Genome-Wide Association Study Reveals Genetic Mechanisms Underlying Intersex and Aproctia in Large White Pigs
Yajun Li,
Jiaxin Shi,
Yingshan Yang,
Donglin Ruan,
Jie Wu,
Danyang Lin,
Zihao Liao,
Xinrun Hong,
Fuchen Zhou,
Langqing Liu,
Jie Yang,
Ming Yang,
Enqin Zheng,
Zhenfang Wu,
Gengyuan Cai,
Zebin Zhang
Affiliations
Yajun Li
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Jiaxin Shi
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Yingshan Yang
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Donglin Ruan
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Jie Wu
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Danyang Lin
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Zihao Liao
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Xinrun Hong
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Fuchen Zhou
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Langqing Liu
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Jie Yang
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Ming Yang
College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
Enqin Zheng
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Zhenfang Wu
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Gengyuan Cai
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Zebin Zhang
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Congenital developmental abnormalities in piglets, such as intersex and aproctia, adversely affect survival rates, growth performance, and genetic breeding efficiency in pig populations. To elucidate their genetic basis, we performed a genome-wide association study (GWAS) on 1030 Large White pigs. We combined 50 K SNP chip data with SWIM-based genotype imputation to enhance the resolution of genetic variation detection, followed by MLM analysis. Our results identified 53 significant SNPs, with 52 associated with intersex and 1 with aproctia. Key candidate genes included MAD1L1, ID4, EFNA5, and PPP1R16B for intersex and ARNT2 for aproctia. Functional enrichment analysis highlighted pathways related to gonadal development (e.g., progesterone-mediated oocyte maturation) and embryonic morphogenesis. Collectively, the identification of these SNPs and candidate genes advances our understanding of the genetic architecture of intersex and aproctia in piglets. These findings provide actionable insights for optimizing genetic breeding strategies and improving health management in Large White pig production, with potential implications for reducing economic losses caused by congenital disorders.
