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Scrotal hernia in pigs is a complex trait likely affected by genetic and environmental factors. A large-scale association analysis of positional and functional candidate genes was conducted in four previously identified genomic regions linked to hernia susceptibility on  Sus scrofa  chromosomes 2 and 12, as well as the fifth region around 67 cM on chromosome 2, respectively. In total, 151 out of 416 SNPs discovered were genotyped successfully. Using a family-based analysis we found that four regions surrounding  ELF5 ,  KIF18A ,  COL23A1  on chromosome 2, and  NPTX1  on chromosome 12, respectively, may contain the genetic variants important for the development of the scrotal hernia in pigs. These findings were replicated in another case-control dataset. The SNPs around the  ELF5  region were in high linkage disequilibrium with each other, and a haplotype containing SNPs from  ELF5  and  CAT  was highly significantly associated with hernia development. Extensive re-sequencing work focused on the  KIF18A  gene did not detect any further SNPs with extensive association signals. These genes may be involved in the estrogen receptor signaling pathway ( KIF18A  and  NPTX1 ), the epithelial-mesenchymal transition ( ELF5 ) and the collagen metabolism pathway ( COL23A1 ), which are associated with the important molecular characteristics of hernia pathophysiology. Further investigation on the molecular mechanisms of these genes may provide more molecular clues on hernia development in pigs.

Association and Haplotype Analyses of Positional Candidate Genes in Five Genomic Regions Linked to Scrotal Hernia in Commercial Pig Lines