We performed QTL analyses with the revised chromosome 2 map using a statistical model2 testing for the presence of an imprinting effect as expected for IGF2. There was evidence for a paternally expressed QTL located at the distal tip of 2p. The QTL had large effects on lean meat content in ham and explained 30% of the residual phenotypic variance in the F2 population. Large effects on the area of the longissimus dorsi muscle, heart weight and backfat thickness (subcutaneous fat) were also noted, as well as a moderate effect on one meat quality trait, reflectance value. There are indications that new mutations may also contribute substantially to long-term selection responses. We propose that the presence of multiple alleles and multiple consecutive mutations may be common at major trait loci under selection for many generations in domestic animals, crops or natural populations.