Association of Alleles at the Leptin Receptor Gene Locus with Leptin Receptor Expression and Carcass Composition Phenotypes in a Pig Resource Population

The leptin receptor (LEPR) is a type I cytokine receptor that binds the leptin protein known to regulate food intake and energy metabolism, and is a functional candidate gene for regulating economically important phenotypic traits in pigs. The objective of our research is to determine the effect of a single nucleotide polymorphism (SNP) in exon 14 of the LEPR gene on adipose tissue LEPR transcript abundance and carcass composition phenotypes in the Michigan State University Pig Resource Population. This population is a F2 cross between Duroc and Pietrain breeds. A total of 51 female pigs were selected based on LEPR exon 14 SNP genotypes (n=17 per CC, CT, and TT genotype). Total RNA was isolated from subcutaneous fat tissue samples and analyzed using real-time RT-PCR to obtain LEPR expression levels, with SDHA and ACTB as controls. A conditional analysis was performed using Genomic Best Linear Unbiased Prediction with the LEPR exon 14 genotypes as fixed effects, and LEPR gene expression and carcass composition phenotypes as response variables. A significant dominance effect was identified with the TT genotype showing significantly lower expression than the CC and CT genotypes (p=1.20e-02 and 4.05e-02, respectively). The presence of a C allele was associated with significantly higher LEPR expression than the T allele (p=8.61e-03). The heritability of LEPR gene expression was found to be moderate at 0.29. However, the proportion of variance explained by the LEPR SNP was 12% of the total gene expression variance. Conditional analysis for carcass composition phenotypes identified significant dominance effects for eight phenotypic traits including marbling, carcass loin muscle area, ham and loin weight and four backfat thickness measures (p≤0.05). The T allele was significantly associated with decreased backfat thickness and increased carcass loin muscle area, and ham and loin weight. A genome-wide association analysis identified two quantitative trait loci (QTL) for tenth-rib and last-lumbar backfat phenotypes on SSC6. The heritability of these traits were moderate at 0.43. The conditional analysis for these two backfat phenotypes completely removed the significance of the QTLs on SSC6, accounting for up to 8% of the phenotypic variance. This study highlights the LEPR exon 14 SNP as a candidate marker regulating variation in LEPR transcript abundance, and backfat and muscle phenotypes, with the C allele associated with increased LEPR gene expression and backfat thickness, and decreased muscle mass.