Genome-wide association study for intramuscular fatty acid composition in an Iberian × Landrace cross1

Abstract

The lipid content and fatty acid (FA) profile have an important impact in human health as well as in the technological transformation and nutritional and organoleptic quality of meat. A genome-wide association study (GWAS) on 144 backcross pigs (25% Iberian × 75% Landrace) was performed for 32 traits associated with intramuscular FA composition and indices of FA metabolism. The GWAS was carried out using Qxpak 5.0 and the genotyping information obtained from the Porcine SNP60K BeadChip (Illumina Inc., San Diego, CA). Signals of significant association considering a false- discovery rate (q-value < 0.05) were observed in 15 of the 32 analyzed traits, and a total of 813 trait-associated SNP (TAS), distributed in 43 chromosomal intervals on almost all autosomes, were annotated. According to the clustering analysis based on functional classification, several of the annotated genes are related to FA composition and lipid metabolism. Some interesting positional concordances among TAS and previously reported QTL for FA compositions and/or other lipid traits were also found. These common genomic regions for different traits suggest pleiotropic effects for FA composition and were found primarily on SSC4, SSC8, and SSC16. These results contribute to our understanding of the complex genetic basis of FA composition and FA metabolism.

A genome-wide association analysis for porcine serum lipid traits reveals the existence of age-specific genetic determinants

“…One additional limiting factor of GWAS studies performed in livestock is that sample sizes are usually much smaller than those employed in humans. Although the size of our Duroc population is comparable to those described in previous porcine GWAS studies [26–28], the detection of loci with small effects or rare variants with strong effects might be feasible only with larger sample sizes. Despite this limitation, much larger studies performed in humans (in the order of 60,000-100,000 individuals) are consistent with the data outlined in our work.…”

Intermuscular and intramuscular adipose tissues: Bad vs. good adipose tissues

“…142,145 Genomewide-association studies (GWAS) and the liver RNA-Seq on female pigs with extreme phenotypes for IM showed differential expression of transposable elements, long non-coding RNAs. 151,164,165 Furthermore, these studies established the role of putative protein-coding genes including Endotoxin lipopolysaccharide/pro-inflammatory cytokines (LPS/IL-1) in mediating inhibition of retinoid X receptors (RXR) function to regulate cholesterol homeostasis and bile acid homeostasis ( Table 3). Besides changes in abundance of markers for lipid Metabolic enzymes Increased expression of Insulin growth factor-1 (IGF-1) and IGFBP3 with higher body fat…”

Effect of UBE3C polymorphisms on intramuscular fat content and fatty acid composition in Duroc pigs

“…Many studies have reported that E3 ubiquitin protein ligases are involved in fat deposition, lipid metabolism, energy homeostasis, insulin resistance, and immune responses in mammals (Qi et al, 2006;Pasaje et al, 2011;Song et al, 2013;Abe et al, 2014). Although there is little published information regarding UBE3C and its possible functions related to fat deposition in muscle, it is of significant interest as a positional candidate gene for fat deposition in muscle due to its location on SSC18, near the QTLs for IMF content and FA composition (Pérez-Montarelo et al, 2012;Ramayo-Caldas et al, 2012;Uemoto et al, 2012).…”

“…Significant quantitative trait loci (QTLs) for fatness, including IMF content and FA composition, are located on SSC18 (Lee et al, 2003;Choi et al, 2010;Kim et al, 2011;Rückert et al, 2012;Uemoto et al, 2012;Muñoz et al, 2013). Several QTLs for IMF content and FA composition (C14:0, C16:0, C18:2, and C20:5) in muscle tissue and subcutaneous fat are located at position 1-26 Mb of SSC18 (Sanchez et al, 2007;Pérez-Montarelo et al, 2012;Ramayo-Caldas et al, 2012;Uemoto et al, 2012;Nonneman et al, 2013). Interestingly, within this region, several potential candidate genes for fat deposition traits are present, such as leptin (LEP), insulin-induced gene 1 (INSIG1), and ubiquitin protein ligase E3C (UBE3C).…”