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Intramuscular fat (IMF) content and fatty acids (FA) profile determine important sensory and technological characteristics of the meat, being interesting traits to be included in breeding programs for Iberian pig. In a previous study, we analyzed the longissimus dorsi transcriptome of Iberian pigs with divergent breeding values for IMF identifying 63 and 12 functional candidate genes and long non-coding RNA being differentially expressed. The first objective of this work was to use the RNA-seq data generated in that study in order to design a low-density panel with 50 single-nucleotide polymorphisms (SNP). The second aim was to evaluate the effects of this SNP panel on IMF content and backfat FA profile in a closed commercial population of Iberian pigs. The IMF content and backfat FA composition were determined in 940 Iberian pigs. A total of 837 SNPs were identified in the selection of genes and lncRNA. Out of the 50 selected SNP, 11 were monomorphic in the population and 2 failed in their genotyping. Association analyses were carried out for the 37 SNP segregating in the population (minor allele frequency, MAF > 0.05). Regarding IMF content, a significant additive effect (q-value < 0.05) was observed for ADIPOQ:g.124646194T > G SNP, in which the G allele was linked to an increase of 7.59% (additive effect expressed as a percentage of the mean of the trait). For the backfat FA composition, we observed 24 SNP with significant associations. The strongest effects were detected for the ELOVL6:g.112186423A > G and FASN_rs331694510G > A SNP. The A allele of both SNPs were associated to a lower percentage of palmitic (C16:0) and palmitoleic (C16:1) acids and an increase in oleic acid (C18:1). In addition, the AMPD3:g.49043886C > G SNP had significant effects on C16:0, stearic (C18:0), C18:1 and on the sum of saturated and monounsaturated fatty acids. Finally, significant effects of the EGR2:66286345G > T SNP on C18:0 and C18:1 and other minor FA were observed. Our finding

Meat quality of Iberian pigs is defined by the combination of their genetic characteristics and the particular production system. To carry out a genetic analysis of the main meat quality traits, we estimated their heritabilities, genetic correlations and the association effects of 32 selected SNPs of 12 candidate genes. A total of ten traits were measured in longissimus dorsi samples from 1,199 Iberian pigs fattened in the traditional free-range system: water holding capacity (thawing, cooking and centrifuge force water losses), instrumental colour (lightness L*, redness a* and yellowness b*), myoglobin content, shear force on cooked meat, and shear force and maximum compression force on dry-cured loin. Estimated heritability values were low to moderate (0.01 to 0.43) being the lowest for L* and the highest for cooking loss. Strong genetic correlations between water holding capacity traits (0.93 to 0.96) and between myoglobin content and a* (0.94) were observed. The association analyses revealed 19 SNPs significantly associated with different traits. Consistent and strong effects were observed between PRKAG3 SNPs (rs319678464G > C and rs330427832C > T), MYH3_rs81437544T > C, CASP3_rs319658214G > T and CTSL_rs332171512A > G and water losses. Also for CAPN1_rs81358667G > A and CASP3_rs319658214G > T and shear force. The SNPs mapping on PRKAG3 showed the highest effects on Minolta colour traits. Genotyping of these SNPs could be useful for the selection of Iberian young boars with similar estimated breeding values for productive traits.