Abstract
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.
Highlights
Two different approaches are being used for the application of DNA technology to ascertain the genetic basis of production and quality traits and the development of DNA tests as selection tools in farm animals
The linkage map obtained with the seven microsatellites of chromosome 6, heart fatty acid binding protein (H-FABP)-HaeIII RFLP and leptin receptor gene (LEPR)-HpaII RFLP was in agreement with those of other studies with respect to the order and distances between markers
Results of the H-FABP and LEPR association analysis are shown in Tables III and IV, respectively, and important discrepancies were observed for the two compared methods of statistical analysis
Summary
Two different approaches are being used for the application of DNA technology to ascertain the genetic basis of production and quality traits and the development of DNA tests as selection tools in farm animals. We have previously reported the results of a QTL detection project, aimed at the identification of productive and quality QTLs on an F2 cross between Iberian and Landrace pigs With this material, we were able to identify a QTL on chromosome 6 affecting backfat thickness, intramuscular fat percentage and eye muscle area with a high significance level [24]. We were able to identify a QTL on chromosome 6 affecting backfat thickness, intramuscular fat percentage and eye muscle area with a high significance level [24] This trait is one of the main factors influencing the eating quality (tenderness, juiciness and flavor) of pork meat and products [23] and it is presently receiving more attention in pig breeding schemes [16]. The presence of intramuscular fat has been reduced and a lot of criticisms have been raised by consumers about the decline of pig meat quality [28]
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