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

Area of Science:

• Animal Genetics
• Quantitative Trait Loci (QTL) Analysis
• Molecular Genetics

Background:

• A QTL influencing backfat thickness (BF), intramuscular fat (IMF), and eye muscle area (MA) was previously identified on porcine chromosome 6.
• Positional candidate genes, H-FABP and LEPR, were selected for further investigation within this QTL region.

Purpose of the Study:

• To evaluate the effects of H-FABP and LEPR gene polymorphisms on economically important fatness traits in pigs.
• To assess the suitability of different statistical models for analyzing candidate gene effects in populations with linkage disequilibrium.

Main Methods:

• QTL mapping was refined using a regression method with seven microsatellites and two PCR-RFLPs.
• Linkage analysis determined the positions of H-FABP and LEPR genes at 85.4 cM and 107 cM, respectively.
• Candidate gene polymorphism effects were analyzed using an animal model and QTL regression analysis.

Main Results:

• The animal model approach indicated significant effects of H-FABP on IMF and MA, and LEPR on BF and IMF.
• QTL regression analysis, however, did not reveal significant associations for these candidate genes.
• Discrepancies suggest H-FABP and LEPR are likely not the causal mutations for the identified QTL.

Conclusions:

• The animal model approach can be inadequate for evaluating positional candidate genes in populations with linkage disequilibrium.
• Accounting for the probabilities of parental origin of QTL alleles is crucial when using animal models in such populations.
• Further studies are needed to identify the causal mutations responsible for the QTL on porcine chromosome 6.