SNPs detection in DHPS-WDR83 overlapping genes mapping on porcine chromosome 2 in a QTL region for meat pH

Abstract

BackgroundThe pH is an important parameter influencing technological quality of pig meat, a trait affected by environmental and genetic factors. Several quantitative trait loci associated to meat pH are described on PigQTL database but only two genes influencing this parameter have been so far detected: Ryanodine receptor 1 and Protein kinase, AMP-activated, gamma 3 non-catalytic subunit. To search for genes influencing meat pH we analyzed genomic regions with quantitative effect on this trait in order to detect SNPs to use for an association study.ResultsThe expressed sequences mapping on porcine chromosomes 1, 2, 3 in regions associated to pork pH were searched in silico to find SNPs. 356 out of 617 detected SNPs were used to genotype Italian Large White pigs and to perform an association analysis with meat pH values recorded in semimembranosus muscle at about 1 hour (pH1) and 24 hours (pHu) post mortem.The results of the analysis showed that 5 markers mapping on chromosomes 1 or 3 were associated with pH1 and 10 markers mapping on chromosomes 1 or 2 were associated with pHu. After False Discovery Rate correction only one SNP mapping on chromosome 2 was confirmed to be associated to pHu. This polymorphism was located in the 3’UTR of two partly overlapping genes, Deoxyhypusine synthase (DHPS) and WD repeat domain 83 (WDR83). The overlapping of the 3’UTRs allows the co-regulation of mRNAs stability by a cis-natural antisense transcript method of regulation. DHPS catalyzes the first step in hypusine formation, a unique amino acid formed by the posttranslational modification of the protein eukaryotic translation initiation factor 5A in a specific lysine residue. WDR83 has an important role in the modulation of a cascade of genes involved in cellular hypoxia defense by intensifying the glycolytic pathway and, theoretically, the meat pH value.ConclusionsThe involvement of the SNP detected in the DHPS/WDR83 genes on meat pH phenotypic variability and their functional role are suggestive of molecular and biological processes related to glycolysis increase during post-mortem phase. This finding, after validation, can be applied to identify new biomarkers to be used to improve pig meat quality.

From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results

“…Such genetic overlaps are well known, and they are important for the biological interpretation of the outcome from GWAS studies. In such cases the knowledge of the function of the associated genes can be used to decide which relations are more plausible [ 47 ]. For this purpose we collected gene-disease associations with T2DM and their scores from the DisGeNET database regarding the 41 genes present in the 19 structures, genes with such scores are shown as black triangles in Fig 2 , and we also report the DisGeNET score that indicate strength of the gene-disease association in S4 Table .…”

Copy number variation-based genome wide association study reveals additional variants contributing to meat quality in Swine

“…Meat quality traits are complex and usually influenced by multiple genes or QTLs, therefore, the genetic improvement of these traits is rather slow. However, genome-wide association studies (GWAS), linkage mapping, and selective sweep analysis have been successfully employed to investigate significant gene markers for pH, tenderness, meat color, intramuscular fat (IMF) content 1 2 3 4 5 6 7 8 9 .…”

MDM4 (Murine Double Minute 4)

“…Finally, a very interesting finding regarding MORG1 and DHPS has been recently published: the finding is not related to disease but to the technological quality of pig meat (Zambonelli et al 2013). Analysis of genomic regions with genes influencing pork pH, which is an important parameter for the quality assessment of fresh and seasoned meat products, offered SNPs in 3 0 UTR of the partly overlapping genes DHPS and MORG1 (Zambonelli et al 2013).…”