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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 > GSNP, 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 > Gand FASN_rs331694510G > ASNP. 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 > GSNP 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 > TSNP on C18:0 and C18:1 and other minor FA were observed. Our findings reveal ADIPOQ:g.124646194T > G, ELOVL6:g.112186423A > G, and FASN_rs331694510G > Amay be useful in breeding programs for Iberian pigs including FA profile and IMF content as selection goals, provided that their potential effects on other traits of interest are controlled.The proposed single-nucleotide polymorphisms in this work could be used in Iberian breeding schemes for selection of young boars according to their intramuscular fat content and fatty acid profile.Fat infiltration of muscle and fatty acid profile of cover fat are essential traits in Iberian pig industry. However, their inclusion in genetic selection schemes can be tangled, since their determination is laborious and expensive. Molecular markers can be a useful alternative to improve these traits. In a previous study, we analyzed the longissimus dorsi transcriptome of Iberian pigs with divergent breeding values for intramuscular fat (IMF) identifying 63 and 12 functional candidate genes and long non-coding RNA being differentially expressed. From this information, we designed a low-density panel with 50 single-nucleotide polymorphisms, which we subsequently evaluated for IMF content and fatty acids (FA) backfat profile of 940 pigs. The present research identified five polymorphisms mapped to ADIPOQ, ELOVL6, FASN, AMPD3, and EGR2genes that are associated to IMF content and backfat FA profile.