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

Simple Summary: Lipid metabolism has a substantial impact on the quality of meat in swine farming. PPAR gamma has a close association with lipid metabolism and displays high expression in adipose tissues. It is of paramount importance to control lipid metabolism to regulate PPAR gamma expression and activity in pigs. In this study, the association between the expression of the PPAR gamma gene and the backfat thickness of pigs was investigated. In recent years, retrotransposon insertion polymorphisms (RIPs), a new type of molecular marker, have emerged as a potentially valuable tool for genetic breeding in livestock and poultry. In this study, a combined retrotransposon insertion in the PPAR gamma gene of pigs was discovered that could be used as an efficient marker in selecting pigs for growth rate and lean percentage. 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 andWestern commercial breeds. Individuals with the PPAR alpha -ERV-RIP+/+ genotype (+/+ indicated homozygous with insertion) among Large White pigs had significantly higher (p < 0.05) corrected backfat thickness compared to those with the other two genotypes. Similarly, those with the PPAR gamma-COM-RIP (-/-) genotype had significantly higher (p < 0.05) corrected backfat thickness than those with the other two genotypes in Large White pigs. Moreover, in 30-day-old Sujiang piglets, the PPARg gene expression in the backfat of those with the PPAR gamma-COM-RIP-/- genotype (-/- indicated homozygous without insertion) was significantly greater (p < 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 < 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.