Accelerated discovery of functional genomic variation in pigs

The genotype-phenotype link is a major research topic in the life sciences but remains highly complex to disentangle. Part of the complexity arises from the number of genes contributing to the observed phenotype. Despite the vast increase of molecular data, pinpointing the causal variant underlying a phenotype of interest is still challenging. In this study, we present an approach to map causal variation and molecular pathways underlying important phenotypes in pigs. We prioritize variation by utilizing and integrating predicted variant impact scores (pCADD), functional genomic information, and associated phenotypes in other mammalian species. We demonstrate the efficacy of our approach by reporting known and novel causal variants, of which many affect non-coding sequences. Our approach allows the disentangling of the biology behind important phenotypes by accelerating the discovery of novel causal variants and molecular mechanisms affecting important phenotypes in pigs. This information on molecular mechanisms could be applicable in other mammalian species, including humans.

AMPK in skeletal muscle function and metabolism

Skeletal muscle possesses a remarkable ability to adapt to various physiologic conditions. AMPK is a sensor of intracellular energy status that maintains energy stores by fine-tuning anabolic and catabolic pathways. AMPK’s role as an energy sensor is particularly critical in tissues displaying highly changeable energy turnover. Due to the drastic changes in energy demand that occur between the resting and exercising state, skeletal muscle is one such tissue. Here, we review the complex regulation of AMPK in skeletal muscle and its consequences on metabolism (e.g., substrate uptake, oxidation, and storage as well as mitochondrial function of skeletal muscle fibers). We focus on the role of AMPK in skeletal muscle during exercise and in exercise recovery. We also address adaptations to exercise training, including skeletal muscle plasticity, highlighting novel concepts and future perspectives that need to be investigated. Furthermore, we discuss the possible role of AMPK as a therapeutic target as well as different AMPK activators and their potential for future drug development.—Kjøbsted, R., Hingst, J. R., Fentz, J., Foretz, M., Sanz, M.-N., Pehmøller, C., Shum, M., Marette, A., Mounier, R., Treebak, J. T., Wojtaszewski, J. F. P., Viollet, B., Lantier, L. AMPK in skeletal muscle function and metabolism.

Animal Models to Study AMPK

AMPK is an evolutionary conserved energy sensor involved in the regulation of energy metabolism. Based on biochemical studies, AMPK has brought much of interest in recent years due to its potential impact on metabolic disorders. Suitable animal models are therefore essential to promote our understanding of the molecular and functional roles of AMPK but also to bring novel information for the development of novel therapeutic strategies. The organism systems include pig (Sus scrofa), mouse (Mus musculus), fly (Drosophila melanogaster), worm (Caenorhabditis elegans), and fish (Danio rerio) models. These animal models have provided reliable experimental evidence demonstrating the crucial role of AMPK in the regulation of metabolism but also of cell polarity, autophagy, and oxidative stress. In this chapter, we update the new development in the generation and application of animal models for the study of AMPK biology. We also discuss recent breakthroughs from studies in mice, flies, and worms showing how AMPK has a primary role in initiating or promoting pathological or beneficial impact on health.

Fiber hypertrophy and increased oxidative capacity can occur simultaneously in pig glycolytic skeletal muscle

An inverse relationship between skeletal muscle fiber cross-sectional area (CSA) and oxidative capacity suggests that muscle fibers hypertrophy at the expense of oxidative capacity. Therefore, our objective was to utilize pigs possessing mutations associated with increased oxidative capacity [AMP-activated protein kinase (AMPKγ3(R200Q))] or fiber hypertrophy [ryanodine receptor 1 (RyR1(R615C))] to determine if these events occur in parallel. Longissimus muscle was collected from wild-type (control), AMPKγ3(R200Q), RyR1(R615C), and AMPKγ3(R200Q)-RyR1(R615C) pigs. Regardless of AMPK genotype, RyR(R615C) increased fiber CSA by 35%. In contrast, AMPKγ3(R200Q) pig muscle exhibited greater citrate synthase and β-hydroxyacyl CoA dehydrogenase activity. Isolated mitochondria from AMPKγ3(R200Q) muscle had greater maximal, ADP-stimulated oxygen consumption rate. Additionally, AMPKγ3(R200Q) muscle contained more (∼50%) of the mitochondrial proteins succinate dehydrogenase and cytochrome c oxidase and more mitochondrial DNA. Surprisingly, RyR1(R615C) increased mitochondrial proteins and DNA, but this was not associated with improved oxidative capacity, suggesting that altered energy metabolism in RyR1(R615C) muscle influences mitochondrial proliferation and protein turnover. Thus pigs that possess both AMPKγ3(R200Q) and RyR(R615C) exhibit increased muscle fiber CSA as well as greater oxidative capacity. Together, our findings support the notion that hypertrophy and enhanced oxidative capacity can occur simultaneously in skeletal muscle and suggest that the signaling mechanisms controlling these events are independently regulated.

SNP variation in the promoter of the PRKAG3 gene and association with meat quality traits in pig

Background

The PRKAG3 gene encodes the γ3 subunit of adenosine monophosphate activated protein kinase (AMPK), a protein that plays a key role in energy metabolism in skeletal muscle. Non-synonymous single nucleotide polymorphisms (SNPs) in this gene such as I199V are associated with important pork quality traits. The objective of this study was to investigate the relationship between gene expression of the PRKAG3 gene, SNP variation in the PRKAG3 promoter and meat quality phenotypes in pork.

Results

PRKAG3 gene expression was found to correlate with a number of traits relating to glycolytic potential (GP) and intramuscular fat (IMF) in three phenotypically diverse F1 crosses comprising of 31 Large White, 23 Duroc and 32 Pietrain sire breeds. The majority of associations were observed in the Large White cross. There was a significant association between genotype at the g.-311A>G locus and PRKAG3 gene expression in the Large White cross. In the same population, ten novel SNPs were identified within a 1.3 kb region spanning the promoter and from this three major haplotypes were inferred. Two tagging SNPs (g.-995A>G and g.-311A>G) characterised the haplotypes within the promoter region being studied. These two SNPs were subsequently genotyped in larger populations consisting of Large White (n = 98), Duroc (n = 99) and Pietrain (n = 98) purebreds. Four major haplotypes including promoter SNP’s g.-995A>G and g.-311A>G and I199V were inferred. In the Large White breed, HAP1 was associated with IMF% in the M. longissmus thoracis et lumborum (LTL) and driploss%. HAP2 was associated with IMFL% GP-influenced traits pH at 24 hr in LTL (pHULT), pH at 45 min in LTL (pH₄₅LT) and pH at 45 min in the M. semimembranosus muscle (pH₄₅SM). HAP3 was associated with driploss%, pHULT pH₄₅LT and b* Minolta. In the Duroc breed, associations were observed between HAP1 and driploss% and pHUSM. No associations were observed with the remaining haplotypes (HAP2, HAP3 and HAP4) in the Duroc breed. The Pietrain breed was monomorphic in the promoter region. The I199V locus was associated with several GP-influenced traits across all three breeds and IMF% in the Large White and Pietrain breed. No significant difference in promoter function was observed for the three main promoter haplotypes when tested in vitro.

Conclusion

Gene expression levels of the porcine PRKAG3 are associated with meat quality phenotypes relating to glycolytic potential and IMF% in the Large White breed, while SNP variation in the promoter region of the gene is associated with PRKAG3 gene expression and meat quality phenotypes.