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Progeny-testing of full-sibs IBD in a SSC2 QTL region highlights epistatic interactions for fatness traits in pigs

Flavie Tortereau12*, Marie-Pierre Sanchez3, Katia Fève1, Hélène Gilbert13, Nathalie Iannuccelli1, Yvon Billon4, Denis Milan1, Jean-Pierre Bidanel3 and Juliette Riquet1

Author affiliations

1 INRA, UMR444 Laboratoire de Génétique Cellulaire, 31326 Castanet-Tolosan, France

2 Wageningen University, Animal Breeding and Genetics Group, 6700AH Wageningen, The Netherlands

3 INRA, UMR1313 Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France

4 INRA, UE967 Génétique Expérimentale en Productions Animales, 17700 Surgères, France

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Citation and License

BMC Genetics 2011, 12:92  doi:10.1186/1471-2156-12-92

Published: 27 October 2011



Many QTL have been detected in pigs, but very few of them have been fine-mapped up to the causal mutation. On SSC2, the IGF2-intron3-G3072A mutation has been described as the causative polymorphism for a QTL underlying muscle mass and backfat deposition, but further studies have demonstrated that at least one additional QTL should segregate downstream of this mutation. A marker-assisted backcrossing design was set up in order to confirm the segregation of this second locus, reduce its confidence interval and better understand its mode of segregation.


Five recombinant full-sibs, with genotype G/G at the IGF2 mutation, were progeny-tested. Only two of them displayed significant QTL for fatness traits although four inherited the same paternal and maternal chromosomes, thus exhibiting the same haplotypic contrast in the QTL region. The hypothesis of an interaction with another region in the genome was proposed to explain these discrepancies and after a genome scan, four different regions were retained as potential interacting regions with the SSC2 QTL. A candidate interacting region on SSC13 was confirmed by the analysis of an F2 pedigree, and in the backcross pedigree one haplotype in this region was found to mask the SSC2 QTL effect.


Assuming the hypothesis of interactions with other chromosomal regions, the QTL could be unambiguously mapped to a 30 cM region delimited by recombination points. The marker-assisted backcrossing design was successfully used to confirm the segregation of a QTL on SSC2 and, because full-sibs that inherited the same alleles from their two parents were analysed, the detection of epistatic interactions could be performed between alleles and not between breeds as usually done with the traditional Line-Cross model. Additional analyses of other recombinant sires should provide more information to further improve the fine-mapping of this locus, and confirm or deny the interaction identified between chromosomes 2 and 13.