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 findings reveal ADIPOQ:g.124646194T > G, ELOVL6:g.112186423A > G, and FASN_rs331694510G > A may 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 Author(s) 2023. Published by Oxford University Press on behalf of the American Society of Animal Science.Palma-GranadosPatriciaP0000-0002-5240-2832Centro de I+D en Cerdo Ibérico, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra. EX101 km 4,7, 06300 Zafra, Spain.Dpto. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra La Coruña km 7,5, 28040 Madrid, Spain.García-CascoJuan MaríaJMCentro de I+D en Cerdo Ibérico, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra. EX101 km 4,7, 06300 Zafra, Spain.Dpto. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra La Coruña km 7,5, 28040 Madrid, Spain.CaraballoCarmenCCentro de I+D en Cerdo Ibérico, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra. EX101 km 4,7, 06300 Zafra, Spain.Dpto. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra La Coruña km 7,5, 28040 Madrid, Spain.Vázquez-OrtegoPedroPDpto. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra La Coruña km 7,5, 28040 Madrid, Spain.Gómez-CarballarFernandoFSánchez Romero Carvajal Jabugo SA, Ctra. San Juan del Puerto, 21290 Huelva, Spain.Sánchez-EsquilicheFernandoFSánchez Romero Carvajal Jabugo SA, Ctra. San Juan del Puerto, 21290 Huelva, Spain.ÓviloCristinaCDpto. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra La Coruña km 7,5, 28040 Madrid, Spain.MuñozMaríaMDpto. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra La Coruña km 7,5, 28040 Madrid, Spain.engCON15-078Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaSánchez Romero Carvajal JabugoIDI-20171141Centro para el Desarrollo Tecnológico IndustrialJournal ArticleUnited StatesJ Anim Sci80030020021-88120Fatty Acids0Fatty Acids, MonounsaturatedIMSwinegeneticsAnimalsFatty AcidsPolymorphism, Single NucleotideFatty Acids, MonounsaturatedPhenotypeMeatanalysisFat 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 EGR2 genes that are associated to IMF content and backfat FA profile.