Variation in the IGF2 gene promoter region is associated with intramuscular fat content in porcine skeletal muscle.

Intramuscular fat (IMF) and subcutaneous fat (back fat-BF) are two of the major fat depots in livestock. A QTN located in the insulin-like growth factor 2 gene (IGF2) has been associated with a desirable reduction in BF depth in pigs. Given that the lipid metabolism of intramuscular adipocytes differs from that of subcutaneous fat adipocytes, this study aimed to search for genetic variation in the IGF2 gene that may be associated with IMF, as well as BF, in diverse pig breeds. Four proximal promoter regions of the IGF2 gene were characterised and the association of IGF2 genetic variation with IMF and BF was assessed. Six promoter SNPs were identified in four promoter regions (P1-P4; sequence coverage 945, 866, 784 and 864 bp, respectively) in phenotypically diverse F1 cross populations. Three promoter SNPs were subsequently genotyped in three pure breeds (Pietrain = 98, Duroc = 99 and Large White = 98). All three SNPs were >95% monomorphic in the Pietrain and Duroc breeds but minor alleles were at moderate frequencies in the Large White breed. These SNPs were linked and one was located in a putative transcription factor binding site. Five haplotypes were inferred and three combined diplotypes tested for association with IMF and BF in the Large White. As expected haplotype 1 (likely in LD with the beneficial QTN allele) was superior for BF level. In contrast, the heterozygote diplotype of the most common haplotypes (1 and 2) was associated with higher IMF and marbling scores compared to either homozygote. Gene expression analysis of divergent animals showed that IGF2 was 1.89 fold up-regulated in muscle with higher compared to lower IMF content. These findings suggest that genetic variation in the promoter region of the IGF2 gene is associated with IMF content in porcine skeletal muscle and that greater expression of the IGF2 gene is associated with higher IMF content.