Genome-wide study on intramuscular fat in Italian Large White pig breed using the 4 PorcineSNP60 BeadChip

Genome-wide association study results are presented for intramuscular fat in Italian Large White pig breed. 886 individuals were genotyped with PorcineSNP60 BeadChip. After quality control performed with Plink software and in R environment, 49,208 markers remained for the association 22 analysis. The GWAS was conducted using linear mixed model implemented in GenABEL. We detected 7 new SNPs of genes till now not found associated to IMF. Three markers map in a wide intergenic region rich of QTL linked to fat traits, one map 388 kb upstream gene SDK1, one map inside PPP3CA gene, one inside SCPEP1 gene and the last is not mapped in the porcine genome yet. Associations here presented indicate a moderate effect of these genes on IMF. In particular PPP3CA, that is involved in the oxidative metabolism of skeletal muscle, could be considerate as an interesting candidate gene for IMF content in pigs. However further studies are needed to clarify the role of these genes on the physiological processes involved in IMF regulation. These results may be useful to control this trait that is important in terms of nutritional, technological and organoleptic characteristics of fresh meat and processed products.