Abstract
Glycolytic potential (GP) in skeletal muscle is economically important in the pig industry because of its effect on pork processing yield. We have previously mapped a major quantitative trait loci (QTL) for GP on chromosome 3 in a White Duroc × Erhualian F2 intercross. We herein performed a systems genetic analysis to identify the causal variant underlying the 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. The PHKG1 gene encodes a catalytic subunit of the phosphorylase kinase (PhK), which functions in the cascade activation of glycogen breakdown. 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 GP and a decrease of>20% in water-holding capacity of pork. These effects were consistent across the F2 and Sutai populations, as well as Duroc × (Landrace × Yorkshire) hybrid pigs. The unfavorable allele exists predominantly in Duroc-derived pigs. The findings provide new insights into understanding risk factors affecting glucose metabolism, and would greatly contribute to the genetic improvement of meat quality in Duroc related pigs.
Highlights
In past decades, thousands of quantitative trait loci (QTLs) have been detected for economically important traits in livestock through genetic linkage studies [1]
Glycogen storage diseases (GSD) are a group of inherited disorders characterized by storage of excess glycogen, which are mainly caused by the abnormality of a particular enzyme essential for releasing glucose from glycogen
We reported a loss-of-function mutation in the PHKG1 gene that causes the deficiency of the glycogen breakdown, leading to GSD and acid meat in Duroc-sired pigs
Summary
Thousands of quantitative trait loci (QTLs) have been detected for economically important traits in livestock through genetic linkage studies [1]. The recent availability of livestock genome sequences and high-density SNP chips has allowed detection of significant association of nucleotide polymorphisms with complex traits, and effective identification of causal mutations for some monogenic traits [2,3,4]. Despite these progresses, uncovering the quantitative trait genes (QTGs) or nucleotides (QTNs) for complex traits remains a challenging task. Some researchers have identified a number of promising candidate genes for muscle traits and blood lipid traits of pig by integrative analyses of GWAS (or linkage mapping), eQTL and trait-correlated expression [11,12,13,14]
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