A splicing mutation in PHKG 1 decreased its expression in skeletal muscle and caused PSE meat in Duroc × Luchuan crossbred pigs

Summary 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 RYR 1 and PRKAG 3 but identified the existence of an unfavorable allele of a splicing mutation (g.8283C>A) in PHKG 1 in two Duroc boars and three Duroc × Luchuan crossbred pigs with PSE meat. An association analysis with 425 Duroc × Luchuan crossbred pigs revealed that the polymorphism of the splicing site of PHKG 1 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 PHKG 1 was identified in 189 Duroc × Luchuan crossbred pigs, and the splicing mutation was proven to be significantly associated with the expression of PHKG 1 ( 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 ± 7.28, and 58 CA heterozygotes had two types of transcripts (T1 and T2), with FPKM of 19.63 ± 5.11 and 9.20 ± 2.39 respectively. Based on the association and eQTL analysis results, we concluded that PSE meat in Duroc × Luchuan crossbred pigs is caused by the splicing mutation in PHKG 1 . Our findings further support the effect of the causative mutation in PHKG 1 on meat quality. The GEO accession number for the data is GSE 124315.