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A splicing mutation in PHKG 1 decreased its expression in skeletal muscle and caused PSE meat in Duroc × Luchuan crossbred pigs
Author(s) -
Liu Y.,
Liu Y.,
Ma T.,
Long H.,
Niu L.,
Zhang X.,
Lei Y.,
Wang L.,
Chen Y.,
Wang Q.,
Zheng Z.,
Xu Xuewen
Publication year - 2019
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12807
Subject(s) - crossbreed , biology , rna splicing , genetics , allele , alternative splicing , gene , microbiology and biotechnology , exon , zoology , rna
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.