Abstract
BackgroundIn 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.ResultsHigh-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.ConclusionsOur 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 materialThe online version of this article (doi:10.1186/s12711-015-0111-y) contains supplementary material, which is available to authorized users.
Highlights
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 quantitative trait locus (QTL) on pig chromosome 8 for palmitic and palmitoleic acid contents in muscle and backfat
Six bacterial artificial chromosome (BAC) clones that contain at least one of these three regions were identified by PCR: BAC 651E12, 650D01 and 385A04 were positive for the promoter region, BAC 201D05, 95C02, 754E02 and 385A04 were positive for exon 2 and BAC 754E02 was positive for exon 4
Association studies support the major role of the ELOVL6: c.-533C > T polymorphism Previously, we found that single nucleotide polymorphism (SNP) ELOVL6:c.-533C > T in the promoter region of ELOVL6 was associated with a QTL on SSC8 that affects palmitic and palmitoleic acid contents in muscle and backfat [2]
Summary
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. Results of our previous analysis on the promoter of pig ELOVL6 [2] showed that: (1) pig and mouse ELOVL6 promoters share SRE and E-box motifs, and in the pig ELOVL6 promoter, SRE elements are present at positions −18, −450 and −524 and an E-box motif at position −331; (2) a single nucleotide polymorphism (SNP) i.e. ELOVL6:c.-533C > T is located close to the most distal SRE element and is highly associated with percentages of palmitic and palmitoleic acids in muscle and backfat and with the expression level of ELOVL6 in backfat; (3) the pig ELOVL6 promoter contains binding sites for other transcription factors i.e. for SP1 transcription factor (SP1) at position −470 with a SNP at position −480 i.e. ELOVL6:c.480C > T and for MLX interacting protein-like (MLXIPL) at position −322 ( called carbohydrate response element binding protein or ChREBP); (4) the pig ELOVL6 promoter contains five additional SNPs (ELOVL6:c.-574C > T, ELOVL6:c.-534C > T, ELOVL6:c.-492G > A, ELOVL6:c.394G > A and ELOVL6:c.-313C > T); and (5) expression of ELOVL6 varies between various lipogenic tissues (liver, adipose tissue and muscle), which suggests that the mechanisms that regulate the expression of this gene differ in each tissue. One cannot exclude the possibility that microRNAs, a class of short noncoding RNAs with a key role in gene expression, may affect expression of ELOVL6, since the 3’UTR of porcine ELOVL6 gene has not been fully characterized
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