A selective genotyping approach identifies single nucleotide polymorphisms in porcine chromosome 2 genes associated with production and carcass traits in Italian heavy pigs.

Several studies have shown that porcine chromosome 2 (SSC2) harbors important quantitative trait loci (QTL) for production traits. In particular, an imprinted QTL for muscle mass production is determined by a mutation in the IGF2 gene (intron3-g.3072G>A). We recently identified and analysed single nucleotide polymorphisms (SNPs) in genes (cathepsin D, CTSD g.70G>A; cathepsin F, CTSF g.22G>C; lactate dehydrogenase A, LDHA g.46G>T) localized on SSC2 (including the IGF2 intron3-g.3072G>A SNP) showing association with production traits in Italian Large White pigs and/or localizing them on QTL regions. Here we analysed these markers applying a selective genotyping approach based on estimated breeding values (EBVs). Three groups of Italian Large White pigs each made by animals with the most positive (n. 50) and most negative (n. 50) EBVs for average daily gain (ADG), backfat thickness (BFT) or weight of lean cuts (LC) and one group of Italian Duroc pigs made by 50 animals with most positive and 50 animals with most negative EBV for visible intermuscular fat (VIF) were genotyped. In Italian Large White pigs, allele frequency differences for the IGF2 intron3-g.3072G>A SNP between the two extreme tails for all groups were highly significant (considering all analysed animals: P=9.85E-20 for LC; P=3.16E-15 for BFT; P=4.41E-6 for ADG). Significant allele frequency differences were also observed for the CTSD g.70G>A (P=0.0002 for ADG; P=0.00068) and LDHA g.46G>T (P=2.32E-5 for ADG) polymorphisms. These results provide further support on the effects of these polymorphisms or genes whose application on marker assisted selection programs could be envisaged.