A new approach in association study of sinlge nucleotide polymorphism of genes for carcass and quality traits in commercial pigs.

Six batches of four commercial hybrids of heavy pigs, reared for the production of Italian dry-cured hams, were identified for having homogeneous feeding and farm conditions. For a total of 235 pigs, slaughtered in the same slaughterhouse, carcass traits and muscle composition were measured. The pigs were genotyped for single nucleotide polymorphisms (SNPs) of Na+, K+-ATPase subunit alpha 2 (ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide; ATP1A2), cystatin B (CSTB), mitochondrial 2,4-dienoyl-CoA reductase 1 (DECR1), leptin (LEP; 3 SNPs), melanocortin receptor 4 (MC4R), melanocortin receptor 5 (MC5R), sarcolipin (SLN) and titin (TTN) genes. All genes showed biallelic polymorphisms and the alleles were differently distributed between the six batches. Pigs were subsequentely clustered in “lean” and “fat” using either carcass traits (lean percentage, backfat thickness, loin muscle thickness, ham weight and ham cover fat thickness: 100 lean and 135 fat) or meat composition data (dry matter, protein, fat and ash of Biceps femoris and Vastus lateralis and pH after 24 hours: 126 lean and 109 fat). The association of gene polymorphisms with leaness and fatness of pigs was thus investigated using a logistic regression. ATP1A2, LEP (HinfI polymorphism) and MC4R, together with sex and ham weight were, included in the model to screen lean and fat pigs classified according to carcass traits data, yielding a correct classification of 71%. For the lean and fat pigs classified according to muscle composition, sex, CSTB, DECR1, MC5R and LEP (AciI/TaqI polymorphisms) were included in the regression analysis, that yielded a 66% of pigs correctly classified. These preliminary results may indicate that some of the selected candidate genes could be associated to production traits and are worth of further investigations.