Combined GWAS and LDLA approaches to improve genome-wide quantitative trait loci detection affecting carcass and meat quality traits in pig.

Many QTL affecting meat quality and carcass traits have been reported. However, in most of the cases these QTL have been detected in non-commercial populations. Therefore, a family structured population of 457 F2 pigs issued from an inter-cross between 2 commercial sire lines was used to detect QTL affecting meat quality and carcass traits. All animals were genotyped using the Illumina PorcineSNP60 BeadChip platform. Genome-wide association studies were used in combination with linkage disequilibrium-linkage analysis to identify QTL. A total of 32 QTL were detected. Nine of these QTL exceeded the genome-wide 5% significance threshold. We detected 18 QTL affecting carcass composition traits and 16 QTL affecting meat quality traits. Using post-QTL bioinformatics analysis we highlighted 26 functional candidate genes related to fatness, muscle development, meat color and meat pH. Finally, our results shed light on the advantage of using different QTL detection methodologies to get a global overview of the QTL present in the studied population.

The Longissimus and Semimembranosus muscles display marked differences in their gene expression profiles in pig.

BACKGROUND: Meat quality depends on skeletal muscle structure and metabolic properties. While most studies carried on pigs focus on the Longissimus muscle (LM) for fresh meat consumption, Semimembranosus (SM) is also of interest because of its importance for cooked ham production. Even if both muscles are classified as glycolytic muscles, they exhibit dissimilar myofiber composition and metabolic characteristics. The comparison of LM and SM transcriptome profiles undertaken in this study may thus clarify the biological events underlying their phenotypic differences which might influence several meat quality traits. METHODOLOGY/PRINCIPAL FINDINGS: Muscular transcriptome analyses were performed using a custom pig muscle microarray: the 15 K Genmascqchip. A total of 3823 genes were differentially expressed between the two muscles (Benjamini-Hochberg adjusted P value ≤0.05), out of which 1690 and 2133 were overrepresented in LM and SM respectively. The microarray data were validated using the expression level of seven differentially expressed genes quantified by real-time RT-PCR. A set of 1047 differentially expressed genes with a muscle fold change ratio above 1.5 was used for functional characterization. Functional annotation emphasized five main clusters associated to transcriptome muscle differences. These five clusters were related to energy metabolism, cell cycle, gene expression, anatomical structure development and signal transduction/immune response. CONCLUSIONS/SIGNIFICANCE: This study revealed strong transcriptome differences between LM and SM. These results suggest that skeletal muscle discrepancies might arise essentially from different post-natal myogenic activities.

High ambient temperature alleviates the inflammatory response and growth depression in pigs challenged with Escherichia coli lipopolysaccharide.

Pig production has increased in hot climate countries over recent years, but the effect of exposure to high temperatures on the health status of farm animals has not been investigated thoroughly. It is not clear how the ambient temperature (Ta) might influence responses to inflammatory challenge in pigs. The aim of the present study was to evaluate the effects of high Ta on performance and physiological parameters of growing pigs, subjected to repeated administration of Escherichia coli lipopolysaccharide (LPS). Thirty-seven pigs, each fitted with a jugular catheter, were assigned to one of two Ta conditions: thermo-neutral (TN, 24 °C) or high (HT, 30 °C). After a 14-day adaptation period, and a 7-day measurement period, pigs were administered five repeated injections of LPS at 48 h intervals. Irrespective of Ta, the LPS challenge reduced feed consumption and increased plasma pro-inflammatory cytokines, haptoglobin and cortisol. However, the extent of these responses was greater in pigs at TN than HT. In both groups, plasma thyroxine and triiodothyronine concentrations decreased, following the first LPS injection and thereafter returned to baseline, which occurred faster at HT than at TN. Moreover, the LPS challenge decreased growth and feed efficiency in pigs kept at TN, which was not observed in pigs kept at HT. The results suggest a greater capacity of pigs to limit the physiological and metabolic disturbances caused by inflammatory challenge, when kept at HT, compared to TN.

Associations between muscle gene expression pattern and technological and sensory meat traits highlight new biomarkers for pork quality assessment.

Meat quality (MQ) results from complex phenomenon and despite improved knowledge on MQ development, its variability remains high. The identification of biomarkers and the further development of rapid tests would thus be helpful to evaluate MQ in pork industries. Using transcriptomics, the present study aimed at identifying biomarkers of eight pork quality traits: ultimate pH, drip loss, lightness, redness, hue angle, intramuscular fat, shear force and tenderness, based on an experimental design inducing a high variability in MQ. Associations between microarray gene expression and pork traits (n=50 pigs) highlighted numerous potential biomarkers of MQ. Using quantitative RT-PCR, 113 transcript-trait correlations including 40 of these genes were confirmed (P<0.05, |r|≤0.73), out of which 60 were validated (P<0.05, |r|≤0.68) on complementary experimental data (n=50). Multiple regression models including 3 to 5 genes explained up to 59% of MQ trait variability. Moreover, functional analysis of correlated-trait genes provided information on the biological phenomena underlying MQ.

Mitochondrial function, fatty acid metabolism, and immune system are relevant features of pig adipose tissue development.

The molecular mechanisms underlying the genetic control of fat development in humans and livestock species still require characterization. To gain insights on gene expression patterns associated with genetic propensity for adiposity, we compared subcutaneous adipose tissue (SCAT) transcriptomics profiles from two contrasted pig breeds for body fatness. Samples were obtained from Large White (LW; lean phenotype) and Basque pigs (B; low growth and high fat content) at 35 kg (n = 5 per breed) or 145 kg body weight (n = 10 per breed). Using a custom adipose tissue microarray, we found 271 genes to be differentially expressed between the two breeds at both stages, out of which 123 were highly expressed in LW pigs and 148 genes were highly expressed in B pigs. Functional enrichment analysis based on gene ontology (GO) terms highlighted gene groups corresponding to the mitochondrial energy metabolism in LW pigs, whereas immune response was found significantly enriched in B pigs. Genes associated with lipid metabolism, such as ELOVL6, a gene involved in fatty acid elongation, had a lower expression in B compared with LW pigs. Furthermore, despite enlarged adipocyte diameters and higher plasma leptin concentration, B pigs displayed reduced lipogenic enzyme activities compared with LW pigs at 145 kg. Altogether, our results suggest that the development of adiposity was associated with a progressive worsening of the metabolic status, leading to a low-grade inflammatory state, and may thus be of significant interest for both livestock production and human health.

Comparison of muscle transcriptome between pigs with divergent meat quality phenotypes identifies genes related to muscle metabolism and structure.

BACKGROUND: Meat quality depends on physiological processes taking place in muscle tissue, which could involve a large pattern of genes associated with both muscle structural and metabolic features. Understanding the biological phenomena underlying muscle phenotype at slaughter is necessary to uncover meat quality development. Therefore, a muscle transcriptome analysis was undertaken to compare gene expression profiles between two highly contrasted pig breeds, Large White (LW) and Basque (B), reared in two different housing systems themselves influencing meat quality. LW is the most predominant breed used in pig industry, which exhibits standard meat quality attributes. B is an indigenous breed with low lean meat and high fat contents, high meat quality characteristics, and is genetically distant from other European pig breeds. METHODOLOGY/PRINCIPAL FINDINGS: Transcriptome analysis undertaken using a custom 15 K microarray, highlighted 1233 genes differentially expressed between breeds (multiple-test adjusted P-value<0.05), out of which 635 were highly expressed in the B and 598 highly expressed in the LW pigs. No difference in gene expression was found between housing systems. Besides, expression level of 12 differentially expressed genes quantified by real-time RT-PCR validated microarray data. Functional annotation clustering emphasized four main clusters associated to transcriptome breed differences: metabolic processes, skeletal muscle structure and organization, extracellular matrix, lysosome, and proteolysis, thereby highlighting many genes involved in muscle physiology and meat quality development. CONCLUSIONS/SIGNIFICANCE: Altogether, these results will contribute to a better understanding of muscle physiology and of the biological and molecular processes underlying meat quality. Besides, this study is a first step towards the identification of molecular markers of pork quality and the subsequent development of control tools.

Joint analysis of quantitative trait loci and major-effect causative mutations affecting meat quality and carcass composition traits in pigs.

BACKGROUND: Detection of quantitative trait loci (QTLs) affecting meat quality traits in pigs is crucial for the design of efficient marker-assisted selection programs and to initiate efforts toward the identification of underlying polymorphisms. The RYR1 and PRKAG3 causative mutations, originally identified from major effects on meat characteristics, can be used both as controls for an overall QTL detection strategy for diversely affected traits and as a scale for detected QTL effects. We report on a microsatellite-based QTL detection scan including all autosomes for pig meat quality and carcass composition traits in an F2 population of 1,000 females and barrows resulting from an intercross between a Pietrain and a Large White-Hampshire-Duroc synthetic sire line. Our QTL detection design allowed side-by-side comparison of the RYR1 and PRKAG3 mutation effects seen as QTLs when segregating at low frequencies (0.03-0.08), with independent QTL effects detected from most of the same population, excluding any carrier of these mutations. RESULTS: Large QTL effects were detected in the absence of the RYR1 and PRKGA3 mutations, accounting for 12.7% of phenotypic variation in loin colour redness CIE-a* on SSC6 and 15% of phenotypic variation in glycolytic potential on SSC1. We detected 8 significant QTLs with effects on meat quality traits and 20 significant QTLs for carcass composition and growth traits under these conditions. In control analyses including mutation carriers, RYR1 and PRKAG3 mutations were detected as QTLs, from highly significant to suggestive, and explained 53% to 5% of the phenotypic variance according to the trait. CONCLUSIONS: Our results suggest that part of muscle development and backfat thickness effects commonly attributed to the RYR1 mutation may be a consequence of linkage with independent QTLs affecting those traits. The proportion of variation explained by the most significant QTLs detected in this work is close to the influence of major-effect mutations on the least affected traits, but is one order of magnitude lower than effect on variance of traits primarily affected by these causative mutations. This suggests that uncovering physiological traits directly affected by genetic polymorphisms would be an appropriate approach for further characterization of QTLs.

Differentially-expressed genes in pig Longissimus muscles with contrasting levels of fat, as identified by combined transcriptomic, reverse transcription PCR, and proteomic analyses.

Intramuscular fat content is important for many meat quality parameters. This work is aimed at identifying functional categories of genes associated with natural variation among individuals in intramuscular fat content to help the design of genetic schemes for high marbling potential. Taking advantage of the global nature of transcriptomic and proteomic technologies, 40 genes were identified as differently expressed between high fat and low fat pig Longissimus muscles at slaughter weight. They are involved in metabolic processes, cell communication, binding, and response to stimulus. Using real-time PCR in muscle biopsies taken earlier in the fattening period, the group with a high intramuscular fat content was also characterized by the down-expression of genes playing a negative role in adipogenesis, such as architectural transcription factor high-motility hook A1, mitogen activated protein-kinase14, and cyclin D1. These results suggest that interindividual variability in intramuscular fat content might arise essentially from differences in early adipogenesis.

Comparison of sarcoplasmic proteomes between two groups of pig muscles selected for shear force of cooked meat.

Two-dimensional electrophoresis was used to compare Longissimus sarcoplasmic protein abundance between two groups (tough meat and tender meat), defined on the basis of extreme Warner-Bratzler shear force values measured on cooked pork. Fourteen protein spots differed in quantity (P<0.05) between the two groups and were identified. Adypocyte fatty acid binding protein and acyl-CoA binding protein involved in lipid traffic and in the control of gene expression regulating cell proliferation and differentiation, and Enoyl-CoA hydratase, aldose reductase and triosephosphate isomerase indirectly related to lipid metabolism were overrepresented in the tender group. The tender group was further characterized by increased levels of proteins involved in protein folding and polymerization (initiation factor elf-3beta, chaperonin subunit 2, profilin II). The results suggest that the lower post-cooking shear force could at least in part be related to muscle adipogenetic and/or myogenetic status of which the possible underlying mechanisms are discussed.

Cellular and biochemical features of skeletal muscle in obese Yucatan minipigs.

OBJECTIVE: To examine cellular and biochemical features of skeletal muscle in response to dietary-induced obesity in a novel Yucatan minipig model of childhood obesity. RESEARCH METHODS AND PROCEDURES: From 4 to 16 months of age, minipigs were fed either a recommended human-type diet (NF; n = 4) or were overfed a western-type diet with saturated fat and high-glycemic index carbohydrates (OF, n = 4). Muscle samples (biceps femoris) were histochemically stained for the identification of intramuscular adipocytes, intramyocellular lipid aggregates (oil red O), and myofiber types (myosin ATPase, succinate dehydrogenase). Gene expressions and/or activities of factors involved in lipogenesis, lipolysis, or energetic metabolism were quantified in muscle. RESULTS: Cross-sectional areas of myofibers paralleled pig body weight (r = 0.86, p < 0.01). The size of intramuscular adipocytes, the relative proportion of oil red O-stained fibers, and total muscle lipid content tended (p < or = 0.10) to increase in response to OF diet. Hormone-sensitive lipase, carnitine palmityl transferase-I, and uncoupling protein 2 mRNA levels were lower (p < 0.05) in OF pigs than in NF pigs. Activities of beta-hydroxyacyl-coenzyme A dehydrogenase and citrate synthase assessing post-carnitine palmityl transferase I events and the proportion of oxidative myofibers were not altered by OF diet. Activity and gene expression of fatty acid synthase were lower (p < 0.02) in OF pigs than in NF pigs. DISCUSSION: Overfeeding in Yucatan minipigs reduced the expression levels of three catabolic steps in skeletal muscle that are involved also in the etiology of human obesity.

Potential involvement of mammalian and avian uncoupling proteins in the thermogenic effect of thyroid hormones.

Thyroid hormones (THs) have long been known to be involved in the control of thermoregulation in birds and mammals. In particular, they are reported to play a role in the regulation of heat production. The underlying mechanisms could be the stimulation of the nuclear and mitochondrial transcription of several genes involved in energy metabolism and/or a direct action on the activity of components of the mitochondrial respiratory chain. Attention has recently been focussed on a subfamily of mitochondrial anion carriers called uncoupling proteins (UCPs). These proteins are suspected to be involved in a partial dissipation of the mitochondrial proton electrochemical gradient that would uncouple phosphorylations from oxidations and hence produce heat. However, the involvement of uncoupling mechanisms in thermogenesis and particularly in the thermogenic effect of TH is still unclear. The thermogenic role of UCP1, specifically expressed in brown adipose tissue, and its regulation by TH in rodents is quite well recognised, but the involvement in heat production of its mammalian homologues UCP2, ubiquitously expressed, and UCP3, muscle and adipose tissue-specific, as well as the role of the muscular avian UCP (avUCP), are to be further investigated. The expression of the UCP2 and UCP3 genes was shown to be enhanced by TH in muscle of several rodent species, and to be increased in situations where thermogenesis is stimulated, whereas results are more contrasted in pig. There is now increasing evidence that the physiological role of the mammalian UCP3 and UCP2 is rather related to lipid oxidation and/or prevention of reactive oxygen species accumulation than to heat production by uncoupling. The expression of avUCP was also recently demonstrated to be strongly regulated by thyroid status in chicken, and overexpressed in experimental conditions favouring high triiodothyronine concentrations and thermogenesis. However, its real uncoupling activity and contribution to thermogenesis remain to be established.

Unusual metabolic characteristics in skeletal muscles of transgenic rabbits for human lipoprotein lipase.

BACKGROUND: The lipoprotein lipase (LPL) hydrolyses circulating triacylglycerol-rich lipoproteins. Thereby, LPL acts as a metabolic gate-keeper for fatty acids partitioning between adipose tissue for storage and skeletal muscle primarily for energy use. Transgenic mice that markedly over-express LPL exclusively in muscle, show increases not only in LPL activity, but also in oxidative enzyme activities and in number of mitochondria, together with an impaired glucose tolerance. However, the role of LPL in intracellular nutrient pathways remains uncertain. To examine differences in muscle nutrient uptake and fatty acid oxidative pattern, transgenic rabbits harboring a DNA fragment of the human LPL gene (hLPL) and their wild-type littermates were compared for two muscles of different metabolic type, and for perirenal fat. RESULTS: Analyses of skeletal muscles and adipose tissue showed the expression of the hLPL DNA fragment in tissues of the hLPL group only. Unexpectedly, the activity level of LPL in both tissues was similar in the two groups. Nevertheless, mitochondrial fatty acid oxidation rate, measured ex vivo using [1-(14C)]oleate as substrate, was lower in hLPL rabbits than in wild-type rabbits for the two muscles under study. Both insulin-sensitive glucose transporter GLUT4 and muscle fatty acid binding protein (H-FABP) contents were higher in hLPL rabbits than in wild-type littermates for the pure oxidative semimembranosus proprius muscle, but differences between groups did not reach significance when considering the fast-twitch glycolytic longissimus muscle. Variations in both glucose uptake potential, intra-cytoplasmic binding of fatty acids, and lipid oxidation rate observed in hLPL rabbits compared with their wild-type littermates, were not followed by any modifications in tissue lipid content, body fat, and plasma levels in energy-yielding metabolites. CONCLUSIONS: Expression of intracellular binding proteins for both fatty acids and glucose, and their following oxidation rates in skeletal muscles of hLPL rabbits were not fully consistent with the physiology rules. The modifications observed in muscle metabolic properties might not be directly associated with any LPL-linked pathways, but resulted likely of transgene random insertion into rabbit organism close to any regulatory genes. Our findings enlighten the risks for undesirable phenotypic modifications in micro-injected animals and difficulties of biotechnology in mammals larger than mice.

Age-related changes in glucose utilization and fatty acid oxidation in a muscle-specific manner during rabbit growth.

The optimal utilization of energy substrates in muscle fibers is of primary importance for muscle contraction and whole body physiology. This study aimed to investigate the age-related changes in some indicators of glucose catabolism and fatty acid oxidation in muscles of growing rabbits. Longissimus lumborum (fast-twitch, LL) and semimembranosus proprius (slow-twitch, SMP) muscles were collected at 10 or 20 weeks of age ( n=6 per age). Glucose transporter GLUT4 content was investigated by immunoblot assay. Activity levels of five enzymes were measured: lactate dehydrogenase (LDH) and phosphofructokinase (PFK) for glycolysis; citrate synthase (CS), isocitrate dehydrogenase (ICDH) and -3-hydroxyacyl-coenzyme A dehydrogenase (HAD) for oxidation. Mitochondrial and peroxisomal oxidation rates were assessed on fresh homogenates using [1-14C]-oleate as substrate. At both ages, mitochondrial and peroxisomal oxidations rates, as well as activities of oxidative enzymes were higher in SMP than in LL. In both muscles, the apparent rate of fatty acid oxidation by the mitochondria did not differ between the two ages. However, a decrease in the activities of the three oxidative enzymes was observed in LL, whereas activities of CS and HAD and peroxisomal oxidation rate of oleate increased between the two ages in SMP muscle. In both muscles, LDH activity increased between 10 and 20 weeks, without variations in glucose uptake (GLUT4 transporter content) and in the first step of glucose utilization (PFK activity). In conclusion, mitochondrial oxidation rate of fatty acids and activities of selected mitochondrial enzymes were largely unrelated. Moreover, regulation of energy metabolism with advancing age differed between muscle types.

Cloning and tissue distribution of a carnitine palmitoyltransferase I gene in rainbow trout (Oncorhynchus mykiss).

The carnitine palmitoyltransferase I (EC.2.3.1.21; CPT I) mediates the transport of fatty acids across the outer mitochondrial membrane. In mammals, there are two different proteins CPT I in the skeletal muscle (M) and liver (L) encoded by two genes. The carnitine palmitoyltransferase system of lower vertebrates received little attention. With the aim of improving knowledge on the CPT family in fish, we examined CPT I cDNA and CPT activity in different tissues of rainbow trout (Oncorhynchus mykiss). Using RT-PCR, we successfully cloned a partial CPT I cDNA sequence (1650 bp). The predicted protein sequence revealed identities of 63% and 61% with human L-CPT I and M-CPT I, respectively. This mRNA is expressed in liver, white and red skeletal muscles, heart, intestine, kidney and adipose tissue of trout. This is in good agreement with the measurement of the CPT activity in the same tissues. The [IC(50)] that reflects the sensitivity to malonyl-CoA inhibition was 0.116+/-0.004 microM for the liver and 0.426+/-0.041 microM for the white muscle. These results demonstrate for the first time the existence of at least one gene encoding for CPT I present in both the liver and the muscle of rainbow trout.