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Open Access Research article

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

Paolo Zambonelli1*, Roberta Davoli1, Mila Bigi1, Silvia Braglia1, Luigi Francesco De Paolis1, Luca Buttazzoni23, Maurizio Gallo3 and Vincenzo Russo1

Author Affiliations

1 Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL), Università di Bologna, Via Fratelli Rosselli, 107, 42123 Reggio Emilia, Italia

2 Consiglio per la Ricerca e la sperimentazione in Agricoltura, Via Salaria 31, Monterotondo Scalo, 00015 Roma, Italia

3 Associazione Nazionale Allevatori Suini (ANAS), via Lazzaro Spallanzani 4/6, 00161 Roma, Italia

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BMC Genetics 2013, 14:99  doi:10.1186/1471-2156-14-99

Published: 8 October 2013

Abstract

Background

The 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.

Results

The 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.

Conclusions

The 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.

Keywords:
Swine; Meat pH; Single nucleotide polymorphism; DHPS; WDR83; Overlapping genes