Muscle glycogen level and occurrence of acid meat in commercial hybrid pigs are regulated by two low-frequency causal variants with large effects and multiple common variants with small effects

Abstract

Background Meat production from the commercial crossbred Duroc × (Landrace × Yorkshire) (DLY) pig is predominant in the pork industry, but its meat quality is often impaired by low ultimate pH (pHu). Muscle glycogen level at slaughter is closely associated with pHu and meat technological quality, but its genetic basis remains elusive. The aim of this study was to identify genes and/or causative mutations associated with muscle glycogen level and other meat quality traits by performing a genome-wide association study (GWAS) and additional analyses in a population of 610 DLY pigs. Results Our initial GWAS identified a genome-wide significant ( P = 2.54e−11) quantitative trait locus (QTL) on SSC15 (SSC for Sus scrofa chromosome) for the level of residual glycogen and glucose (RG) in the longissimus muscle at 45 min post-mortem. Then, we demonstrated that a low-frequency (minor allele frequency = 0.014) R200Q missense mutation in the PRKAG3 ( RN ) gene caused this major QTL effect on RG. Moreover, we showed that the 200Q ( RN – ) allele was introgressed from the Hampshire breed into more than one of the parental breeds of the DLY pigs. After conditioning on R200Q, re-association analysis revealed three additional QTL for RG on SSC3 and 4, and on an unmapped scaffold (AEMK02000452.1). The SSC3 QTL was most likely caused by a splice mutation (g.8283C>A) in the PHKG1 gene that we had previously identified. Based on functional annotation, the genes TMCO1 on SSC4 and CKB on the scaffold represent promising candidate genes for the other two QTL. There were significant interaction effects of the GWAS tag SNPs at those two loci with PRKAG3 R200Q on RG. In addition, a number of common variants with potentially smaller effects on RG ( P < 10 −4 ) were uncovered by a second conditional GWAS after adjusting for the two causal SNPs, R200Q and g.8283C>A. Conclusions We found that the RN – allele segregates in the parental lines of our DLY population and strongly influences its meat quality. Our findings also indicate that the genetic basis of RG in DLY can be mainly attributed to two major genes ( PRKAG3 and PHKG1 ), along with many minor genes. Electronic supplementary material The online version of this article (10.1186/s12711-019-0488-0) contains supplementary material, which is available to authorized users.

Enhancer-promoter interaction maps provide insights into skeletal muscle-related traits in pig genome

“…Altogether, this multi-omics approach identified novel trait-related genes and candidate functional SNPs. For example, the previously detected candidate target gene related to muscle physiology traits (such as glycogen content, meat color, and drip loss) was PRKAG3 [31][32][33], which harbored one nonconservative substitution (rs1109104772, known as R200Q), in contrast, our models identified one novel candidate functional SNP (rs327909991) (Fig. 4c).…”

Genome-Wide Association Analysis Reveals Novel Loci Related with Visual Score Traits in Nellore Cattle Raised in Pasture–Based Systems

“…For CONF, genomic regions were found close to six genes: TMCO1 , UCK2 , ALDH9A1 , MGST3 , LRRCR2 , and RXRG . Under the influence of the TMCO1 gene, this region may be related to calcium ion homeostasis in endoplasmic reticulum membranes and to energy homeostasis [ 39 ], as previously reported for commercial pigs [ 40 ]. In cattle, an association with TMCO1 was demonstrated related with the efficiency of the humoral immune response to infection with Ostertagia ostertagi , a gastrointestinal nematode with a high incidence in tropical herds [ 41 ].…”

Research progress and applications of genome‐wide association study in farm animals

“…However, this dilemma has been addressed as different types of software and algorithms, such as REMMAX [68], MatrixEpistasis [69], and Epi-MEIF [70] have developed. Liu et al have found that two SNPs in the pig genome have significant roles in muscular residual glucose content by interacting with the causal subtitution PRKAG R200Q that mediates this phenotype [71]. Li et al discovered a significant epistatic effect of SNPs affecting the body weight and found 18 pairs of interacting gene sets such as IGF2BP1 and TYRP1 [72].…”