Evaluation Of Effects Of Positional Candidate Genes HMGA1, C6orf106and ENSSDCG00000023160on Pig Leg Soundness Traits

Leg weakness is a serious problem in the pig industry. It causes pigs lame and unablestanding, and deteriorates pig’s welfare. All of these hinder pig’s development and growth.The unwilling culling boars and sows results in huge economic loss. Thus, deciphering thegenetic architecture of leg soundness in pigs will not only contribute to pig breed program,but also provide an animal model of leg and arm diseases in human.Leg soundness is a complex trait, and many factors give rise to it, such as breed,microbial infections, imbalanced nutrition, artificial selection and environmental factors. Itis a common view that leg soundness has its genetic architecture, but it is still unclear,expect serval QTL and few GWAS reports. In our previous study, we had performed awhole genome scan in White Duroc×Erhualian resource population using183microsatellite markers, and a total of16QTL of leg soundness traits are detected at the1%genome-wide significant level, the QTL on SSC7is the most significant one. Agenome-wide association study was performed to fine mapping the QTL using the porcine60K SNP chip in the F2and Sutai populations, and the QTL was fine mapping in a2.15Mbinterval.In this study, three positional candidate genes were selected, namely HMGA1,C6orf106and ENSSSCG00000023160. To search the polymorphic loci in the three genes,their sequences were determined in serval F1boars by a short-gun DNA sequence methodin the F2population. A total of174SNPs were identified in C6orf106, including9in theconservative region. Three of9SNPs were selected to genotype in F2, Sutai and DLYcommercial populations using Taqman methods. Five polymorphic loci inENSSSCG00000023160were detected, and all of them were genotyped by using genotypeimputation in the F2population. The searching and genotyping of polymorphic loci inHMGA1were described by Shen in his master thesis. In the F2and Sutai populations, the11polymorphic loci were merged into the SNPs on SSC7screened from the porcine60KSNP chip, and GenABEL package of R was used to perform the association analysis. Theassociations between the3SNPs of C6orf106and the leg soundness traits were performedby SAS.The association results showed that two loci g.2029C>T and g.3155A>G of HMGA1are significantly associated with length and weight of the biceps brachii and gait score, andthe difference between them and the most significant locus is very little, so HMGA1ismost likely causal gene of leg soundness. The3SNPs of C6orf106significantly associatewith leg soundness traits in F2population, but they don’t associate with any leg soundnesstraits in Sutai and DLY commercial populations. Considering there are171SNPs without analysis, therefore, it cannot exclude as the causal gene of leg soundness. All ofpolymorphic loci of ENSSSCG00000023160are analyzed in F2population, only one SNPassociates with forelimb gait score, and the association is not strong as the top ones, thus itis excluded as the causal gene of leg soundness.