Associations of Polymorphisms in Leptin and Leptin Receptor Genes with Meat Quality in Pigs of the Ukrainian Large White Breed

The associations of SNP in leptin gene ( LEP g.2845A>T, LEP g.3996T>C, LEP g.3469T>C) and leptin receptor gene ( LEPR c.232A>T, LEPR c.2856C>T, LEPR c.915C>T) with meat quality traits were studied in pigs of Ukrainian Large White breed (ULW). A computational analysis (SIFT, PolyPhen-2, and I-Mutant bioinformatic services) of the effect of mutations that cause SNPs (both for the selected SNP and for those missense SNPs, for which they can be potential linkage disequilibrium (LD) markers) on the structure and function of leptin and leptin receptor was carried out. The LEP c.3469T>C SNP (exon 3, rs45431504) was associated with the protein content in meat and moisture content in the back fat. The LEP g.2845A>T SNP (rs344615147), which is associated with the water-holding capacity of meat and moisture content in back fat, is located in the second intron and, as well as c.3469T>C SNP, can be presumably considered as an LD marker of the LEP rs701423985 SNP missense polymorphism. The LEPR c.232A>T SNP (exon 4, rs45435517) is a missense mutation, which causes the S52I amino acid substitution. The estimations obtained using SIFT and PolyPhen-2 indicate a significant effect of the rs45435517 on functional characteristics of leptin receptor. Indeed, an association of c.232A>T SNP with the thickness of back-fat was established in our work. At the same time, c.2856C>T SNP (exon 20, rs694660564, a synonymous substitution), which demonstrated in our work an association with the loss of moisture in the meat in ULW pigs, can be a potential LD marker and be in linkage disequilibrium with the LEPR rs1113972516, rs792804682, and rs1109261799 missense SNPs. SNP, for which the associations with meat quality indices were established in our work, can obviously be considered as potential markers for breeding ULW pigs and possibly other breeds aimed at obtaining genotypes with improved characteristics of meat quality.