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Background  In previous studies on an Iberian x Landrace cross, we have provided evidence that supported the porcine  ELOVL6  gene as the major causative gene of the QTL on pig chromosome 8 for palmitic and palmitoleic acid contents in muscle and backfat. The single nucleotide polymorphism (SNP)  ELOVL6:c.-533C > T  located in the promoter region of  ELOVL6  was found to be highly associated with  ELOVL6  expression and, accordingly, with the percentages of palmitic and palmitoleic acids in  longissimus dorsi  and adipose tissue. The main goal of the current work was to further study the role of  ELOVL6  on these traits by analyzing the regulation of the expression of  ELOVL6  and the implication of  ELOVL6  polymorphisms on meat quality traits in pigs.    Results  High-throughput sequencing of BAC clones that contain the porcine  ELOVL6  gene coupled to RNAseq data re-analysis showed that two isoforms of this gene are expressed in liver and adipose tissue and that they differ in number of exons and 3’UTR length. Although several SNPs in the 3’UTR of  ELOVL6  were associated with palmitic and palmitoleic acid contents, this association was lower than that previously observed with SNP  ELOVL6:c.-533C > T . This SNP is in full linkage disequilibrium with SNP  ELOVL6:c.-394G > A  that was identified in the binding site for estrogen receptor alpha (ERα). Interestingly, the  ELOVL6:c.-394G  allele is associated with an increase in methylation levels of the  ELOVL6  promoter and with a decrease of  ELOVL6  expression. Therefore, ERα is clearly a good candidate to explain the regulation of  ELOVL6  expression through dynamic epigenetic changes in the binding site of known regulators of  ELOVL6  gene, such as SREBF1 and SP1.    Conclusions  Our results strongly suggest the  ELOVL6:c.-394G > A  polymorphism as the causal mutation for the QTL on pig chromosome 8 that affects fatty acid composition in pigs.    Electronic supplementary material  The online version of this article (doi:10.1186/s12711-015-0111-y) contains supplementary material, which is available to authorized users.

Epigenetic regulation of the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs