Genome-wide Association Study Identifies Related Sites For Pig Scrotal Hernia On SLAF-seq Technology And Replication Testing Of Some Candidate Gene

Pig inguinal/scrotal hernia is one of the hereditary diseases which have been paid more attention in the modern pig industry. It had led to poor animal welfare and enormous economic loss. Inguinal/scrotal hernia is a complex disease which is caused by the interaction of multiple genes with environmental factors, so its research has been developing slowly. Currently, many research groups had used different methods to study the principles and identify the susceptible loci and positional candidate genes for inguinal/scrotal hernia. However, those results were inconsistent and had not been widely validated. In this study, we had identified candidate susceptible loci with pig inguinal/scrotal hernia on the base of SLAF-seq genome-wide association study. We had also verified possible candidate genes including SOX9、COL2A1、MMP2 and INSL3 by PCR-RFLP. The main discoveries were shown as follows:1. A total of 270 samples had been gathered, which were composed of the French Large White,the French Landrace,the US Department of pigs and hybrid pigs. 59 affected individuals and 61 normal individuals had been picked out from 270 samples, which had been sequenced by SLAF-seq. According to integrity-degree>0.8 and MAF>0.05, we had screened 218,460 highly consistent SNPs. Taking into account the complexity of the group structure, we had analyzed sample group structure by SNPs. Based on a linear model of TASSEL software, the significant locus had not been detected whether in the total group or in the French Large White. Then, we had performed the case-control genome-wide linkage analysis by using QQ plot for veridation. 7 significant SNPs had been identified to be associated with pig inguinal/scrotal hernia in the total group, 9 significant SNPs had been gotten in the French Large White.2. According to the associated SNPs, functional gene had been exploited. Two positional candidate genes, CPNE5 and MAP7D2, were found in the 120 sequenced samples, while one positional candidate gene MYCN was found in the French Large White. By analysing the polymorphism of CPNE5’s and MAP7D2’s in the 270 samples, the result showed that there were significant differences in the frequencies of genotypes and alleles between the affected individuals and the normal individuals(P<0.01).3. Four candidate genes, SOX9, COL2A1, MMP2 and INSL3, had been chosen for polymorphism analysis in the group. For the SOX9, significant differences existed in the frequencies of genotypes and alleles between the affected individuals and the normal individuals(P<0.01). And for the COL2A1, there were only significant differences in the frequencies of genotypes(P<0.01) in the French Large White, and no significant differences in the 270 samples(P>0.05). For MMP2 and INSL3, there were significant differences neither genotype frequencies nor alleles frequencies.