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The genetic landscape of intramuscular fat content and composition in pigs
Intramuscular fat content and composition are relevant selection goals in pig breeding schemes because of their significant influence on meat tenderness, juiciness and flavor. Muscle lipid phenotypes are determined by both nutritional and genetic factors, displaying moderate heritabilities and a polygenic architecture. In this way, genome scans with microsatellites have revealed the existence of more than 200 intramuscular fat content QTL scattered throughout the pig genome. Unfortunately, experimental limitations related with population size and marker density have prevented the identification of mutations with causal effects. The comparison of QTL maps amongst muscles and fat depots has evidenced a modest positional concordance, suggesting that the penetrance of polymorphisms with causal effects on lipid metabolism is modulated by tissue-specific factors. This is an important consideration that should be kept in mind when implementing gene-assisted or genomic selection schemes aimed to improve intramuscular fat content and composition in swine. Gene expression studies based on microarrays have also provided valuable clues about the biology of muscle fat deposition in pigs, showing that it is modulated by a complex network of pathways related with lipid (lipogenesis, lipolysis, PPAR signaling) and carbohydrate (insulin signaling) metabolism. However, microarrays have a limited power because they do not allow exploring transcript structure or the expression patterns of non-coding RNAs. The recent advent of high-throughput genotyping and sequencing technologies has made possible to circumvent many of these limitations. Now, genome-wide association studies take advantage of the information provided by tens of thousands of SNP markers to fine map genomic regions associated with intramuscular fat content and composition in pigs. In parallel, the RNA-seq technology is expanding the analysis of differential expression to mRNA splicing variants as well as to many non-coding RNAs with functions yet to be discovered. Particularly powerful are those approaches integrating genome-wide polymorphism and expression data, since they can offer and unprecedented view about the molecular mechanisms that regulate lipid deposition in the porcine skeletal muscle.
Keywords: intramuscular fat, pig, genomics