A splicing mutation in PHKG1 decreased its expression in skeletal muscle and caused PSE meat in Duroc × Luchuan crossbred pigs

Abstract

In recent years, Luchuan pigs in southern China have been used to produce high-quality meat by crossbreeding them with Duroc boars; however, PSE (pale, soft and exudative) meat was frequently reported in the crossbred pigs, and the underlying reason remains unknown. We excluded the possibility of the well-known causative mutations in RYR1 and PRKAG3 but identified the existence of an unfavorable allele of a splicing mutation (g.8283C>A) in PHKG1 in two Duroc boars and three Duroc 9 Luchuan crossbred pigs with PSE meat. An association analysis with 425 Duroc 9 Luchuan crossbred pigs revealed that the polymorphism of the splicing site of PHKG1 has significant association with the ultimate meat pH value (P = 0.035) and color score (P = 0.004). In addition, a strong cis-eQTL (expression QTL) signal for the expression of PHKG1 was identified in 189 Duroc 9 Luchuan crossbred pigs, and the splicing mutation was proven to be significantly associated with the expression of PHKG1 (P = 4.01e-11). Furthermore, RNA-sequencing data analysis confirmed that 131 CC homozygotes had only one transcript (T1), with FPKM (fragments per kilobase of transcript per million) of 35.40 AE 7.28, and 58 CA heterozygotes had two types of transcripts (T1 and T2), with FPKM of 19.63 AE 5.11 and 9.20 AE 2.39 respectively. Based on the association and eQTL analysis results, we concluded that PSE meat in Duroc 9 Luchuan crossbred pigs is caused by the splicing mutation in PHKG1. Our findings further support the effect of the causative mutation in PHKG1 on meat quality. The GEO accession number for the data is GSE124315.

Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits

“…Among these 63 candidate genes, the most famous one is PHKG1 , in which a splicing mutation (g.8283C > A) in Duroc pigs leads to increased glycolytic potential and rapid pH decline in meat [ 6 ]. In a previous study, we confirmed that the splicing mutation g.8283C > A is the causative mutation for the eQTL signal and that pigs that carry the mutant allele have a high risk of pale, soft, and exudative meat [ 30 ]. Other identified candidate genes that are of interest include NUDT7 , which was assigned to a QTL for meat color [ 47 – 49 ], and FADS2 and DGAT2 , which are involved in the regulation of lipid metabolism and fat deposition [ 50 – 52 ].…”

“…Instead, for DNA-chip SNPs, we set a threshold of 19 for the median of the number of each genotype at each site to avoid an extreme distribution of genotypes. For ASE analysis with RNAseq data, Table 1 The overlap between eQTL analysis, ASE analysis and correlation analysis "Num_Het" represents the total number of observed heterozygotes, and "Num_ASE" means the number of heterozygotes that displayed ASE we applied the N-masking alignment strategy to eliminate allelic mapping bias and set filtering conditions for both total read counts (10) and allele-specific read counts (3), as well as the minimum sample size of heterozygotes (30) and the count of ASE heterozygotes (10), which ensured higher reliability. We found that 43.8% (378/863) of the trans-genes had a cis-eQTL on the same chromosome, such as SLC5A4.…”

“…The experimental population was described in our previous study [30]. Briefly, 425 animals (hereafter referred to as DL) produced by crossing eight Duroc boars with 158 Luchuan sows were fed following the same protocol and slaughtered by a standardized procedure at the age of 210 ± 6 days.…”

A mutation in PHKG1 causes high drip loss and low meat quality in Chinese Ningdu yellow chickens

“…Diseases associated with PHKG1 include glycogen storage disease ( Kishnani et al, 2019 ). Several studies have also demonstrated that PHKG1 is a strong candidate gene for meat quality traits in pigs ( Liu et al, 2019 ; Liu et al, 2020 ) and residual feed intake and feed conversion ratio in chickens ( Shah et al, 2016 ; Liu et al, 2018 ). Furthermore, a previous study demonstrated that the PHKG1 gene is a causative gene for meat quality traits in White Duroc × Erhualian F2 intercross and Sutai pigs, which could lead to a less active Phosphorylase Kinase ( PhK ) protein ( Ma et al, 2014 ).…”

Landscape of tissue-specific RNA Editome provides insight into co-regulated and altered gene expression in pigs (Sus-scrofa)

“…Duroc is a famous lean-type pig breed with high muscle mass and growth rate. However, there are remarkable phenotype differences in muscle mass, growth rate, back-fat thickness and intramuscular fat content between these two breeds [ 19 , 20 ]. Even so, the RNA editing sites contributing to the phenotype have rarely been reported in animals.…”