Insertion of 643bp Retrotransposon Upstream of PPARγ CDS Is Associated with Backfat of Large White Pigs

PPARs are essential regulators of mammalian fatty acid and lipid metabolism. Although the effects of genetic variations, including single nucleotide polymorphisms (SNPs) in PPARs genes on the phenotype of domestic animals have been investigated, there is limited information on the impact of retrotransposon insertion polymorphisms (RIPs). In this study, a combined comparative genome and polymerase chain reaction (PCR) was used to excavate the RIPs in porcine PPARs. We also investigated the potential effects of retrotransposon insertion on phenotype and expression patterns. This study identified the two RIPs in PPARs genes, namely an ERV in intron 1 of PPAR&alpha: and a combined retrotransposon in intron 2 of PPAR&gamma:, designated as PPAR&alpha:-ERV-RIP and PPAR&gamma:-COM-RIP, respectively. These RIPs exhibited different distribution patterns among Chinese indigenous breeds and Western commercial breeds. Individuals with the PPAR&alpha:-ERV-RIP+/+ genotype (+/+ indicated homozygous with insertion) among Large White pigs had significantly higher (p &lt: 0.05) corrected backfat thickness compared to those with the other two genotypes. Similarly, those with the PPAR&gamma:-COM-RIP&minus:/&minus: genotype had significantly higher (p &lt: 0.05) corrected backfat thickness than those with the other two genotypes in Large White pigs. Moreover, in 30-day-old Sujiang piglets, the PPAR&gamma: gene expression in the backfat of those with the PPAR&gamma:-COM-RIP&minus:/&minus: genotype (&minus:/&minus: indicated homozygous without insertion) was significantly greater (p &lt: 0.01) than those with other genotypes. The dual luciferase reporter gene assay demonstrated that the combined retrotransposon insertion significantly reduced the activity of the MYC promoter in both C2C12 and 3T3-L1 cells (p &lt: 0.01). Therefore, the combined retrotransposon insertion could function as a repressor to decrease the expression of PPAR&gamma:, making PPAR&gamma:-COM-RIP a valuable molecular marker for assisted selection of backfat thickness in pig breeding.