Beef tenderness and intramuscular fat proteomic biomarkers: muscle type effect

Functional study and epigenetic targets analyses of SIRT1 in intramuscular preadipocytes via ChIP-seq and mRNA-seq

The SIRT1 epigenetic regulator is involved in hepatic lipid homoeostasis. However, the role of SIRT1 in regulating intramuscular fat deposition as well as the pathways and potential epigenetic targets involved remain unknown. Herein, we investigate SIRT1 function, its genome-wide epigenetic target profile, and transcriptomic changes under SIRT1 overexpression during yak intramuscular preadipocytes differentiation. To this end, we analysed the relationship between SIRT1 and intramuscular fat content as well as lipid metabolism-related genes in longissimus dorsi tissue. We found that SIRT1 expression negatively correlates with intramuscular fat content as well as with the expression of genes related to lipid synthesis, while positively correlating with that of fatty acid oxidation-involved genes. SIRT1 overexpression in intramuscular preadipocytes significantly reduced adipose differentiation marker expression, intracellular triacylglycerol content, and lipid deposition. Chromatin immunoprecipitation coupled with high-throughput sequencing of H3K4ac (a known direct target of SIRT1) and high-throughput mRNA sequencing results revealed that SIRT1 may regulate intramuscular fat deposition via three potential new transcription factors (NRF1, NKX3.1, and EGR1) and four genes (MAPK1, RXRA, AGPAT1, and HADH) implicated in protein processing within the endoplasmic reticulum pathway and the MAPK signalling pathway in yaks. Our study provides novel insights into the role of SIRT1 in regulating yak intramuscular fat deposition and may help clarify the mechanistic determinants of yak meat characteristics.

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.

Molecular mechanisms contributing to the development of beef sensory texture and flavour traits and related biomarkers: Insights from early post-mortem muscle using label-free proteomics

Beef sensory quality comprises a suite of traits, each of which manifests its ultimate phenotype through interaction of muscle physiology with environment, both in vivo and post-mortem. Understanding variability in meat quality remains a persistent challenge, but omics studies to uncover biological connections between natural variability in proteome and phenotype could provide validation for exploratory studies and offer new insights. Multivariate analysis of proteome and meat quality data from Longissimus thoracis et lumborum muscle samples taken early post-mortem from 34 Limousin-sired bulls was conducted. Using for the first-time label-free shotgun proteomics combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS), 85 proteins were found to be related with tenderness, chewiness, stringiness and flavour sensory traits. The putative biomarkers were classified in five interconnected biological pathways; i) muscle contraction, ii) energy metabolism, iii) heat shock proteins, iv) oxidative stress, v) regulation of cellular processes and binding. Among the proteins, PHKA1 and STBD1 correlated with all four traits, as did the GO biological process 'generation of precursor metabolites and energy'. Optimal regression models explained a high level (58-71%) of phenotypic variability with proteomic data for each quality trait. The results of this study propose several regression equations and biomarkers to explain the variability of multiple beef eating quality traits. Thanks to annotation and network analyses, they further suggest protein interactions and mechanisms underpinning the physiological processes regulating these key quality traits. SIGNIFICANCE: The proteomic profiles of animals with divergent quality profiles have been compared in numerous studies; however, a wide range of phenotypic variation is required to better understand the mechanisms underpinning the complex biological pathways correlated with beef quality and protein interactions. We used multivariate regression analyses and bioinformatics to analyse shotgun proteomics data to decipher the molecular signatures involved in beef texture and flavour variations with a focus on multiple quality traits. We developed multiple regression equations to explain beef texture and flavour. Additionally, potential candidate biomarkers correlated with multiple beef quality traits are suggested, which could have utility as indicators of beef overall sensory quality. This study explained the biological process responsible for determining key quality traits such as tenderness, chewiness, stringiness, and flavour in beef, which will provide support for future beef proteomics studies.

Altering the ratio of palmitic, stearic, and oleic acids in dietary fat affects nutrient digestibility, plasma metabolites, growth performance, carcass, meat quality, and lipid metabolism gene expression of Angus bulls

This study evaluated the effects of changing the ratio of palmitic, stearic, and oleic acids in dietary fat on nutritional metabolism, growth performance, and meat quality of finishing Angus bulls. Bulls received the following three treatments: (1) a control diet without fat supplement (CON), (2) CON + mixed fatty acid supplement (58% C16:0 + 28% cis-9 C18:1; MIX), (3) CON + saturated fatty acid supplement (87% C16:0 + 10% C18:0; SFA). In summary, both fat treatment diets simultaneously increased saturated fatty acids C16:0 (P = 0.025), C18:0 (P < 0.001) and total monounsaturated fatty acids (P = 0.008) in muscle, thus balancing the ratio of unsaturated to saturated fatty acids in muscle. MIX diet increased the digestibility of dry matter (P = 0.014), crude protein (P = 0.038), and ether extract (P = 0.036). SFA diet increased the daily gain (P = 0.032) and intramuscular fat content (P = 0.043). The high content of C16:0 and C18:0 in the SFA diet promoted weight gain and fat deposition of beef cattle by increasing feed intake, up-regulating the expression of lipid uptake genes and increasing deposition of total fatty acids, resulting in better growth performance and meat quality.

Relationships between the abundance of 29 proteins and several meat or carcass quality traits in two bovine muscles revealed by a combination of univariate and multivariate analyses

We aimed to evaluate the relationships between meat or carcass properties and the abundance of 29 proteins quantified in two muscles, Longissimus thoracis and Rectus abdominis, of Rouge des Prés cows. The relative abundance of the proteins was evaluated using a high throughput immunological method: the Reverse Phase Protein array. A combination of univariate and multivariate analyses has shown that small HSPs (CRYAB, HSPB6), fast glycolytic metabolic and structural proteins (MYH1, ENO3, ENO1, TPI1) when assayed both in RA and LT, were related to meat tenderness, marbling, ultimate pH, as well as carcass fat-to-lean ratio or conformation score. In addition to some small HSP, ALDH1A1 and TRIM72 contributed to the molecular signature of muscular and carcass adiposity. MYH1 and HSPA1A were among the top proteins related to carcass traits. We thus shortened the list to 10 putative biomarkers to be considered in future tools to manage both meat and carcass properties. SIGNIFICANCE: In three aspects this manuscript is notable. First, this is the first proteomics study that aims to evaluate putative biomarkers of both meat and carcass qualities that are of economic importance for the beef industry. Second, the relationship between the abundance of proteins and the carcass or meat traits were evaluated by a combination of univariate and multivariate analyses on 48 cows that are representative of the biological variability of the traits. Third, we provide a short list of ten proteins to be tested in a larger population to feed the pipeline of biomarker discovery.

Differences in meat quality between Angus cattle and Xinjiang brown cattle in association with gut microbiota and its lipid metabolism

Gut microbiota plays important roles in mediating fat metabolic events in humans and animals. However, the differences of meat quality traits related to the lipid metabolism (MQT-LM) in association with gut microbiota involving in lipid metabolism have not been well explored between Angus cattle (AG) and Xinjiang brown cattle (BC). Ten heads of 18-month-old uncastrated male AG and BC (5 in each group) raised under the identical conditions were selected to test MQT-LM, i.e., the backfat thickness (BFT), the intramuscular fat (IMF) content, the intramuscular adipocyte areas (IAA), the eye muscle area (EMA), the muscle fiber sectional area (MFSA) and the muscle shear force after sacrifice. The gut microbiota composition and structure with its metabolic function were analyzed by means of metagenomics and metabolomics with rectal feces. The correlation of MQT-LM with the gut microbiota and its metabolites was analyzed. In comparison with AG, BC had significant lower EMA, IMF content and IAA but higher BFT and MFSA. Chao1 and ACE indexes of α-diversity were lower. β-diversity between AG and BC were significantly different. The relative abundance of Bacteroidetes, Prevotella and Blautia and Prevotella copri, Blautia wexlerae, and Ruminococcus gnavus was lower. The lipid metabolism related metabolites, i.e., succinate, oxoglutaric acid, L-aspartic acid and L-glutamic acid were lower, while GABA, L-asparagine and fumaric acid were higher. IMF was positively correlated with Prevotella copri, Blautia wexlerae and Ruminococcus gnavus, and the metabolites succinate, oxoglutaric acid, L-aspartic acid and L-glutamic acid, while negatively with GABA, L-asparagine and fumaric acid. BFT was negatively correlated with Blautia wexlerae and the metabolites succinate, L-aspartic acid and L-glutamic acid, while positively with GABA, L-asparagine and fumaric acid. Prevotella Copri, Blautia wexlerae, and Ruminococcus gnavus was all positively correlated with succinate, oxoglutaric acid, while negatively with L-asparagine and fumaric acid. In conclusion, Prevotella copri, Prevotella intermedia, Blautia wexlerae, and Ruminococcus gnavus may serve as the potential differentiated bacterial species in association with MQT-LM via their metabolites of oxoglutaric acid, succinate, fumaric acid, L-aspartic acid, L-asparagine, L-glutamic acid and GABA between BC and AG.

Proteomics Unveils Post-Mortem Changes in Beef Muscle Proteins and Provides Insight into Variations in Meat Quality Traits of Crossbred Young Steers and Heifers Raised in Feedlot

Proteomics has been widely used to study muscle biology and meat quality traits from different species including beef. Beef proteomics studies allow a better understanding of the biological processes related to meat quality trait determination. This study aimed to decipher by means of two-dimensional electrophoresis (2D-PAGE), mass spectrometry and bioinformatics the changes in post-mortem muscle with a focus on proteins differentially expressed in the Longissimus thoracis (LT) muscle of immunocastrated young heifers and steers. Carcass traits, chemical composition, pH, instrumental color (L*, a*, b*), cooking loss and Warner-Bratzler shear force (WBSF) of meat from F1 Montana-Nellore cattle were also evaluated. Backfat thickness (BFT) and intramuscular fat content (IMF) were 46.8% and 63.6% higher in heifers (p < 0.05), respectively, while evaporation losses (EL) were 10.22% lower compared to steers. No differences (p > 0.05) were observed for tenderness evaluated by WBSF (3, 10, and 17 days post-mortem), pH, and color traits (L*, a* and b*) between the experimental groups. The study revealed several proteins to be differentially expressed proteins in heifers compared steers (p < 0.05). In heifers, proteins involved in nutrient transport (TF, ALB, and MB), energy metabolism (ALDOA, GAPDH, and PKM), and oxidative stress and response to stress (HSPA8 and CA3) were associated with a greater BFT and IMF deposition. The higher expression of these proteins indicated greater oxidative capacity and lower glycolytic activity in the LT muscle of heifers. In steers, there was greater abundance of protein expression related to muscle contraction and proteins of structure (ACTA1, TPM2 and TNNT3), energy metabolism (ENO1, ENO3, PYGM, PGM1 and TPI1) and ATP metabolism (ATP5F1B, PEBP1 and AK1), indicating greater glycogenolysis in LT muscle, suggesting a shift in the glycolytic/oxidative fibers of steers.

Tandem mass tag labeling to assess proteome differences between intermediate and very tender beef steaks

Tenderness is considered as one of the most important quality attributes dictating consumers' overall satisfaction and future purchasing decisions of fresh beef. However, the ability to predict and manage tenderness has proven very challenging due to the numerous factors that contribute to variation in end-product tenderness. Proteomic profiling allows for global examination of differentially abundant proteins in the meat and can provide new insight into biological mechanisms related to meat tenderness. Hence, the objective of this study was to examine proteomic profiles of beef longissimus lumborum (LL) steaks varying in tenderness, with the intention to identify potential biomarkers related to tenderness. For this purpose, beef LL muscle samples were collected from 99 carcasses at 0 and 384 h postmortem. Based on Warner-Bratzler shear force values at 384 h, 16 samples with the highest (intermediate tender, IT) and lowest (very tender, VT) values were selected to be used for proteomic analysis in this study (n = 8 per category). Using tandem mass tag-based proteomics, a total of 876 proteins were identified, of which 51 proteins were differentially abundant (P < 0.05) between the tenderness categories and aging periods. The differentially identified proteins encompassed a wide array of biological processes related to muscle contraction, calcium signaling, metabolism, extracellular matrix organization, chaperone, and apoptosis. A greater (P < 0.05) relative abundance of proteins associated with carbohydrate metabolism and apoptosis, and a lower (P < 0.05) relative abundance of proteins involved in muscle contraction was observed in the VT steaks after aging compared with the IT steaks, suggesting that more proteolysis occurred in the VT steaks. This may be explained by the greater (P < 0.05) abundance of chaperonin and calcium-binding proteins in the IT steaks, which could have limited the extent of postmortem proteolysis in these steaks. In addition, a greater (P < 0.05) abundance of connective tissue proteins was also observed in the IT steaks, which likely contributed to the difference in tenderness due to added background toughness. The established proteomic database obtained in this study may provide a reference for future research regarding potential protein biomarkers that are associated with meat tenderness.

Proteomic and parallel reaction monitoring approaches to evaluate biomarkers of mutton tenderness

Intensive fattening usually results in the changes of meat quality. Tenderness is a central attribute for mutton sensory qualities and consumers' choice. Here, we reported that intensive fattening mutton was more tender than that of traditionally raised sheep. By proteomic approach, we found 49 differentially expressed proteins in longissimus dorsi muscle. After bioinformatics analysis, 5 cytoskeletal proteins, 3 protein binding proteins and 7 metabolic enzymes were identified as potential biomarkers for mutton tenderness. Finally, we verified the expression of these abundant proteins by parallel reaction monitoring (PRM). Collectively, our results reveal that the mutton of sheep raised by intensive fattening is more tender than that of traditionally raised sheep. Myosin-2, myosin-13, vimentin, carbonic anhydrase, carbonic anhydrase-2, Glutathione S-transferase and Microtubule-associated protein 4 isoform X1 can be candidate biomarkers for mutton tenderness. Our data also indicate a central role of cytoskeletal proteins and metabolic enzymes in determining mutton tenderness.

Combining label-free and label-based accurate quantifications with SWATH-MS: Comparison with SRM and PRM for the evaluation of bovine muscle type effects

Mass spectrometry has proven to be a valuable tool for the accurate quantification of proteins. In this study, the performances of three targeted approaches, namely selected reaction monitoring (SRM), parallel reaction monitoring (PRM) and sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS), to accurately quantify ten potential biomarkers of beef meat tenderness or marbling in a cohort of 64 muscle samples were evaluated. So as to get the most benefit out of the complete MS2 maps that are acquired in SWATH-MS, an original label-free quantification method to estimate protein amounts using an I-spline regression model was developed. Overall, SWATH-MS outperformed SRM in terms of sensitivity and dynamic range, while PRM still performed the best, and all three strategies showed similar quantification accuracies and precisions for the absolute quantification of targets of interest. This targeted picture was extended by 585 additional proteins for which amounts were estimated using the label-free approach on SWATH-MS; thus, offering a more global profiling of muscle proteomes and further insights into muscle type effect on candidate biomarkers of beef meat qualities as well as muscle metabolism.

Combined transcriptome and proteome analyses reveal differences in the longissimus dorsi muscle between Kazakh cattle and Xinjiang brown cattle

Objective

With the rapid development of proteomics sequencing and RNA sequencing technology, multi-omics analysis has become a current research hotspot. Our previous study indicated that Xinjiang brown cattle have better meat quality than Kazakh cattle. In this study, Xinjiang brown cattle and Kazakh cattle were used as the research objects.

Methods

Proteome sequencing and RNA sequencing technology were used to analyze the proteome and transcriptome of the longissimus dorsi muscle of the two breeds of adult steers (n = 3).

Results

In this project, 22,677 transcripts and 1,874 proteins were identified through quantitative analysis of the transcriptome and proteome. By comparing the identified transcriptome and proteome, we found that 1,737 genes were identified at both the transcriptome and proteome levels. The results of the study revealed 12 differentially expressed genes and proteins: troponin I1, crystallin alpha B, cysteine, and glycine rich protein 3, phosphotriesterase-related, myosin-binding protein H, glutathione s-transferase mu 3, myosin light chain 3, nidogen 2, dihydropyrimidinase like 2, glutamate-oxaloacetic transaminase 1, receptor accessory protein 5, and aspartoacylase. We performed functional enrichment of these differentially expressed genes and proteins. The Kyoto encyclopedia of genes and genomes results showed that these differentially expressed genes and proteins are enriched in the fatty acid degradation and histidine metabolism signaling pathways. We performed parallel reaction monitoring (PRM) verification of the differentially expressed proteins, and the PRM results were consistent with the sequencing results.

Conclusion

Our study provided and identified the differentially expressed genes and proteins. In addition, identifying functional genes and proteins with important breeding value will provide genetic resources and technical support for the breeding and industrialization of new genetically modified beef cattle breeds.

Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

BACKGROUND

Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on the lncRNAs involved in sheep IMF deposition is still in its infancy. Aohan fine-wool sheep (AFWS), one of China's most important meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of IMF deposition. We identified lncRNAs by RNA sequencing in Longissimus thoracis et lumborum (LTL) samples of sheep at two ages: 2 months (Mth-2) and 12 months (Mth-12).

RESULTS

We identified a total of 26,247 genes and 6935 novel lncRNAs in LTL samples of sheep. Among these, 199 mRNAs and 61 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained target genes of differentially expressed lncRNAs (DELs) and performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We found that target mRNAs were enriched in metabolic processes and developmental pathways. One pathway was significantly enriched, namely tight junction. Based on the analysis of critical target genes, we obtained seven candidate lncRNAs that potentially regulated lipid deposition and constructed a lncRNA-mRNA co-expression network that included MSTRG.4051.3-FZD4, MSTRG.16157.3-ULK1, MSTRG.21053.3-PAQR3, MSTRG.19941.2-TPI1, MSTRG.12864.1-FHL1, MSTRG.2469.2-EXOC6 and MSTRG.21381.1-NCOA1. We speculated that these candidate lncRNAs might play a role by regulating the expression of target genes. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR.

CONCLUSIONS

Our study identified the differentially expressed mRNAs and lncRNAs during intramuscular lipid deposition in Aohan fine-wool sheep. The work may widen the knowledge about the annotation of the sheep genome and provide a working basis for investigating intramuscular fat deposition in sheep.

Understanding the Determination of Meat Quality Using Biochemical Characteristics of the Muscle: Stress at Slaughter and Other Missing Keys

Despite increasingly detailed knowledge of the biochemical processes involved in the determination of meat quality traits, robust models, using biochemical characteristics of the muscle to predict future meat quality, lack. The neglecting of various aspects of the model paradigm may explain this. First, preslaughter stress has a major impact on meat quality and varies according to slaughter context and individuals. Yet, it is rarely taken into account in meat quality models. Second, phenotypic similarity does not imply similarity in the underlying biological causes, and several models may be needed to explain a given phenotype. Finally, the implications of the complexity of biological systems are discussed: a homeostatic equilibrium can be reached in countless ways, involving thousands of interacting processes and molecules at different levels of the organism, changing over time and differing between animals. Consequently, even a robust model may explain a significant part, but not all of the variability between individuals.

Characterization of the promoter region of bovine ATP5B: roles of MyoD and GATA1 in the regulation of basal transcription

Intramuscular fat (IMF) content is a key determinant of beef quality, making it a key topic of research interest. ATP5B serves as the catalytic component of the mitochondrial ATP synthase complex and plays essential roles in controlling fat contents and oxidative metabolism in bovine skeletal muscle. In this study, we determined that bovine ATP5B was highly expressed in longissimus thoracis. To elucidate the molecular mechanisms involved in bovine ATP5B regulation, we cloned and characterized the promoter region of ATP5B. Applying 5'-rapid amplification of cDNA end analysis (RACE), we identified two transcriptional start sites (TSSs) in its promoter region. Using a series of 5'-deletion promoter plasmids in luciferase reporter assay, we found that the proximal minimal promoter of ATP5B was located within the region -539/220 relative to the TSS. Site-directed mutation in combination with chromatin immunoprecipitation (ChIP) assays demonstrated that MyoD and GATA1 binding to the promoter region drives bovine ATP5B transcription. Taken together, these results provide new insight into the regulatory mechanisms of ATP5B transcription in mediating the IMF content of beef.

Molecular signatures of beef tenderness: Underlying mechanisms based on integromics of protein biomarkers from multi-platform proteomics studies

Over the last two decades, proteomics have been employed to decipher the underlying factors contributing to variation in the quality of muscle foods, including beef tenderness. One such approach is the application of high-throughput protein analytical platforms in the identification of meat quality biomarkers. To broaden our understanding about the biological mechanisms underpinning meat tenderization across a large number of studies, an integromics study was performed to review the current status of protein biomarker discovery targeting beef tenderness. This meta-analysis is the first to gather and propose a comprehensive list of 124 putative protein biomarkers derived from 28 independent proteomics-based experiments, from which 33 robust candidates were identified worthy of evaluation using targeted or untargeted data-independent acquisition proteomic methods. We further provide an overview of the interconnectedness of the main biological pathways impacting tenderness determination after multistep analyses including Gene Ontology annotations, pathway and process enrichment and literature mining, and specifically discuss the major proteins and pathways most often reported in proteomics research.

Wójciak K. Peptides from Different Carcass Elements of Organic and Conventional Pork-Potential Source of Antioxidant Activity

The growing consumer interest in organic foods, as well as, in many cases, the inconclusiveness of the research comparing organic and conventional foods, indicates a need to study this issue further. The aim of the study was to compare the effects of meat origin (conventional vs. organic) and selected elements of the pork carcass (ham, loin, and shoulder) on the meat proteome and the antioxidant potential of its peptides. The peptidomic approach was used, while the ability of antioxidants to scavenge 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulfonic acid (ABTS), to chelate Fe(II) ions, and to reduce Fe(III) was determined. Most peptides were derived from myofibrillary proteins. The meat origin and the element of the pork carcass did not have a significant effect on the proteome. On the other hand, the pork origin and the carcass element significantly affected the iron ion-chelating capacity (Fe(II)) and the reducing power of peptides. In particular, pork ham from conventional rearing systems had the best antioxidant properties in relation to potential antioxidant peptides. This could be a factor for human health, as well as for stabilized meat products (e.g., toward lipid oxidation).

Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction

This study evaluated the potential of a panel of 20 protein biomarkers, quantified by Reverse Phase Protein Array (RPPA), to explain and predict two important meat quality traits, these being beef tenderness assessed by Warner-Bratzler shear force (WBSF) and the intramuscular fat (IMF) content (also termed marbling), in a large database of 188 Protected Designation of Origin (PDO) Maine-Anjou cows. Thus, the main objective was to move forward in the progression of biomarker-discovery for beef qualities by evaluating, at the same time for the two quality traits, a list of candidate proteins so far identified by proteomics and belonging to five interconnected biological pathways: (i) energy metabolic enzymes, (ii) heat shock proteins (HSPs), (iii) oxidative stress, (iv) structural proteins and (v) cell death and protein binding. Therefore, three statistical approaches were applied, these being Pearson correlations, unsupervised learning for the clustering of WBSF and IMF into quality classes, and Partial Least Squares regressions (PLS-R) to relate the phenotypes with the 20 biomarkers. Irrespective of the statistical method and quality trait, seven biomarkers were related with both WBSF and IMF, including three small HSPs (CRYAB, HSP20 and HSP27), two metabolic enzymes from the oxidative pathway (MDH1: Malate dehydrogenase and ALDH1A1: Retinal dehydrogenase 1), the structural protein MYH1 (Myosin heavy chain-IIx) and the multifunctional protein FHL1 (four and a half LIM domains 1). Further, three more proteins were retained for tenderness whatever the statistical method, among which two were structural proteins (MYL1: Myosin light chain 1/3 and TNNT1: Troponin T, slow skeletal muscle) and one was glycolytic enzyme (ENO3: β-enolase 3). For IMF, two proteins were, in this trial, specific for marbling whatever the statistical method: TRIM72 (Tripartite motif protein 72, negative) and PRDX6 (Peroxiredoxin 6, positive). From the 20 proteins, this trial allowed us to qualify 10 and 9 proteins respectively as strongly related with beef tenderness and marbling in PDO Maine-Anjou cows.

Association of hormone-sensitive lipase (HSL) gene polymorphisms with the intramuscular fat content in two Chinese beef cattle breeds

Hormone-sensitive lipase (HSL) was considered as an essential enzyme in glucolipid metabolism. It has been proposed to be a lead candidate gene for genetic markers of lipid deposition in livestock. The aim of this study was to identify sequence variants (SVs) of the bovine HSL gene and evaluate the relations to intramuscular fat in two indigenous Chinese beef cattle breeds. Expression analysis by quantitative real-time polymerase chain reactions (qPCR) indicated that expression levels of bovine HSL gene were highest in the perirenal fat and heart within two different age stage (adult and calf), respectively. Five SVs were identified by direct DNA sequencing, which included four missense mutations (g.16563C>T, g.16734G>A, g.16896A>G, g.17388G>T) in exon 8 and a synonymous mutation (g.17402C>T) in exon 9. Population genetic analysis showed that except for g.16563C>T and g.17402C>T, all the other detected SVs strongly affected the bovine intramuscular fat content (P < 0.01 or P < 0.05). The individuals with Hap5/5 diplotypes (CC-GG-GG-GG-CC) was highly significantly associated with intramuscular fat content than the other diplotypes (P < 0.01). The above results suggested that the HSL gene can used as potential candidate markers gene for the beef breed improvement through marker assisted selection in Chinese cattle breeds.

Muscle Fiber Properties in Cattle and Their Relationships with Meat Qualities: An Overview

The control of meat quality traits constitutes an important target for any farm animal production, including cattle. Therefore, better understanding of the biochemical properties that drive muscle development and final outcomes constitutes one of the main challenging topics of animal production and meat science. Accordingly, this review has focused on skeletal muscle fibers in cattle and their relationships with beef qualities. It aimed to describe the chemical and structural properties of muscle fibers as well as a comprehensive review of their contractile and metabolic characteristics during the life of the animal. The existing methods for the classification of muscle fibers were reviewed, compared, and discussed. Then, the different stages of myogenesis in cattle were defined. The main factors regulating fetal and postnatal growth and the plasticity of muscle fibers were evidenced, especially the role of myostatin growth factor and the impact of nutritional factors. This review highlights that the knowledge about muscle fibers is paramount for a better understanding of how to control the muscle properties throughout the life of the animal for better management of the final eating qualities of beef. Accordingly, the associations between bovine muscle fibers and different meat eating qualities such as tenderness, pH decline, and color traits were further presented.

The inclusion of de-oiled wet distillers grains in feedlot diets reduces the expression of lipogenic genes and fat content in Longissimus muscle from F1 Angus-Nellore cattle

The inclusion of agro-industry by-products originated from corn ethanol production has increased in animal nutrition in Brazil, reducing formulation costs. In the literature, there is no consensus on how the high inclusion of de-oiled wet distillers grains can affect beef quality and the expression of lipogenic genes in Longissimus muscle. The aim of this study was to evaluate the effects of WDG in the diet of F1 Angus-Nellore cattle on meat quality characteristics, chemical composition and expression of genes involved in lipid metabolism. A hundred F1 Angus-Nellore bulls, with average initial body weight (BW) of 369.5 ± 49 kg were used. The experiment was carried out in a randomized block design, and the animals were divided into two blocks (light and heavy) according to the initial body weight. The animals were fed diets containing levels of 0 (control), 15, 30 and 45% of WDG replacing dry corn and soybean meal. After 129 days of feedlot, the animals were slaughtered and samples of the longissimus thoracis (LT) muscle were collected for quality analyzes such as shear force (3, 10 and 17 aging days), color (luminosity, red, Chroma and Hue), cooking losses, pH and chemical composition (moisture, protein, lipids and ash contents). In addition, the expression of the PPARα, PPARγ, SREBP-1c, SCD1, LPL, FABP4, FASN, ACOX, CPT2, GPX1 and ACACA genes was investigated in the LT muscle by real-time reverse transcription polymerase chain reaction (RT-PCR). Data were analyzed using polynomial contrasts (linear, quadratic and control vs. WDG). There was no interaction (P > 0.05) between aging times and the inclusion of WDG in the diets on the meat quality (pH, cooking losses, coloration and tenderness). However, diets with increasing levels of WDG caused a linear reduction (P = 0.01) in the intramuscular fat of LT. The lipogenic genes SCD1, PPARγ, FASN and CPT2 were less expressed (P < 0.05) in response to the inclusion of WDG. These results suggest that the inclusion of WDG reduced the expression of lipogenic genes and consequently the marbling of LT muscle without affecting tenderness (shear force) and meat color traits.

Review: Enhancing intramuscular fat development via targeting fibro-adipogenic progenitor cells in meat animals

In the livestock industry, subcutaneous and visceral fat pads are considered as wastes, while intramuscular fat or marbling fat is essential for improving flavor and palatability of meat. Thus, strategies for optimizing fat deposition are needed. Intramuscular adipocytes provide sites for lipid deposition and marbling formation. In the present article, we addressed the origin and markers of intramuscular adipocyte progenitors - fibro-adipogenic progenitors (FAPs), as well as the latest progresses in mechanisms regulating the proliferation and differentiation of intramuscular FAPs. Finally, by targeting intramuscular FAPs, possible nutritional manipulations to improve marbling fat deposition are discussed. Despite recent progresses, the properties and regulation of intramuscular FAPs in livestock remain poorly understood and deserve further investigation.

Application of proteomic to investigate the post-mortem tenderization rate of different horse muscles

The aim of this study was to evaluate the effect of post-mortem aging on tenderness development and proteolysis of myofibrillar proteins in 3 different horse muscles. Warner-Bratzler shear force decreased during aging in all muscles, showing the lowest values in longissimus lumborum (LL) in all sampling points. Myofibril fragmentation index significantly increased in LL and semimembranosus (SM) muscles throughout aging time whereas in semitendinosus (ST) it increased after 14 days of aging. Proteomics analysis revealed the major content of intact myofibrillar proteins with high molecular weight in ST muscle in the first phase of aging, while, after 14 days a higher accumulation of TnT-derived polypeptides and spots isoforms ascribed to MLC2 and MLC1 proteins were found. Data highlight that aging affects the meat tenderness and proteolysis with different intensities in each muscle and suggest that a more extensive post-mortem proteolysis occurred in ST muscle.

A proteomic-based approach for the search of biomarkers in Iberian wild deer (Cervus elaphus) as indicators of meat quality

The positive perception of deer meat among consumers is growing. Consequently, further efforts are needed to control its meat quality. Specifically, the aim of this study was to search protein biomarkers in connection with tenderness and intramuscular fat (IMF) content of Iberian wild red deer (Cervus elaphus) meat. Twelve venison samples classified as tender, intermediate and tough meat, as well as with different IMF were studied, using quantitative proteomic by SWATH-MS combined with bioinformatic analyses. The study of muscle proteome showed significant differences among these three groups of meat samples, since five differentially abundant proteins (IVD, LAMB1, MYL3, SDHC and SDHA) and six (FABP4, IVD, LAMB1, MYL3, CRYZ and SERPINB6) were strongly correlated with tenderness and IMF, respectively. The proteomic approach provides protein biomarkers linked to venison meat quality and marked changes in proteins related to oxidoreductase complex in skeletal muscle. SIGNIFICANCE: Meat tenderness and IMF are major concerns in game meat. The proteomic approach demonstrated a strong correlation between proteins and these quality traits, despite the complexity of samples (wild animals hunted at different ages). Our results suggest that several proteins can be biomarkers and provide a molecular insight.

Association of calpain and calpastatin activity to postmortem myofibrillar protein degradation and sarcoplasmic proteome changes in bovine Longissiumus lumborum and Triceps brachii

The aim of this study was to determine the extent to which calpastatin (CASN) variants (based on two chromatographic peaks; CASN-P1 and CASN-P2) explain variation in μ-calpain autolysis, protein degradation, and changes in the sarcoplasmic proteome observed during postmortem aging of beef. The Longissimus lumborum (LL) and Triceps brachii (TB) muscles were obtained from six crossbred steers and samples prepared from day 0, 1 and 7 postmortem (pm). The decline of CASN activity during aging was due to decrease of CASN-P2 in both muscles. The CASN-P2:μ-calpain ratio at day 0 was greater for TB, which presented lesser calpain autolysis, myofibrillar protein degradation, and fewer sarcoplasmic proteome changes during aging. Changes in abundance of Heat shock protein 70 family in the sarcoplasmic fraction were positively associated to proteolysis during aging, with greater differences in LL.

Beef tenderness and intramuscular fat proteomic biomarkers: Effect of gender and rearing practices

This study analyzed the effect of gender on the abundances of 20 protein biomarkers of tenderness and/or intramuscular fat content in five muscles: Longissimus thoracis, previously identified as biomarkers of tenderness and/or intramuscular Semimembranosus, Rectus abdominis, Triceps brachii and Semitendinosus, from cows and steers of the Protected Designation Origin Maine Anjou. The protein abundances were quantified using Reverse Phase Protein Array with specific validated antibodies. Among the 20 studied proteins, the abundance of 8 biomarkers involved in energetic metabolism, contraction and cellular stress, was different according to gender. The gender effect was different depending on the muscle type with greater abundances in Semitendinosus, Rectus abdominis and Longissimus thoracis muscles. On the basis of animal characteristics and rearing factors, three rearing practices classes were identified for cows. Among the factors, fattening duration modified the abundance of 12 proteins mainly in Triceps brachii muscle. A positive correlation between the abundance of the small HSP20 and slaughter age was observed in the 5 muscles. Two proteins, Four and a half LIM domains 1 (FHL1) and Glycogen phosphorylase (PYGB) appeared to be muscle, gender and rearing practices independent. These results constitute valuable data to understand how to manage beef quality by controlling these different factors. SIGNIFICANCE: This study is the first to compare the relative abundance of 20 proteins previously identified as biomarkers of tenderness and/or intramuscular fat (IMF) content of beef meat between cows and steers among 5 different muscles. Its originality is in the use of Reverse Phase Protein Array for fast quantification of the proteins and the integration of data from rearing factors, carcass characteristics and biomarkers of meat qualities. The findings provide evidence for modulating biomarker levels by controlling the choice of animal type and rearing factors according to the type of muscle that would produce animals with the desired meat qualities.

Comparing SRM and SWATH Methods for Quantitation of Bovine Muscle Proteomes

Mass spectrometry (MS) has become essential for efficient and accurate quantification of proteins and proteomes and, thus, a key technology throughout all biosciences. However, validated MS methods are still scarce for meat quality research applications. The objective of this work was to develop and compare two targeted proteomic methods, namely, selected reaction monitoring (SRM) and sequential window acquisition of all theoretical spectra (SWATH), for the quantification of 11 bovine muscle proteins that may be indicators of meat color. Both methods require evaluation of spectra from proteotypic and quantotypic peptides, and we here report our evaluation of which peptides and MS parameters are best suited for robust quantification of these 11 proteins. We observed that the SRM approach provides better reproducibility, linearity, and sensitivity than SWATH and is therefore ideal for targeted quantification of low-abundance proteins, while the SWATH approach provides a more time-efficient method for targeted protein quantification of high-abundance proteins and, additionally, supports the search for novel biomarkers.

Assessment of muscle Longissimus thoracis et lumborum marbling by image analysis and relationships between meat quality parameters

The intramuscular fat (IMF), recognized by the consumer as marbling, is an important meat quality trait. The objective of this study was to validate a new method of beef marbling evaluation by image analysis. The new assessment was compared with two known marbling measurements: chemical IMF and USDA scores. Moreover, the relationship between marbling measurements and other meat quality parameters was investigated. Samples of Longissimus thoracis et lumborum (LTL) muscle were obtained from carcasses of 39 Italian crossbred heifers and 62 Angus bred heifers, that underwent two different dietary treatments. The use of various breeds and diets was chosen to obtain different intramuscular fat levels, in order to validate the use of Image J software for the analysis of different type of beef meat. The images of fresh cuts were appraised by experienced beef graders, and the samples were used to determine fat content by chemical Soxhlet extraction. Carcasses measurements according to the EUROP system, and other physical meat proprieties were also assessed. The results demonstrated that the marbling measurements obtained by computer image analysis, such as the number of marbling particles, the average particle size (mm), and the percentage of marbling particles (%), significantly (P < 0.05) correlated with USDA scores and IMF content. Moreover, the principal component analysis (PCA) showed three principal meat components, identified as 1) color, 2) fat, and 3) water release. The second principal component (PC) explained 24.94% of variance, and was positively correlated with image analysis measures, USDA score, and IMF, while negatively correlated with the Warner–Bratzler shear force (WBSF).