Abstract: Based on previous data from comparative genomics, a structural variation (SV) with 189 bp in length was identified from the intron 15 of mitogen-activated protein kinase kinase kinase 4 (MAP3K4) gene in Xiang pig, which was defined as MAP3K4-I15-sv189. To explore the SV polymorphism in pig populations and its effects on gene expression, a PCR method was established using specific primers to discriminate SV genotypes and the gene expression level was determined via RT-qPCR technology. There found two genotypes, DD and ID, at the MAP3K4-I15-sv189 locus in Xiang pig population, in which the gene without SV region was indicated as D, while the reference gene containing the SV region was termed to be gene I. Of those, the frequency was 97.35% of allele D in Xiang pig population. In Yorkshire pig population, three genotypes, DD, ID and II, were measured with frequency of 80% in allele D. And frequency of allele D in Xiang pigs was significantly higher than that in Yorkshire pigs (P<0.05). The elements in the SV region were analyzed via Bioinformatics methods. The deletion of SV might lead to the loss of several repeat elements, which might change the expression of MAP3K4. A higher expression level of MAP3K4 mRNA was then tested from the lung of Xiang pigs compared with other tissues. And the highest level of MAP3K4 was found in the lung with genotype DD and the lowest from samples with genotype II. It indicated that the deletion of SV MAP3K4-I15-sv189 could accelerate the expression of MAP3K4 in pig lung. The results illustrated that the SV MAP3K4-I15-sv189 in MAP3K4 gene was dominated with genotype of deletion which resulted in the increase of gene expression in the lung, and would benefit to better undestanding the mechanism of susceptibility to diseases in Xiang pig lung.

Key words: Xiang pig, structural variation, MAP3K4 gene, polymorphism, lung