An association analysis between a polymorphism in the <i>SEC24A</i> gene and lipid traits recorded in Duroc pigs

By regulating the expression of low-density lipoprotein receptors (LDLR), the SEC24A protein modulates the clearance of plasma cholesterol in mice. The whole-genome sequencing of five Duroc boars that sired a Duroc purebred experimental population (LIPGEN population, 350 individuals) revealed the segregation of one putative nonsense mutation located at the SEC24A (rs336401826, c.44G>A) gene. Genotyping of this polymorphic site in the LIPGEN population highlighted the existence of a significant departure from the Hardy Weinberg equilibrium (χ2 = 5.05, p-value = 0.024527). Despite the fact that SEC24A inactivation should affect serum lipid concentrations, we did not observe an association between SEC24A genotype and such traits. A thorough revision of the annotation of the SEC24A rs336401826 SNP revealed that this polymorphism is probably located in the 5’UTR of the SEC24A gene, rather than at the beginning of the first exon, hence not introducing the predicted premature stop codon that could truncate the SEC24A protein. Given that the annotation of loss-of-function mutations in pigs is far from perfect, careful manual curation of such mutations is recommended before undertaking the analysis of their effects at the experimental level.HIGHLIGHTSOne mutation (c.44 G>A) predicted to disrupt the SEC24A protein segregates in a Duroc pig population.This polymorphism is not associated with serum lipid levels despite its expected effect on such traits.Manual curation of the annotation of this putative nonsense polymorphism has revealed that it maps to the 5’UTR of the SEC24A gene. One mutation (c.44 G>A) predicted to disrupt the SEC24A protein segregates in a Duroc pig population. This polymorphism is not associated with serum lipid levels despite its expected effect on such traits. Manual curation of the annotation of this putative nonsense polymorphism has revealed that it maps to the 5’UTR of the SEC24A gene.</p

Additional file 7: Figure S1. of Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles

Validation by RT-qPCR of the differential expression of mRNA isoforms corresponding to the RXRG, SCD, MAFF and ITGA5 genes in HIGH vs LOW pigs. (PPT 132 kb

Distribution of genome-wide expression QTL amongst pig chromosomes.

<p>(A) Total number of eQTL and (B) <i>cis-</i>acting (▪) and <i>trans-</i>acting (▴) eQTL.</p

Porcine genomic regions with eQTL regulating more than four genes (eQTL hotspots).

<p>Porcine genomic regions with eQTL regulating more than four genes (eQTL hotspots).</p

List of genes regulated by each one of the 11 <i>trans-</i>regulatory hotspots regions.

<p>List of genes regulated by each one of the 11 <i>trans-</i>regulatory hotspots regions.</p

DAVID analysis of pathways significantly enriched in the list of <i>cis-</i> and <i>trans-</i>regulated genes.

<p>In bold, pathways related to lipid and muscle metabolism and fat deposition.</p

Genome-wide significant <i>trans-</i>eQTL for <i>gluteus medius</i> expression traits whose target genes are functionally related to lipid metabolism and fat deposition.

1<p>Positional genes fitting in the confidence interval of the eQTL are indicated.</p>2<p>IMF – intramuscular fat content; FA – Fatty Acid content (%); SFA – % saturated fatty acids.</p

Additional file 3: Table S3. of Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles

Alternatively spliced mRNA isoforms identified in the porcine gluteus medius muscle of Duroc pigs by CLC Bio and/or STAR/RSEM/ DESEq2. (XLSX 569 kb

Effect of the genome-wide <i>P</i>-value cutoff on the relative frequencies of <i>trans</i>- and <i>cis</i>-eQTL.

<p>Effect of the genome-wide <i>P</i>-value cutoff on the relative frequencies of <i>trans</i>- and <i>cis</i>-eQTL.</p

Additional file 2: Table S2. of Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles

Primers employed in the validation of four differentially expressed isoforms by RT-qPCR. (XLSX 10 kb