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Open Access Research

Test for positional candidate genes for body composition on pig chromosome 6

Óvilo Cristina1*, Angels Oliver2, José Luis Noguera3, Alex Clop4, Carmen Barragán1, Luis Varona3, Carmen Rodríguez1, Miguel Toro1, Armand Sánchez4, Miguel Pérez-Enciso3 and Luis Silió1

Author Affiliations

1 Departamento de Mejora Genética Animal, SGIT-INIA, 28040 Madrid, Spain

2 Centre de Tecnologia de la Carn, IRTA, 17121 Monells, Girona, Spain

3 Area de Producció Animal, Centre UdL-IRTA, 25198 Lleida, Spain

4 Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain

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Genetics Selection Evolution 2002, 34:465-479  doi:10.1186/1297-9686-34-4-465

The electronic version of this article is the complete one and can be found online at:

Received:9 August 2001
Accepted:14 February 2002
Published:15 July 2002

© 2002 INRA, EDP Sciences


One QTL affecting backfat thickness (BF), intramuscular fat content (IMF) and eye muscle area (MA) was previously localized on porcine chromosome 6 in an F2 cross between Iberian and Landrace pigs. This work was done to study the effect of two positional candidate genes on these traits: H-FABP and LEPR genes. The QTL mapping analysis was repeated with a regression method using genotypes for seven microsatellites and two PCR-RFLPs in the H-FABP and LEPR genes. H-FABP and LEPR genes were located at 85.4 and 107 cM respectively, by linkage analysis. The effects of the candidate gene polymorphisms were analyzed in two ways. When an animal model was fitted, both genes showed significant effects on fatness traits, the H-FABP polymorphism showed significant effects on IMF and MA, and the LEPR polymorphism on BF and IMF. But when the candidate gene effect was included in a QTL regression analysis these associations were not observed, suggesting that they must not be the causal mutations responsible for the effects found. Differences in the results of both analyses showed the inadequacy of the animal model approach for the evaluation of positional candidate genes in populations with linkage disequilibrium, when the probabilities of the parental origin of the QTL alleles are not included in the model.

candidate gene; H-FABP; LEPR; QTL; pigs


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