Pig Longissimus lumborum proteome: Part II: Relationships between protein content and meat quality

The color of fresh pork: Consumers expectations, underlying farm-to-fork factors, myoglobin chemistry and contribution of proteomics to decipher the biochemical mechanisms

The color of fresh pork is a crucial quality attribute that significantly influences consumer perception and purchase decisions. This review first explores consumer expectations and discrimination regarding pork color, as well as an overview of the underlying factors that, from farm-to-fork, contribute to its variation. Understanding the husbandry factors, peri- and post-mortem factors and consumer preferences is essential for the pork industry to meet market demands effectively. This review then delves into current knowledge of pork myoglobin chemistry, its modifications and pork discoloration. Pork myoglobin, which has certain peculiarities comparted to other meat species, plays a weak role in determining pork color, and a thorough understanding of the biochemical changes it undergoes is crucial to understand and improve color stability. Furthermore, the growing role of proteomics as a high-throughput approach and its application as a powerful research tool in meat research, mainly to decipher the biochemical mechanisms involved in pork color determination and identify protein biomarkers, are highlighted. Based on an integrative muscle biology approach, the available proteomics studies on pork color have enabled us to provide the first repertoire of pork color biomarkers, to shortlist and propose a list of proteins for evaluation, and to provide valuable insights into the interconnected biochemical processes implicated in pork color determination. By highlighting the contributions of proteomics in elucidating the biochemical mechanisms underlying pork color determination, the knowledge gained hold significant potential for the pork industry to effectively meet market demands, enhance product quality, and ensure consistent and appealing pork color.

In-depth characterization of the sarcoplasmic muscle proteome changes in lambs fed with hazelnut skin by-products: Relationships with meat color

This study investigated the effect of agro-industrial hazelnut skin by-products supplementation on lamb meat color variation and the changes in the sarcoplasmic muscle proteome during post-mortem storage (0, 4 and 7 days). Gel-based proteomics and bioinformatics approaches were applied to better understand the potential role of feeding strategies in modulating the mechanisms underpinning meat discoloration and post-mortem changes during storage. Therefore, twenty-two Valle del Belice male lambs were randomly assigned to two dietary treatments: control (C), lambs fed with maize-barley diet, and hazelnut skin (H), lambs fed hazelnut skin by-product as maize partial replacer in the concentrate diet. Hazelnut dietary treatment led to better lamb meat color stability as evidenced by the lowest decrease in redness and saturation index values. Proteomics and bioinformatics results revealed changes in the abundance of 41 proteoforms, which were mainly involved in glycolytic processes, responses to oxidative stress, and immune and endocrine system. The proteins allowed revealing interconnected pathways to be behind meat color variation as a consequence of using hazelnut skin by-products to sustainable feed lamb. The proteins can be used as potential predictors of lamb meat color variation. Accordingly, the regression equations developed in this paper revealed triosephosphate isomerase (TPI1) as a reliable candidate biomarker of color stability in lamb meat. SIGNIFICANCE: The use of agro-industrial by-products in animal feeding can be a potential sustainable strategy to reduce the environmental impacts of the food production chain and consequently improve animal welfare and product quality. The inclusion of hazelnut skin by-products in the animal's diet, due to the high concentration of polyphenols, represents an effective strategy to improve the oxidative stability of meat, with significant implications on color. The use of proteomics combined with bioinformatics on the sarcoplasmic proteome is a powerful approach to decipher the underlying mechanism. Accordingly, this approach allowed in this trial a deeper understanding of the molecular mechanisms involved in the post-mortem processes through the discovery of several biological pathways linked with lamb meat color variation. Glycolysis, followed by responses to oxidative stress, and other proteins involved in the immune and endocrine system were found as the major interconnected pathways that could act as potential predictors of lamb meat color stability. Candidate proteins biomarkers were further revealed in this study to be related with multiple meat color traits.

Transcriptomic Analysis of the Porcine Gut in Response to Heat Stress and Dietary Soluble Fiber from Beet Pulp

This study aimed to investigate the impact of heat stress (HS) and the effects of dietary soluble fiber from beet pulp (BP) on gene expression (differentially expressed genes, DEGs) of the porcine jejunum. Out of the 82 DEGs, 47 genes were up-regulated, and 35 genes were downregulated between treatments. The gene ontology (GO) enrichment analysis showed that the DEGs were related mainly to the actin cytoskeleton organization and muscle structure development in biological processes, cytoplasm, stress fibers, Z disc, cytoskeleton, and the extracellular regions in cellular composition, and actin binding, calcium ion binding, actin filament binding, and pyridoxal phosphate binding in the molecular function. The KEGG pathway analysis showed that the DEGs were involved in hypertrophic cardiomyopathy, dilated cardiomyopathy, vascular smooth muscle contraction, regulation of actin cytoskeleton, mucin type O-glycan biosynthesis, and African trypanosomiasis. Several of the genes (HSPB6, HSP70, TPM1, TAGLN, CCL4) in the HS group were involved in cellular oxidative stress, immune responses, and cellular differentiation. In contrast, the DEGs in the dietary BP group were related to intestinal epithelium integrity and immune response to pathogens, including S100A2, GCNT3, LYZ, SCGB1A1, SAA3, and ST3GAL1. These findings might help understand the HS response and the effect of dietary fiber (DF) regarding HS and be a valuable reference for future studies.

Proteomic analysis to understand the relationship between the sarcoplasmic protein patterns and meat organoleptic characteristics in different horse muscles during aging

The study investigates the changes in meat organoleptic characteristics and sarcoplasmic proteins of 3 horse muscles during aging. Longissimus lumborum (LL), semimembranosus (SM) and semitendinosus (ST) muscles, were removed from 12 Italian Heavy Draft Horse carcasses and aged for 1, 3, 6, 9 and 14 days. The lowest values of hardness and chewiness were found in LL muscle. During aging, a decrease of hardness was observed in ST muscle reaching the lowest value at 14 days. 2DE revealed a decrease of 15 sarcoplasmic protein spots in all muscles. Muscle-differences were found at 14 days. An increase of tropomyosin spots was found in LL muscle while, ST was characterized by a rise of superoxide dismutase, phosphoglucomutase-1 and two isoforms of myoglobin. Principal component analysis applied to color, texture parameters and spots volume differentiated the muscles into three different clusters. Data revealed that myofibrillar, glycolytic and mitochondrial proteins are potential muscle-biomarkers to monitor post-mortem processes and meat quality characteristics in horse meat.

TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

Background

Intramuscular adipocytes differentiation is a complex process, which is regulated by various transcription factor, protein factor regulators and signal transduction pathways. However, the proteins and signal pathways that regulates goat intramuscular adipocytes differentiation remains unclear.

Result

In this study, based on nanoscale liquid chromatography mass spectrometry analysis (LC-MS/MS), the tandem mass tag (TMT) labeling analysis was used to investigate the differentially abundant proteins (DAPs) related with the differentiation process of goat intramuscular adipocytes. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes enrichment and protein-protein interaction network analyses were performed for the characterization of the identified DAPs. The candidate proteins were verified by parallel reaction monitoring analysis. As a result, a total of 123 proteins, 70 upregulation proteins and 53 downregulation proteins, were identified as DAPs which may be related with the differentiation process of goat intramuscular adipocytes. Furthermore, the cholesterol metabolism pathway, glucagon signaling pathway and glycolysis / gluconeogenesis pathway were noticed that may be the important signal pathways for goat Intramuscular adipocytes differentiation.

Conclusions

By proteomic comparison between goat intramuscular preadipocytes (P_IMA) and intramuscular adipocytes (IMA), we identified a series protein that might play important role in the goat intramuscular fat differentiation, such as SRSF10, CSRP3, APOH, PPP3R1, CRTC2, FOS, SERPINE1 and AIF1L, could serve as candidates for further elucidate the molecular mechanism of IMF differentiation in goats.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07730-y.

Effect of a Diet Supplemented with Nettle (Urtica dioica L.) or Fenugreek (Trigonella foenum-graecum L.) on the Post-Slaughter Traits and Meat Quality Parameters of Termond White Rabbits

Simple Summary

Herbs can be a perfect supplement in the animal diet. In addition, they improve the functioning of the immune system, regulate the appetite and feed intake of animals, regulate the functioning of the digestive system, stimulate the metabolism of the body as well as quality parameters of meat. In the literature regarding herbal supplements to rabbit fodder, there is not much information on the use of nettle or fenugreek in their nutrition. Both of these herbs are valuable sources of vitamins and minerals. They regulate the digestive system and stimulate appetite. They have a positive impact on the functioning of the immune system and they exhibit antibacterial activity. Nettle improves biochemical, haematological, and immunological parameters. Numerous studies have shown that fenugreek can also have anti-inflammatory, analgesic, and antipyretic properties. The purpose of the study was to analyse the effect of nettle (Urtica dioica L.) leaves and fenugreek (Trigonella foenum-graecum L.) seeds as additives to fodder in order to improve post-slaughter traits and quality parameters Termond White of rabbit meat. Rabbits fed with pellets with the addition of nettle were characterized by a higher slaughter weight, higher weight of hot and cold carcasses, as well as a higher weight of the fore, middle and hind part of the carcass compared to the other two groups. The carcasses of animals fed with fenugreek and nettle had a higher percentage of the fore and hind parts compared to the carcasses of the animals from the control group. For most colour measurement traits, the differences depending on the feeding regime were significant. Summing up, it can be stated that feeding rabbits with herbal supplements, such as nettle or fenugreek, has no negative impact on technological parameters of the meat or the microstructure of the muscles. On the contrary, in the case of nettle, one can speak of a beneficial effect of this herbal supplement on the post-slaughter traits and microstructure of the muscles, as evidenced by the greater share of type I muscle fibres in the composition of muscles, e.g., longissimus lumborum, indicating a more oxidative nature of these muscles, which in turn may translate into the quality of rabbit meat.

Abstract

The purpose of the study was to analyse the effect of nettle (Urtica dioica L.) leaves and fenugreek (Trigonella foenum-graecum L.) seeds as additives to fodder in order to improve post-slaughter traits and quality parameters of Termond White rabbit meat (n = 60; 30♂, 30♀). Three experimental groups were created. The control group (n = 20; 10♂ and 10♀) was fed ad libitum feed containing corn, bran, wheat, dried alfalfa, soybean meal, sunflower meal, dicalcium phosphate, calcium carbonate and vitamin-mineral premix. The animals from the first experimental group (n = 20; 10♂ and 10♀) were fed a complete mixture added with 1% of nettle (Urtica dioica L.) leaves. Rabbits from the second group (n = 20; 10♂ and 10♀) were fed with a complete mixture added with 1% of fenugreek (Trigonella foenum-graecum L.) seeds. Rabbits fed with pellets with the addition of nettle were characterized by a higher slaughter weight, higher weight of hot and cold carcasses, lungs, kidneys and head as well as a higher weight of the fore, middle and hind part of the carcass compared to the other two groups. The carcasses of animals fed with fenugreek and nettle had a higher percentage of the fore and hind parts compared to the carcasses of the animals from the control group. The female carcasses were characterized by a significantly higher percentage of the middle part compared to the male carcasses. For most colour measurement traits, the differences depending on the feeding regime were significant. The effect of gender on meat colour was non significant. The effect of feeding regime and of gender on texture traits such as shear force, hardness, springiness, cohesiveness and chewiness were non significant. Feeding had no effect on muscle fibre diameter, but it affected the muscle fibre type I percentage. Thus, the group fed with pellets containing nettle leaves had higher percentage of type I muscle fibres than the control group. The effect of gender on muscle fibre traits was non significant.

Influence of dietary Spirulina inclusion and lysozyme supplementation on the longissimus lumborum muscle proteome of newly weaned piglets

Arthrospira platensis (Spirulina) is a microalga with a high content of crude protein. It has a recalcitrant cell wall that limits the accessibility of the animal endogenous enzymes to its intracellular nutrients. Enzymatic supplementation aiming to degrade cell walls could benefit microalgae digestibility. The objective of this study was to evaluate the impact of dietary Spirulina and lysozyme supplementation over the muscle proteome of piglets during the post-weaning stage. Thirty piglets were randomly distributed among three diets: control (no microalga), SP (10% Spirulina) and SP + L (10% Spirulina +0.01% lysozyme). After 4 weeks, they were sacrificed and samples of the longissimus lumborum muscle were taken. The muscle proteome was analysed using a Tandem Mass Tag (TMT)-based quantitative approach. A total of 832 proteins were identified. Three comparisons were computed: SP vs Ctrl, SP + L vs Ctrl and SP + L vs SP. They had ten, four and twelve differentially abundant proteins. Glycogen metabolism and nutrient reserves utilization are increased in the SP piglets. Structural muscle protein synthesis increased, causing higher energy requirements in SP + L piglets. Our results demonstrate the usefulness of proteomics to disclose the effect of dietary microalgae, whilst unveiling putative mechanisms derived from lysozyme supplementation. Data available via ProteomeXchange with identifier PXD024083. SIGNIFICANCE: Spirulina, a microalga, is an alternative to conventional crops which could enhance the environmental sustainability of animal production. Due to its recalcitrant cell wall, its use requires additional measures to prevent anti-nutritional effects on the feeding of piglets in the post-weaning period, during which they endure post-weaning stress. One of such measures could be CAZyme supplementation to help degrade the cell wall during digestion. Muscle proteomics provides insightful data on the effect of dietary microalgae and enzyme activity on piglet metabolism.

Application of Proteomic Technologies to Assess the Quality of Raw Pork and Pork Products: An Overview from Farm-To-Fork

The quality assurance of pork meat and products includes the study of factors prior to slaughter such as handling practices, diet and castration, and others during the post-mortem period such as aging, storage, and cooking. The development over the last two decades of high-throughput techniques such as proteomics offer great opportunities to examine the molecular mechanisms and study a priori the proteins in the living pigs and main post-mortem changes and post-translational modifications during the conversion of the muscle into the meat. When the most traditional crossbreeding and rearing strategies to improve pork quality were assessed, the main findings indicate that metabolic pathways early post-mortem were affected. Among the factors, it is well documented that pre-slaughter stress provokes substantial changes in the pork proteome that led to defective meat, and consequently, novel protein biomarkers should be identified and validated. Additionally, modifications in pork proteins had a strong effect on the sensory attributes due to the impact of processing, either physical or chemical. Maillard compounds and protein oxidation should be monitored in order to control proteolysis and volatile compounds. Beyond this, the search of bioactive peptides is becoming a paramount goal of the food and nutraceutical industry. In this regard, peptidomics is a major tool to identify and quantify these peptides with beneficial effects for human health.

TMT-based quantitative proteomic analysis of porcine muscle associated with postmortem meat quality

To explore the molecular mechanisms of meat quality, four high-quality (HQ) samples and four low-quality (LQ) samples from longissimus dorsi muscles were chosen, and tandem mass tag (TMT) labeling combined with mass spectrometry (MS) were performed to find associations between meat quality and proteome profiles. The LQ meats had lower pH, lighter color, and higher drip loss compared to the HQ meats. About 140 differentially expressed proteins were identified. Functional analysis results of differentially expressed proteins showed that decreased release of Ca²⁺, lower contents of type II fibers, lower contents of glycogen, and decreased glycogenolysis in HQ meats indicated a lower degree of glycolysis in HQ as compared to LQ meats. Meanwhile, some differentially expressed proteins suggested that the levels of oxidative stress and apoptosis were lower in HQ meats than in LQ meats. This study reveals physiological changes between HQ and LQ meats according to the proteome profiles.

Myosin Heavy Chain Composition, Rate of Dystrophin and Integrin Degradation and Meat Quality of Pig Longissimus thoracis and psoas major Muscles During Postmortem Aging

This study evaluated myosin heavy chain composition and the effect of aging time (45 min, 24 h, 96 h and 168 h) on meat quality parameters and dystrophin and integrin degradation pattern in longissimus thoracis and psoas major muscles of 24 Polish Landrace fatteners slaughtered at 100 kg body weight. It was found that m. longissimus thoracis had a greater percentage of MyHC-IIB (P≤0.05) and a significantly lower percentage of type I and IIA/IIX (P≤0.05) compared with the m. psoas major. Moreover, psoas major muscle had significantly higher (P≤0.05) pH45, pH24 and lower drip loss values for 45 min to 24 h, 45 min to 96 h and 45 min to 168 h than m. longissimus thoracis. Muscle type also had a significant effect on the rate of dystrophin and integrin degradation postmortem, which were significantly (P≤0.05) more rapidly degraded in the m. longissimus thoracis compared to the m. psoas major. It is concluded from the obtained results that the muscles with a greater percentage of MyHC-IIB show lower pH values, which translates into more rapid rate of integrin and dystrophin degradation. Ultimately, this may contribute to higher drip loss values during refrigerated storage.

TMT-labeled quantitative proteomic analyses on the longissimus dorsi to identify the proteins underlying intramuscular fat content in pigs

The Laiwu pig is famous for its excessively extremely high level of intramuscular fat content (IMF), however, the exact regulatory mechanism underlying intramuscular fat deposition in skeletal muscle is still unknown. As an economically important trait in pigs, IMF is controlled by multiple genes and biological pathways. In this study, we performed an integrated transcriptome-assisted TMT-labeled quantitative proteomic analysis of the longissimus dorsi (LD) muscle in Laiwu pigs at the fastest IMF deposition stage and identified 5074 unique proteins and 52 differentially abundant proteins (DAPs) (>1.5-fold cutoff, p < .05). These DAPs were hierarchically clustered in the LD muscle over two developmental stages from 120 d to 240 d. A comparison between transcriptomic (mRNA) and proteomic data revealed two differentially expressed genes corresponding to the DAPs. Changes in the levels of the nine proteins were further analyzed using RT-qPCR and parallel reaction monitoring (PRM). The proteins identified in this study could serve as candidates for elucidating the molecular mechanism of IMF deposition in pigs. SIGNIFICANCE: The intramuscular fat content (IMF) refers to the amount of fat within muscles and plays an important role in meat quality by affecting meat quality-related traits, such as tenderness, juiciness and flavor. Using the integrated transcriptome-assisted TMT-labeled quantitative proteomic approach to characterize changes in the proteomic profile of the longissimus dorsi muscle, we identified differentially abundant proteins, such as ALDH1B1, OTX2, AnxA6 and Zfp512, that are associated with intramuscular fat deposition and fat biosynthesis in pigs. These proteins could serve as candidates for elucidating the molecular mechanism of IMF deposition in pigs.

Mechanism of continuous high temperature affecting growth performance, meat quality, and muscle biochemical properties of finishing pigs

Background

The mechanism of high ambient temperature affecting meat quality is not clear till now. This study investigated the effect of high ambient temperature on meat quality and nutrition metabolism in finishing pigs.

Methods

All pigs received the same corn-soybean meal diet. A total of 24 Landrace × Large White pigs (60 kg BW, all were female) were assigned to three groups: 22AL (fed ad libitum at 22 °C), 35AL (ad libitum fed at 35 °C), and 22PF (at 22 °C, but fed the amount consumed by pigs raised at 35 °C) and the experiment lasted for 30 days.

Results

Feed intake, weight gain, and intramuscular fat (IMF) content of pigs were reduced, both directly by high temperature and indirectly through reduced feed intake. Transcriptome analysis of longissimus dorsi (LM) showed that downregulated genes caused by feed restriction were mainly involved in muscle development and energy metabolism; and upregulated genes were mainly involved in response to nutrient metabolism or extracellular stimulus. Apart from the direct effects of feed restriction, high temperature negatively affected the muscle structure and development, energy, or catabolic metabolism, and upregulated genes were mainly involved in DNA or protein damage or recombination, cell cycle process or biogenesis, stress response, or immune response.

Conclusion

Both high temperature and reduced feed intake affected growth performance and meat quality. Apart from the effects of reducing feed intake, high temperature per se negatively downregulated cell cycle and upregulated heat stress response. High temperature also decreased the energy or catabolic metabolism level through PPAR signaling pathway.

Electronic supplementary material

The online version of this article (10.1186/s12263-019-0643-9) contains supplementary material, which is available to authorized users.

Differential protein profiles in duck meat during the early postmortem storage period

The present study was designed to investigate proteomic differences in duck breast muscle during the early postmortem storage period. The meat quality was evaluated at 0 hr and 24 hr postmortem at 4°C in Pekin ducks, black Muscovy ducks and Mule ducks. Differentially expressed proteins were detected by two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF/TOF MS) at 0 hr and 24 hr postmortem in the three duck breeds. The results showed that 53 proteins spots were differentially expressed at 0 hr and 24 hr postmortem at 4°C in Pekin ducks, 75 spots in black Muscovy ducks, and 72 spots in Mule ducks. A total of 30 (10 spots for each breed) were selected for identification by mass spectrometry. Seven proteins were identified in Pekin ducks, eight in black Muscovy ducks and seven in Mule ducks. Moreover, the above results obtained by 2-DE and MALDI-TOF/TOF MS were confirmed by western blotting. To our knowledge, this study is the first to provide insights into the protein profiles of ducks during postmortem storage and provides a better understanding of the biochemical processes that contribute to duck meat quality.

Proteomic Profiles of the Longissimus Muscles of Entire Male and Castrated Pigs as Related to Meat Quality

There are indications of reduced meat quality in entire male pigs (EMs) in comparison to surgically castrated pigs (SCs); however, the differences are not strongly confirmed, and the etiology is not clarified. In the present study, samples of the longissimus dorsi, pars lumborum muscle (LL) from EMs (n = 12) and SCs (n = 12) of the same age and weight were evaluated at the physico-chemical and proteomic level. EMs exhibited lower intramuscular fat content, higher collagen content with higher solubility, a higher level of protein carbonyl groups (indicating higher protein oxidation), lower water holding capacity, and tougher meat than SCs. Proteomic analysis revealed differences in heat shock proteins expression, while a greater abundance of several other identified proteins (malate dehydrogenase, Na/K-transporting adenosintriphosphatase (ATP-ase) subunit alpha-1, and blood plasma proteins) indicates that EMs have a more oxidative metabolic profile than that of SCs. More abundant protein fragments (mainly actin and myosin heavy chain) suggest a higher degree of proteolysis in EMs, which was not followed by lower meat toughness.

Associations among Protein Biomarkers and pH and Color Traits in Longissimus thoracis and Rectus abdominis Muscles in Protected Designation of Origin Maine-Anjou Cull Cows

This study investigated the relationships among a list of 23 protein biomarkers with CIE-L*a*b* meat color traits and ultimate pH on Longissimus thoracis (LT) and Rectus abdominis (RA) muscles of 48 protected designation of origin Maine-Anjou cows. The technological parameters were correlated with several biomarkers and were in some cases muscle-dependent. More biomarkers were related to pHu in LT than in RA muscle. Some consistencies were found, by the common correlation of pHu with MyHC-IIa and MyHC-IIx. The pHu of the LT muscle was also correlated with other cytoskeletal entities and proteins belonging to metabolism and cellular stress. In contrast to the relationships found between biomarkers and LT pHu, more proteins were related to the instrumental color coordinates in RA than in LT muscle. The regression equations were parameter- and muscle-dependent. Certain of the retained proteins explained more than one color coordinate. Hsp70-Grp75 was positive in the models of L*, a*, b*, and C* of LT and of b* in the RA muscle. Further heat shock proteins were strongly related with the meat color coordinates in both muscles. The involvement of metabolic enzymes and myofibrillar proteins in the meat color development was also verified in this experiment. This study confirmed once again the importance of numerous biological pathways in beef color.

Integrative analysis of transcriptomics and proteomics of skeletal muscles of the Chinese indigenous Shaziling pig compared with the Yorkshire breed

Background

The Shaziling pig (Sus scrofa) is a well-known indigenous breed in China. One of its main advantages over European breeds is its high meat quality. However, little genetic information is available for the Shaziling pig. To screen for differentially expressed genes and proteins that might be responsible for the meat quality, the longissimus dorsi muscles from Shaziling and Yorkshire pig breeds were investigated using an integrative analysis of transcriptomics and proteomics, involving high-throughput sequencing, the two-dimensional gel electrophoresis, and mass spectrometry.

Results

Sequencing produced 79,320 unigenes by de novo assembly, and 488 differentially expressed genes in the longissimus dorsi muscle of Shaziling pig compared with the Yorkshire breed were identified. Gene Ontology term enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes analysis showed that the gene products were mainly involved in metabolism, protein binding, and regulation of skeletal muscle development. At the protein level, 23 differentially expressed proteins were identified, which were potentially associated with fatty acid metabolism, the glycolytic pathway, and skeletal muscle growth. Eight differentially expressed genes were confirmed by real-time PCR. These results give an insight into the mechanisms underlying the formation of skeletal muscle in the Shaziling pig.

Conclusions

Certain differentially expressed genes and proteins are involved in fatty acid metabolism, intramuscular fat deposition, and skeletal muscle growth in the Shaziling pig. These results provide candidate genes for improving meat quality and will promote further transcriptomic research in Shaziling pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0389-y) contains supplementary material, which is available to authorized users.

Proteomic and peptidomic differences and similarities between four muscle types from New Zealand raised Angus steers

Four muscles from New Zealand-raised Angus steers were evaluated (musculus semitendinosus, m. longissimus thoracis et lumborum, m. psoas major and m. infraspinatus) to test their differences and common features in protein and peptide abundances. The ultimate goal of such a comparison is to match muscle types to products with targeted properties. Protein profiling based on two-dimensional electrophoresis showed that the overall profiles were similar, but, between muscle types, significant (p<0.05) intensity differences were observed in twenty four protein spots. Profiling of endogenous peptides allowed characterisation of 346 peptides. Quantitative analysis showed a clear distinction between the muscle types. Forty-four peptides were identified that showed a statistically significant (p<0.05) and substantial (>2-fold change) difference between at least two muscle types. These analyses demonstrate substantial similarities between these four muscle types, but also clear distinctions in their profiles; specifically a 25% difference between at least two muscles at the peptidomic level, and a 14% difference at the proteomic level.

A hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) based metabolomics study on colour stability of ovine meat

Meat colour is one of the cues available to the consumer to gauge overall meat quality and wholesomeness. Colour stability of meat is determined by several factors both inherent to the animal and post-slaughter conditions, including ageing, storage/packaging and display times. A hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) based metabolomics study was undertaken to identify and compare polar metabolites between ovine meat samples that were exposed to different durations of ageing, storage conditions, and display times. Primary metabolites comprising amino acids, sugars, nucleotides, nucleosides, organic acids and their breakdown products were mainly identified as discriminating factors. For the first time, boron complexes of sugar and malic acid were also tentatively identified. As expected, most compounds identified were related to myoglobin chemistry, and compounds with antioxidant properties were found in higher levels in colour stable samples. Supplementary studies identifying semi-polar, non-polar and volatile compounds will provide a holistic understanding of the chemical basis of colour stability in ovine meat.

Proteomics and the search for welfare and stress biomarkers in animal production in the one-health context

Stress and welfare are important factors in animal production in the context of growing production optimization and scrutiny by the general public.

Understanding Early Post-Mortem Biochemical Processes Underlying Meat Color and pH Decline in the Longissimus thoracis Muscle of Young Blond d'Aquitaine Bulls Using Protein Biomarkers

Many studies on color biochemistry and protein biomarkers were undertaken in post-mortem beef muscles after ≥24 hours. The present study was conducted on Longissimus thoracis muscles of 21 Blond d'Aquitaine young bulls to evaluate the relationships between protein biomarkers present during the early post-mortem and known to be related to tenderness and pH decline and color development. pH values at 45 min, 3 h, and 30 h post-mortem were correlated with three, seven, and six biomarkers, respectively. L*a*b* color coordinates 24 h post-mortem were correlated with nine, five, and eight protein biomarkers, respectively. Regression models included Hsp proteins and explained between 47 and 59% of the variability between individuals in pH and between 47 and 65% of the variability in L*a*b* color coordinates. Proteins correlated with pH and/or color coordinates were involved in apoptosis or had antioxidative or chaperone activities. The main results include the negative correlations between pH45 min, pH3 h, and pHu and Prdx6, which may be explained by the antioxidative and phospholipase activities of this biomarker. Similarly, inducible Hsp70-1A/B and μ-calpain were correlated with L*a*b* coordinates, due to the protective action of Hsp70-1A/B on the proteolytic activities of μ-calpain on structural proteins. Correlations existed further between MDH1, ENO3, and LDH-B and pH decline and color stability probably due to the involvement of these enzymes in the glycolytic pathway and, thus, the energy status of the cell. The present results show that research using protein indicators may increase the understanding of early post-mortem biological mechanisms involved in pH and beef color development.

A genetical genomics approach reveals new candidates and confirms known candidate genes for drip loss in a porcine resource population

In this study lean meat water-holding capacity (WHC) of a Duroc × Pietrain (DuPi) resource population with corresponding genotypes and transcriptomes was investigated using genetical genomics. WHC was characterized by drip loss measured in M. longissimus dorsi. The 60K Illumina SNP chips identified genotypes of 169 F2 DuPi animals. Whole-genome transcriptomes of muscle samples were available for 132 F2 animals using the Affymetrix 24K GeneChip® Porcine Genome Array. Performing genome-wide association studies of transcriptional profiles, which are correlated with phenotypes, allows elucidation of cis- and trans-regulation. Expression levels of 1,228 genes were significantly correlated with drip loss and were further analyzed for enrichment of functional annotation groups as defined by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. A hypergeometric gene set enrichment test was performed and revealed glycolysis/glyconeogenesis, pentose phosphate pathway, and pyruvate metabolism as the most promising pathways. For 267 selected transcripts, expression quantitative trait loci (eQTL) analysis was performed and revealed a total of 1,541 significant associations. Because of positional accordance of the gene underlying transcript and the eQTL location, it was possible to identify eight eQTL that can be assumed to be cis-regulated. Comparing the results of gene set enrichment and the eQTL detection tests, molecular networks and potential candidate genes, which seemed to play key roles in the expression of WHC, were detected. The α-1-microglobulin/bikunin precursor (AMBP) gene was assumed to be cis-regulated and was part of the glycolysis pathway. This approach supports the identification of trait-associated SNPs and the further biological understanding of complex traits.

Monitoring post mortem changes in porcine muscle through 2-D DIGE proteome analysis of Longissimus muscle exudate

Background

Meat quality is a complex trait influenced by a range of factors with post mortem biochemical processes highly influential in defining ultimate quality. High resolution two-dimensional DIfference Gel Electrophoresis (2-D DIGE) and Western blot were applied to study the influence of post mortem meat ageing on the proteome of pork muscle. Exudate collected from the muscle following centrifugation was analysed at three timepoints representing a seven day meat ageing period.

Results

The intensity of 136 spots varied significantly (p < 0.05) across this post mortem period and 40 spots were identified using mass spectrometry. The main functional categories represented were metabolic proteins, stress-related proteins, transport and structural proteins. Metabolic and structural proteins were generally observed to increase in abundance post mortem and many likely represent the accumulation of the degradation products of proteolytic enzyme activity. In contrast, stress-related proteins broadly decreased in abundance across the ageing period. Stress response proteins have protective roles in maintaining cellular integrity and a decline in their abundance over time may correlate with a reduction in cellular integrity and the onset of meat ageing. Since cellular conditions alter with muscle ageing, changes in solubility may also contribute to observed abundance profiles.

Conclusions

Muscle exudate provided valuable information about the pathways and processes underlying the post mortem ageing period, highlighting the importance of post mortem modification of proteins and their interaction for the development of meat quality traits.

Effect of low voltage electrical stimulation on protein and quality changes in bovine muscles during postmortem aging

This experiment was conducted to determine the influence of low voltage electrical stimulation (ES) on the tenderness development of beef round muscles. Eight steers were slaughtered, and ES applied to one side of each carcass within 90 min of exsanguination. Steaks from M. longissimus dorsi, semimembranosus, adductor, and gracilis were vacuum packaged and aged at 4 °C for 9 d. Star probe, sensory evaluation, Western blot assays of troponin-T and μ-calpain autolysis and 2D-DIGE were conducted. ES resulted in accelerated (P<0.05) pH decline of the longissimus in the first 24h postmortem. ES did not influence (P>0.05) proteolysis and tenderness, but did alter the predominance of metabolic proteins in the soluble fraction of muscle. Aging for 9 d improved tenderness (P<0.05). The data confirmed that low voltage ES at 90 min of exsanguination had no effect on proteolysis and tenderness development in the longissimus dorsi, semimembranosus, adductor or gracilis in beef.

Evaluation of QTL for carcass merit and meat quality traits in a US commercial Duroc population

Putative quantitative trait loci (QTL) regions on 5 chromosomes (SSC3, 6, 12, 15, and 18) were selected from our previous genome scans of a Duroc×Pietrain F(2) resource population for further evaluation in a US commercial Duroc population (n=331). A total of 81 gene-specific single nucleotide polymorphism (SNP) markers were genotyped and 33 markers were segregating. The MDH1 SNP on SSC3 was associated with 45-min and ultimate pH (pHu), and pH decline. PRKAG3 on SSC15 was associated with pHu. The HSPG2 SNP on SSC6 was associated with marbling score and days to 113kg. Markers for NUP88 and FKBP10 on SSC12 were associated with 45-min pH and L*, respectively. The SSC15 marker SF3B1 was associated with L* and LMA, and the SSC18 marker ARF5 was associated with pHu and color score. These results in a commercial Duroc population showed a general consistency with our previous genome scan.

Skeletal muscle proteomics in livestock production

Proteomics allows studying large numbers of proteins, including their post-translational modifications. Proteomics has been, and still are, used in numerous studies on skeletal muscle. In this article, we focus on its use in the study of livestock muscle development and meat quality. Changes in protein profiles during myogenesis are described in cattle, pigs and fowl using comparative analyses across different ontogenetic stages. This approach allows a better understanding of the key stages of myogenesis and helps identifying processes that are similar or divergent between species. Genetic variability of muscle properties analysed by the study of hypertrophied cattle and sheep are discussed. Biological markers of meat quality, particularly tenderness in cattle, pigs and fowl are presented, including protein modifications during meat ageing in cattle, protein markers of PSE meat in turkeys and of post-mortem muscle metabolism in pigs. Finally, we discuss the interest of proteomics as a tool to understand better biochemical mechanisms underlying the effects of stress during the pre-slaughter period on meat quality traits. In conclusion, the study of proteomics in skeletal muscles allows generating large amounts of scientific knowledge that helps to improve our understanding of myogenesis and muscle growth and to control better meat quality.