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Genetic Diversity and Population Structure of Five Pig Breeds from Chongqing, China
by
,
Xi Long
1,†
,
Lidan Zhang
2,†,
Yu Pan
1,
Liang Zhang
1,
Zhi Tu
1,
Lijuan Zhang
1,
Qing Wang
2,
Hongmei Pan
1,* and
Zongyi Guo
1,* 1
Chongqing Academy of Animal Science, Chongqing 402460, China
2
National Center of Technology Innovation for Pigs, Chongqing 402460, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Animals 2025, 15(17), 2610; https://doi.org/10.3390/ani15172610
Submission received: 2 July 2025
/
Revised: 9 August 2025
/
Accepted: 4 September 2025
/
Published: 5 September 2025
(This article belongs to the Section Pigs)
Simple Summary
Chongqing, a municipality directly under the Central Government of China, is located in the southwest of the country and has a subtropical monsoon climate. Five pig breeds with distinct genetic characteristics evolved in this region due to climate, topography, and human activities. These breeds have high-quality meat and are resistant to heat, humidity, and disease. This study used SNP chips to investigate the genetic diversity and population structure of these pig breeds to help conserve livestock diversity and genetic resources, thereby increasing the genetic diversity of pig breeds worldwide.
Abstract
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.
