Diversity and Population Structure of Five Pig Breeds from Chongqing, China

Five pig breeds have been developed in Chongqing and are economically important livestock resources in this region: Hechuan Black pigs (HC), Luopanshan pigs (LP), Penzhou Mountain pigs (PZ), Quxi pigs (QX), and Rongchang pigs (RC). Understanding the genetic diversity and population structure of pig breeds can help improve the conservation and management of their genetic resources. This study sequenced SNPs in 188 pigs from five breeds in Chongqing, China, using a 50K SNP chip. Of the 45,211 detected SNPs, 9442 were excluded after quality control, and 35,769 were included in the analysis. Among the five breeds, QX had the highest genetic diversity. Principal component analysis and phylogenetic trees showed that the five populations were phylogenetically distinct. Population structure analysis identified five subpopulations at K = 5, indicating that RC were genetically independent. RC had the fastest linkage disequilibrium (LD) decay, suggesting weaker selection pressure. In turn, HC exhibited the slowest decay, indicating stronger selection pressure and closer relatedness within this population. The analysis of genetic differentiation indices revealed that LP and HC had the highest degree of differentiation (0.1958), while QX and PZ had the lowest (0.0748). In conclusion, we found differences in population structure among breeds, providing a basis for conserving genetic diversity and improving pig breeds.