Data from: A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle

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.