Abstract: 【Objective】 The objective of this study is to develop a method to access the leg soundness through scoring the joint of limb bone and calculate the simple correlation coefficients among the scores for leg soundness in pigs. Furthermore, the association between three positional and functional candidate genes, namely HMGA1, C6orf106 and ENSSSCG0000023160, and leg soundness was also studied in F2, Laiwu, Erhualian, Sutai and DLY populations.【Method】The joint of five limb bones were scored according to the size and depth of rip on the joint surface and the worn-out degree of the joint. If the rip on the joint surface is very big and deep or the joint is seriously worn out, the joint is scored 1. On the other hand, if there is no rip on the joint surface and the joint doesn’t have any degree of worn-out, the joint is scored 5. Higher the joint score is, healthier the joint is and sounder the leg is. Based on the authors’ previous genome-wide association studies, three genes HMGA1, C6orf106 and ENSSSCG0000023160 were screened as positional and functional candidate genes to leg soundness in a 0.4 Mb region centered on the top SNP on SSC7. To search the polymorphic loci of the three genes in the F2 population, their DNA sequences were determined by a short-gun DNA sequence method. A total of 11 polymorphic loci were picked out according to their conservations among 6 species. The genotypes of 3 loci for HMGA1 and 3 loci for C6orf106 were determined using the Taqman method, and the genotypes of the other 5 loci for the third gene were inferred by genotype imputation just in the F2 population. At last, the GenABEL package of R was used to perform the association analysis between the loci with MAF＞0.05 and the traits.【Result】A total of 174 and 5 polymorphic loci were identified in C6orf106 and ENSSSCG00000023160 genes, respectively. Joint scores were positively correlated with each other and were negatively correlated with the length and weight of biceps brachii, but most of them had no correlation with toe, leg and gait scores. The male’s scapula joint score was significantly lower than the female’s, but arm shoulder joint score and focile hock joint score were significantly higher than the female’s corresponding joint score. In the F2 population, all of the three genes were associated with leg soundness, but ENSSSCG00000023160 was weaker than the other two genes, therefore it was excluded as a candidate gene to leg soundness and was not genotyped in the other 4 populations. In the Erhualian population, two loci g.2029C＞T and g.3155A＞G of HMGA1 were significantly associated with leg soundness, and the other SNP lacked the polymorphism. In the other 3 populations, all of the 3 SNPs of HMGA1 were deficiently polymorphic. Only the g.6953T＞C locus of C6orf106 had enough polymorphic in the Laiwu population, and it was associated with leg soundness. In the Sutai and DLY populations, only two loci g.2054T＞C and g.6953T＞C of C6orf106 were polymorphic, but none was associated with leg soundness.【Conclusion】A method of accessing the leg soundness has been proposed by scoring the joint of limb bones in pigs, and it is a crucial supplement method to access the leg soundness. Because toe, leg and gait scores are not correlation with the joint scores, they can’t replace the joint scores. The association analysis results excluded the ENSSSCG00000023160 gene as candidate gene to leg soundness, but both HMGA1 and C6orf106 genes were not excluded. Therefore, the two genes are worthy for further investigations.

Key words: pig, leg soundness, joint score, association analysis, genotype imputation