Analysis of qtl and candidate genes for porcine meat and fat quality in an iberian by landrace swine cross

Abstract

The general objective of this work was to increase our understanding of the genetic architecture of meat quality traits in the Iberian pig. To that end, we have employed different approaches, from QTL to in vitro protein activity assays, primarily in an Iberian by Landrace swine cross. In the first study, a genome wide QTL scan for muscle fibre traits, we uncovered a considerable contribution of overdominance and epistasis. We also showed that many regions of the genome are likely to be involved in the genetic control of these traits. Interestingly, there was a good agreement in the QTL regions between our study and other literature reports. A second main focus was to refine the FAT1 QTL region in porcine chromosome 4, where a large QTL effect on fatness resides. Specifically, we have analyzed a previously identified candidate gene, FABP4, and characterized and evaluated the FABP5 gene. Our results were not completely conclusive, as neither FABP4 nor FABP5 polymorphisms were able to explain all the QTL genetic variability. However, we showed that the Iberian FABP4-FABP5 haplotypes explained better the QTL than each gene separately. The third study concerned fatty acid composition QTL on porcine chromosome 8. While the FABP2 gene was discarded as the causal factor, a non-synonymous polymorphism in a conserved residue of the MTTP protein was strongly associated with fatty acid composition and protein activity in vitro. Importantly, the effect was confirmed in a commercial hybrid population. This makes it the MTTP polymorphism as a potential causal factor of the QTL. Finally, we have confirmed the effects on fatness of the IGF2 causal mutation in our experimental population, but we have also shown that there exist additional relevant loci in the same porcine chromosome 2. All together, these studies evidence that meat and fat quality exhibits a truly complex genetic architecture, and illustrates the difficulty - but not the impossibility - of revealing the causal responsible mutations.