New insight into the SSC8 genetic determination of fatty acid composition in pigs

Abstract

Background: Fat content and fatty acid composition in swine are becoming increasingly studied because of their effect on sensory and nutritional quality of meat. A QTL (quantitative trait locus) for fatty acid composition in backfat was previously detected on porcine chromosome 8 (SSC8) in an Iberian x Landrace F2 intercross. More recently, a genome-wide association study detected the same genomic region for muscle fatty acid composition in an Iberian x Landrace backcross population. ELOVL6, a strong positional candidate gene for this QTL, contains a polymorphism in its promoter region (ELOVL6:c.-533C < T), which is associated with percentage of palmitic and palmitoleic acids in muscle and adipose tissues. Here, a combination of single-marker association and the haplotype-based approach was used to analyze backfat fatty acid composition in 470 animals of an Iberian x Landrace F2 intercross genotyped with 144 SNPs (single nucleotide polymorphisms) distributed along SSC8.

Results: Two trait-associated SNP regions were identified at 93 Mb and 119 Mb on SSC8. The strongest statistical signals of both regions were observed for palmitoleic acid (C16:1(n-7)) content and C18:0/C16:0 and C18:1(n-7)/C16:1(n-7) elongation ratios. MAML3 and SETD7 are positional candidate genes in the 93 Mb region and two novel microsatellites in MAML3 and nine SNPs in SETD7 were identified. No significant association for the MAML3 microsatellite genotypes was detected. The SETD7:c.700G > T SNP, although statistically significant, was not the strongest signal in this region. In addition, the expression of MAML3 and SETD7 in liver and adipose tissue varied among animals, but no association was detected with the polymorphisms in these genes. In the 119 Mb region, the ELOVL6:c.-533C > T polymorphism showed a strong association with percentage of palmitic and palmitoleic fatty acids and elongation ratios in backfat.

Conclusions: Our results suggest that the polymorphisms studied in MAML3 and SETD7 are not the causal mutations for the QTL in the 93 Mb region. However, the results for ELOVL6 support the hypothesis that the ELOVL6:c.-533C > T polymorphism has a pleiotropic effect on backfat and intramuscular fatty acid composition and that it has a role in the determination of the QTL in the 119 Mb region.

Figure 1

Association study and LDLA of the C18:0/C16:0 elongation ratio in BF. Plot of association study (red points) and LDLA patterns (blue line) for the stearic/palmitic ratio; the X-axis represents positions in Mb on SSC8, and the Y-axis shows the –log10 (p-value); vertical, the pink line represents the position of the MAML3 gene, the blue line represents the position of the SETD7 gene and the green line represents the position of the ELOVL6 gene on SSC8; horizontal, dashed lines mark the association study significance level (FDR-based q-value ≤ 0.05); positions in Mb are relative to the Sscrofa10.2 assembly of the pig genome.

Figure 2

Schematic representation of the elongation pathway of 16 and 18 carbon FAs. Statistically significant FA (red square) and ratios of elongation and desaturation (colored arrows) are shown for BF FA composition in the F₂ generation.