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Intramuscular fat content and its fatty acid composition affect porcine meat quality and its nutritional value. The present work aimed to identify genomic variants regulating the expression in the porcine muscle  (Longissimus dorsi)  of 45 candidate genes for lipid metabolism and fatty acid composition in three experimental backcrosses based on the Iberian breed. Expression genome-wide association studies (eGWAS) were performed between the muscle gene expression values, measured by real-time quantitative PCR, and the genotypes of 38,426 SNPs distributed along all chromosomes. The eGWAS identified 186 eSNPs located in ten  Sus scrofa  regions and associated with the expression of  ACSM5 ,  ACSS2 ,  ATF3 ,  DGAT2 ,  FOS  and  IGF2  (FDR < 0.05) genes. Two expression quantitative trait loci (eQTLs) for  IGF2  and  ACSM5  were classified as  cis -acting eQTLs, suggesting a mutation in the same gene affecting its expression. Conversely, ten eQTLs showed  trans -regulatory effects on gene expression. When the eGWAS was performed for each backcross independently, only three common  trans -eQTL regions were observed, indicating different regulatory mechanisms or allelic frequencies among the breeds. In addition, hotspot regions regulating the expression of several genes were detected. Our results provide new data to better understand the functional regulatory mechanisms of lipid metabolism genes in muscle.

Identification of eQTLs associated with lipid metabolism in Longissimus dorsi muscle of pigs with different genetic backgrounds