A 304 bp insertion/deletion mutation in promoter region induces the increase of porcine IDH3β gene expression.

Obese and lean pig breeds show obvious differences in adipose metabolism/fat deposition; however, the molecular mechanism underlying phenotype variation remains unknown. In order to understand it, we analyzed the differences of gene expression in backfat between Meishan (a typical Chinese indigenous obese breed) and Large White (a lean Western breed) pigs. Here, we cloned porcine β subunit of IDH3 (IDH3B) and 2447 bp 5'-flanking sequence of this gene, and determined the genomic structure. Porcine IDH3B contains three isoforms, IDH3B ( 1 ), IDH3B ( 2 ) and IDH3B ( 3 ). Real-time RT-PCR revealed that these three isoforms were prevalently up-regulated in backfat of western commercial pigs, Large White, Landrace and Duroc, compared with Chinese indigenous breeds, Meishan and Tongcheng pigs. A 304 bp insertion/deletion variant was found in the 5'-flanking region. Dual-luciferase reporter assays showed that in vitro the promoter of IDH3B gene with the insertion had higher luciferase activity as compared with the wild type. Three genotypes AA, AB and BB, due to this insertion, were detected, and the frequency of allele A was dominant in western commercial pigs, whereas allele B predominated in Chinese indigenous breeds. IDH3B mRNA expression in Meishan pigs was more abundant with genotype AA than with genotype AB or BB, as in Large White pigs. In addition, the polymorphism was detected in 317 pigs of a Large White × Meishan F2 resource population. Association analysis showed that pigs with genotype AA possessed higher backfat thickness at buttocks than those with genotype AB (P < 0.05) or BB. These data suggested that the 304 bp insertion mutation in promoter region increased the expression of porcine IDH3β transcripts and this mutation might be a candidate marker for marker assistant selection in swine breeding.