Number and mode of inheritance of QTL influencing backfat thickness on SSC2p in Sino-European pig pedigrees

To study the role of paternal and maternal alleles at the IGF2 locus and to test the hypothesis of a second QTL affecting backfat thickness on the short arm of SSC2 (SSC2p), a QTL mapping analysis was carried out on a combined pedigree including both the French and Dutch F2 populations, on the progeny of F1 males that were heterozygous (A/G) and homozygous (G/G) at the IGF2 locus. Simulations were performed to clarify the relations between the two QTL and to understand to what extent they can explain the discrepancies previously reported.The QTL analyses showed the segregation of at least two QTL on chromosome 2 in both pedigrees, i.e. the IGF2 locus and a second QTL segregating at least in the G/G F1 males and located between positions 30 and 51 cM. Statistical analyses highlighted that the maternally inherited allele at the IGF2 locus had a significant effect but simulation studies showed that this is probably a spurious effect due to the segregation of the second QTL.Our results show that two QTL on SSC2p affect backfat thickness. Differences in the pedigree structures and in the number of heterozygous females at the IGF2 locus result in different imprinting statuses in the two pedigrees studied. The spurious effect observed when a maternally allele is present at the IGF2 locus, is in fact due to the presence of a second closely located QTL. This work confirms that pig chromosome 2 is a major region associated with fattening traits.Many QTL associated with economically important traits like growth, fatness and meat quality have been detected since the 2000 s, as reviewed by Bidanel and Rotschild in 2002 [1]. However, even for those that have been fine-mapped, successful identification of the causal mutation is rare. In 1999, a paternally expressed QTL affecting backfat thickness (BFT) and muscle mass was identified on the short arm of SSC2 close to the IGF2 gene in crosses between Large White (LW) and European Wild Boar [2] and between LW and Pietrain [3]. In 200