OMIA:001128-9823 : Pale soft exudative meat in Sus scrofa (pig) |
In other species: chicken , turkey
Categories: Muscle phene
Mendelian trait/disorder: yes
Disease-related: yes
Key variant known: yes
Year key variant first reported: 2014
Cross-species summary: PSE
Mapping: Duan et al. (2009) mapped a quantitative trait loci (QTL) for glycolytic potential on chromosome 3 in a White Duroc × Erhualian F2 intercross.
Molecular basis: Ma et al. (2014) “performed a systems genetic analysis to identify the causal variant underlying the [glycolytic potential] phenotype QTL (pQTL). We first conducted genome-wide association analyses in the F2 intercross and an F19 Sutai pig population. The QTL was then refined to an 180-kb interval based on the 2-LOD drop method. We then performed expression QTL (eQTL) mapping using muscle transcriptome data from 497 F2 animals. Within the QTL interval, only one gene (PHKG1) has a cis-eQTL that was colocolizated with pQTL peaked at the same SNP. …. Deep sequencing of PHKG1 revealed a point mutation (C>A) in a splice acceptor site of intron 9, resulting in a 32-bp deletion in the open reading frame and generating a premature stop codon. The aberrant transcript induces nonsense-mediated decay, leading to lower protein level and weaker enzymatic activity in affected animals. ... The mutation causes an increase of 43% in glycolytic potential and a decrease of>20% in water-holding capacity of pork.” Liu et al. (2019) investigated the occurrence of pale, soft and exudative meat in Luchuan X Duroc pigs. After excluding the well-known mutations in RYR1 and PRKAG3 they identified that the PHKG1 splice variant identified by Ma et al. (2014) caused PSE meat in this crossbred population.
Prevalence: Ma et al. (2014): “The unfavorable allele exists predominantly in Duroc-derived pigs.”
Breed:
Duroc (Pig) (VBO_0001127).
Breeds in which the phene has been documented. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).
Associated gene:
| Symbol | Description | Species | Chr | Location | OMIA gene details page | Other Links |
|---|---|---|---|---|---|---|
| PHKG1 | phosphorylase kinase, gamma 1 (muscle) | Sus scrofa | 3 | NC_010445.4 (16822042..16831054) | PHKG1 | Homologene, Ensembl , NCBI gene |
Variants
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WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.
Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.
| OMIA Variant ID | Breed(s) | Variant Phenotype | Gene | Allele | Type of Variant | Source of Genetic Variant | Reference Sequence | Chr. | g. or m. | c. or n. | p. | Verbal Description | EVA ID | Year Published | PubMed ID(s) | Acknowledgements |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1288 | Duroc (Pig) | Pale soft exudative meat | PHKG1 | splicing | Naturally occurring variant | Sscrofa11.1 | 3 | g.16830320C>A | c.919-5C>A | ENSSSCT00000008491.4:c.919-5C>A Ma et al. 2014: "a point mutation (C>A) in a splice acceptor site of intron 9, resulting in a 32-bp deletion in the open reading frame and generating a premature stop codon" | rs330928088 | 2014 | 25340394 |
Cite this entry
Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2021). OMIA:001128-9823: Online Mendelian Inheritance in Animals (OMIA) [dataset]. https://omia.org/. https://doi.org/10.25910/2AMR-PV70
References
Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.
| 2019 | Liu, Y., Liu, Y., Ma, T., Long, H., Niu, L., Zhang, X., Lei, Y., Wang, L., Chen, Y., Wang, Q., Zheng, Z., Xu, X. : |
| A splicing mutation in PHKG1 decreased its expression in skeletal muscle and caused PSE meat in Duroc × Luchuan crossbred pigs. Anim Genet 50:395-398, 2019. Pubmed reference: 31179574. DOI: 10.1111/age.12807. | |
| 2014 | Ma, J., Yang, J., Zhou, L., Ren, J., Liu, X., Zhang, H., Yang, B., Zhang, Z., Ma, H., Xie, X., Xing, Y., Guo, Y., Huang, L. : |
| A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle. PLoS Genet 10:e1004710, 2014. Pubmed reference: 25340394. DOI: 10.1371/journal.pgen.1004710. | |
| 2009 | Duan, Y.Y., Ma, J.W., Yuan, F., Huang, L.B., Yang, K.X., Xie, J.P., Wu, G.Z., Huang, L.S. : |
| Genome-wide identification of quantitative trait loci for pork temperature, pH decline, and glycolytic potential in a large-scale White Duroc x Chinese Erhualian resource population. J Anim Sci 87:9-16, 2009. Pubmed reference: 18791141. DOI: 10.2527/jas.2008-1128. |
Edit History
- Created by Frank Nicholas on 19 Sep 2019
- Changed by Frank Nicholas on 19 Sep 2019
- Changed by Frank Nicholas on 20 Sep 2019
- Changed by Frank Nicholas on 23 Sep 2019
- Changed by Imke Tammen2 on 23 Feb 2021