P3018 Gene expression analysis in backfat and identification of eQTL regions for fatness and fatty acid composition candidate genes in pigs

Abstract

Fat content and fatty acid (FA) composition determine important sensory and technological aspects of pork and meat products because of their influence on the melting point and oxidative status of porcine tissues. Artificial selection to increase meat production in pigs has caused a reduction of intramuscular fat and changes in meat FA composition in some breeds. Gene expression levels can be analyzed as a quantitative trait to identify genomic regions regulating its expression. These regions are known as expression quantitative trait loci (eQTLs). The detection of eQTLs has been proposed as a good strategy to deepen the study of the genetic architecture of complex traits. The aim of this work was to study the genetic basis of the backfat expression of 43 lipid-related genes associated with meat quality traits in pigs. We performed an expression genome-wide association (eGWAS) with the backfat gene expression measured by real-time PCR and the PorcineSNP60 BeadChip genotype information in 115 Iberian × Landrace backcross (BC1_LD) animals. The eGWAS identified 224 eSNPs located in 21 chromosomal regions on SSC2-SSC4, SSC6, SSC8-SSC10 and SSC13-SSC15 and associated with the ACSM5, ELOVL6, FABP4, FADS2, and FATP4 genes. Three out of 21 eQTLs corresponding to ACSM5, FABP4, and FADS2 were classified as cis-acting eQTLs, whereas the remaining 18 eQTLs have trans-regulatory effects. In addition, four polymorphisms were identified and genotyped in the BC1_LD animals for the genes with cis-acting eQTLs: two SNPs located in the proximal promoter region of ACSM5 (SSC3) and FADS2 (SSC2), and one Indel and one SNP located in the intron 1 and in the 3’UTR region of FABP4, respectively. It is noteworthy that the strongest association signal for ACSM5 gene expression was shown for the polymorphism located in the promoter region of this gene. For FABP4 gene expression, the SNP in the 3’UTR region showed the lower P-value, and the indel was also one of the most significantly associated, as has been previously described. Thus, these SNPs are strong candidate polymorphisms to explain the mRNA variation of the ACSM5 and FABP4 genes and may have also a role in the determination of the FA composition in the BC1_LD animals. In concordance with these results, FABP4:g.2634_2635insC polymorphism has been associated with the percentage of palmitoleic and eicosatrienoic FA and polyunsaturated FA in muscle. These findings provide resources to decipher the functional regulatory mechanisms implicated in the variation of meat quality traits in pigs.