Análisis de asociación genómico de caracteres relacionados con la calidad de la carne y la grasa intramuscular en cerdos Duroc

The goal of the current work was to perform a genome-wide association analysis (GWAS) in order to identify genomic regions associated with the phenotypic variation of two groups of traits measured in the longissimus dorsi and gluteus medius muscles: 1) Intramuscular fat content and composition (palmitic, stearic, oleic and linoleic); 2) Meat quality: pH at 24 hours post-modem (PH24), electric conductivity and three Minolta values (redness a, lightness L and yellowness b). Although intramuscular fat phenotypes can be considered as meat quality traits, in this study we have treated them separately. About 352 Duroc pigs (Lipgen population) were typed with the PorcineSNP60 BeadChip (IIlumina), that allows the multiplexed analysis of 62,163 single nucleotide polymorphisms (SNPs). Association analyses were carried out with the GenABEL and EMMAX softwares. The amount of phenotypic variance explained by the SNPs for intramuscular fat content (h2sNp), estimated with three different softwares (GenABEL, EMMAX and GEMMA), ranged between 0.48-0.61 (longissimus dorsi) and 0.47-0.52 (gluteus medius). For intramuscular fat composition, h2sNp estimates ranged between 0 and 0.32. In the case of meat quality traits, h2sNp took values between 0 and 0.31 except for redness (h2sNp equal to 0.42-0.48 for the longissimus dorsi and 0.47-0.55 for the gluteus medius). The main associations described in the current work (i.e. those that are genome-wide significant and that are consistently detected by GenABEL and EMMAX) correspond to stearic content at SSC14 (120.9-124.4 Mb, both muscles) and at SSC4 (63.9 Mb, al-11y in the gluteus medius). We have also found genome¬wide significant associations for palmitic content (SSC5, 71.7-80.1 Mb; SSC6, 135.1-136.0 Mb) and intramuscular fat percentage (SSG6, 135,0-136.0 Mb), but these associations were not confirmed by both programs. Chromosome-wide significant associations were detected by both EMMAX and GenABEL for stearic content in the gluteus medius (SSC4 and SSC14) and Iongissimus dorsi (SSC14) as well as for the palmitic content of the gluteus medius (SSC5). With regard to meat quality traits, we only found chromosome-wide significant associations. GenABEL and EMMAX showed concordance for redness (gluteus medius) at the SSC3 (16.6-16.7 Mb, 50.2-56.1 Mb), electric conductivity of the longissimus dorsi at SSC4 (104.2-106.5 Mb) and at SSC5 (14.4-16.1 Mb) as wefl as for the electric conductivity of the gluteus medius, also at SSCS (13.0-15.7 Mb). In general, we observed a limited positional concordance between the GWAS maps generated for the gluteus medius and longissimus dorsi muscles, suggesting that the variation of these phenotypes is influenced by muscle-specific genetic factors. Finally, we have made a list of candidate genes mapping lo the trait ¬associated regions. In this regard, it is worth to mention the stearoyl-CoA desaturase gene located at 5.9 kb of the SSC14 SNP most significantly associated with stearic content