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

Exploring variances in meat quality between Qingyuan partridge chicken and Cobb broiler: Insights from combined multi-omics analysis

Previously, animal breeding prioritized enhancing key economic traits to improve production efficiency, leading to a gradual difference in meat quality. However, the genetic factors influencing meat quality remain unclear. To identify key genetic pathways contributing to meat quality, native Chinese yellow-feathered chicken (Qingyuan Partridge Chicken, QPC; female, n=10), and commercial chicken broiler (Cobb broiler, CB; female, n=10) were used for meat quality assessment through metabolomics, proteomics, and phosphoproteomics sequencing. The results show that QPC had lower pH (93.12%), shear force (81.46%), cooking loss (69.29%), moisture content (93.24%) and muscle fiber area (46.04%), but higher meat color values (a*(163.65%) and b*(250.27%)), drip loss (146.32%), and intramuscular fat content (382.01%) than CB (p < 0.05). Metabolomic, proteomic, and phosphoproteomic analyses were jointly conducted, revealing significant differences in energy metabolism strategies. Higher glycolytic enzyme activity was observed in QPC (ENO1, GAPDH, GPI, PFKM, PKM, and TPI1, p < 0.05), while more energetic phosphate compounds were stored in CB. CB had higher Na+/K+ Pump protein abundance (SCN4A, LOC107051305, ATP1B4, ATP12A, ATP1A1, and ATP1A2, p < 0.05) and phosphorylation (ATP1A2-Ser662, p < 0.05) and Ca2+ channel protein abundance (ATP2B4, SRL, CACNB1, CACNA1S, CACNA2D1, CAMK2G, LOC107050717 and TNNC2, p < 0.05) than QPC. In QPC, CAMKII autophosphorylation activated downstream protein and increased Ca2+. These results suggest CB is more contractile than QPC, contributing to meat quality between CB and QPC.

Flavor characterization of pork cuts in Chalu black pigs using multi-omics analysis

The study investigated the flavor variations in four different fresh pork cuts (longissimus thoracis, LT; trapezius muscle, TM; hamstring muscle, HM; Pork Belly, PB) from Chalu black pigs (ten castrated boars) using multi-omics techniques. The research also explored the influence of muscle fiber type on the flavor profiles of these cuts. Results from quantitative real-time PCR (qRT-PCR) indicated significant differences in muscle fiber type across the four pork cuts in various anatomical locations. Each cut exhibited distinctive volatile organic compounds (VOCs) profiles, with HM displaying a sweet and fruity green flavor, LT showcasing a fatty and nutty taste, PB presenting a fresh, citrusy, and green flavor, and TM offering a floral and bitter note. Variations in fatty acid carbon number and saturation were observed among the cuts, with HM, LT, and PB being rich in fatty acids with C16-18, C19-21, and 3 double bonds, respectively. The metabolites specific to each cut were found to play key roles in different metabolic pathways, such as protein-related pathways for HM, arginine biosynthesis for LT, lysine biosynthesis for PB, and D-arginine and D-ornithine metabolism for TM. Differentially expressed genes (DEGs) were associated with amino acid metabolism for HM, glycolysis/gluconeogenesis for LT, and cellular aromatic compound organization for PB. Notably, HM and PB displayed unique flavor characteristics, while TM exhibited relatively neutral features. The study also identified correlations among VOCs, muscle fiber type, lipids, metabolites, and gene patterns specific to each cut, highlighting the complex interplay of factors influencing pork flavor.

In-depth exploration of the high and normal pH beef proteome: First insights emphasizing the dynamic protein changes in Longissimus thoracis muscle from pasture-finished Nellore bulls over different postmortem times

This study aimed to evaluate for the first time the temporal dynamic changes in early postmortem proteome of normal and high ultimate pH (pHu) beef samples from the same cattle using a shotgun proteomics approach. Ten selected carcasses classified as normal (pHu < 5.8; n = 5) or high (pHu ≥ 6.2; n = 5) pHu beef from pasture-finished Nellore (Bos taurus indicus) bulls were sampled from Longissimus thoracis muscle at 30 min, 9 h and 44 h postmortem for proteome comparison. The temporal proteomics profiling quantified 863 proteins, from which 251 were differentially abundant (DAPs) between high and normal pHu at 30 min (n = 33), 9 h (n = 181) and 44 h (n = 37). Among the myriad interconnected pathways regulating pH decline during postmortem metabolism, this study revealed the pivotal role of energy metabolism, cellular response to stress, oxidoreductase activity and muscle system process pathways throughout the early postmortem. Twenty-three proteins overlap among postmortem times and may be suggested as candidate biomarkers to the dark-cutting condition development. The study further evidenced for the first time the central role of ribosomal proteins and histones in the first minutes after animal bleeding. Moreover, this study revealed the disparity in the mechanisms underpinning the development of dark-cutting beef condition among postmortem times, emphasizing multiple dynamic changes in the muscle proteome. Therefore, this study revealed important insights regarding the temporal dynamic changes that occur in early postmortem of high and normal muscle pHu beef, proposing specific pathways to determine the biological mechanisms behind dark-cutting determination.

microRNA Temporal-Specific Expression Profiles Reveal longissimus dorsi Muscle Development in Tianzhu White Yak

As a class of regulatory factors, microRNAs (miRNAs) play an important role in regulating normal muscle development and fat deposition. Muscle and adipose tissues, as major components of the animal organism, are also economically important traits in livestock production. However, the effect of miRNA expression profiles on the development of muscle and adipose tissues in yak is currently unknown. In this study, we performed RNA sequencing (RNA-Seq) on Tianzhu white yak longissimus dorsi muscle tissue obtained from calves (6 months of age, M6, n = 6) and young (30 months of age, M30, n = 6) and adult yak (54 months of age, M54, n = 6) to identify which miRNAs are differentially expressed and to investigate their temporal expression profiles, establishing a regulatory network of miRNAs associated with the development of muscle and adipose. The results showed that 1191 miRNAs and 22061 mRNAs were screened across the three stages, of which the numbers of differentially expressed miRNAs (DE miRNAs) and differentially expressed mRNAs (DE mRNAs) were 225 and 450, respectively. The expression levels of the nine DE miRNAs were confirmed using a reverse transcription quantitative PCR (RT-qPCR) assay, and the trend of the assay results was generally consistent with the trend of the transcriptome profiles. Based on the expression trend, DE miRNAs were categorized into eight different expression patterns. Regarding the expression of DE miRNAs in sub-trends Profile 1 and Profile 2 (p < 0.05), the gene expression patterns were upregulated (87 DE miRNAs). Gene ontology (GO) and Kyoto Encyclopedia of Genes Genomes (KEGG) analyses showed that the identified DE miRNAs and DE mRNAs were enriched in pathway entries associated with muscle and intramuscular fat (IMF) growth and development. On this basis, we constructed a DE miRNA-mRNA interaction network. We found that some DE mRNAs of interest overlapped with miRNA target genes, such as ACSL3, FOXO3, FBXO30, FGFBP4, TSKU, MYH10 (muscle development), ACOX1, FADS2, EIF4E2, SCD1, EL0VL5, and ACACB (intramuscular fat deposition). These results provide a valuable resource for further studies on the molecular mechanisms of muscle tissue development in yak and also lay a foundation for investigating the interactions between genes and miRNAs.

The effect of the production system on the proteomics profiles of the Longissimus thoracis muscle in Arouquesa cattle

Arouquesa cattle breed is an autochthonous Portuguese breed produced under a traditional mountain system that need improvement without affecting beef quality. The aim of this work is to compare the proteomics profiles of the Longissimus thoracis muscle from Arouquesa animals produced under different production systems. Sixty weaners were produced under the following systems: traditional (TF) and traditional with starter feed supplementation (TF + S1) with weaning and slaughtering at 9 months, the S1 + S2 (weaning at 5 months and grower supplement until slaughter) and two rearing periods with finishing supplementation (TF + S3 and S3). Upon slaughter, samples of L. thoracis were taken and analyzed using a shotgun proteomics workflow. Several putative markers of beef quality for the Arouquesa breed were identified: VIM, FSCN1, SERPINH1, ALDH1A1, NDUFB5, ANXA1, PDK4, CEMIP2, NDUFB9, PDLIM1, OXCT1, MYH4. These proteins are involved in actin binding, skeletal muscle development and in the mitochondrial respiratory chain and they can influence mostly meat tenderness and color. We identified specific proteins for each group related to different metabolisms involved in several aspects that affect meat quality parameters. Our results demonstrate the link between production practices and putative meat characteristics, which have the potential to improve the traceability of certified products. SIGNIFICANCE: Arouquesa breed is produced in a sustainable system using natural resources and contributing to the economy of low-populated rural regions in Northern Portugal. Besides their economic relevance, producing autochthonous breeds can counter rural depopulation and maintain local heritage. Additionally, consumer awareness about product quality is increasing and PDO products contribute to satisfying this demand. However, it is necessary to increase production so that it is possible to sell these products outside the production region. To ensure robust traceability and that PDO label characteristics are maintained despite increasing production yield, product analysis is of paramount importance. For this reason, proteomic approaches can provide insight into how production changes will affect beef quality and generate putative biomarkers of certified production systems.

Transcriptomic analysis of different intramuscular fat contents on the flavor of the longissimus dorsi tissues from Guangling donkey

BACKGROUND

In this study, researchers aimed to explore the impact of intramuscular fat (IMF) concentration on the flavor of donkey meat, specifically in the longissimus dorsi muscle of Guangling donkeys. The internal volatile organic compounds that cause the flavor differences between donkey muscles are not clear at present. Transcriptomic technologies were utilized to analyze gene expression and its relationship to donkey meat flavor.

METHOD

Thirty Guangling donkeys had their IMF content evaluated in the longissimus dorsi muscle. Based on IMF content, 16 donkeys of similar ages were divided into two groups: low-fat (L) and high-fat (H). Headspace solid-phase microextraction Gas chromatography-mass spectrometry (HS-SPME-GC-MS) and headspace solid phase microextraction mass spectrometry were used to identify potential flavor components that differed between the two groups.

RESULTS

Five key volatile substances were identified, and WGCNA and KEGG analysis was conducted to analyze the genes associated with these substances. The results showed that pathways like PPAR signaling, nucleotide excision repair, glucagon signaling, arachidonic acid metabolism, and glycolysis/glycogenesis were involved in lipid deposition. Additionally, a gene-gene interaction network map was constructed, highlighting the importance of hub genes such as EEF2, DDX49, GAP43, SNAP25, NDUFS8, MRPS11, RNASEH2A, POLR2E, POLR2C and ALB in regulating key flavor substances.

CONCLUSION

This study provided valuable insights into the regulation of genes and protein expression related to flavor substances in donkey meat. It also deepened understanding of the influence of IMF on flavor and laid a foundation for future molecular breeding improvements in Guangling donkeys.

Leveraging Functional Genomics for Understanding Beef Quality Complexities and Breeding Beef Cattle for Improved Meat Quality

Consumer perception of beef is heavily influenced by overall meat quality, a critical factor in the cattle industry. Genomics has the potential to improve important beef quality traits and identify genetic markers and causal variants associated with these traits through genomic selection (GS) and genome-wide association studies (GWAS) approaches. Transcriptomics, proteomics, and metabolomics provide insights into underlying genetic mechanisms by identifying differentially expressed genes, proteins, and metabolic pathways linked to quality traits, complementing GWAS data. Leveraging these functional genomics techniques can optimize beef cattle breeding for enhanced quality traits to meet high-quality beef demand. This paper provides a comprehensive overview of the current state of applications of omics technologies in uncovering functional variants underlying beef quality complexities. By highlighting the latest findings from GWAS, GS, transcriptomics, proteomics, and metabolomics studies, this work seeks to serve as a valuable resource for fostering a deeper understanding of the complex relationships between genetics, gene expression, protein dynamics, and metabolic pathways in shaping beef quality.

Lipidomics analysis reveals new insights into crisp grass carp associated with meat texture

Feeding faba beans to grass carp could crisp its muscle texture to avoid softening, the relationship between texture formation throughout the crisping process and the critical lipids regulating the fish quality has not yet been clarified. Herein, an 60-day nutritional trial and untargeted lipidomic analysis was used to study the changes of lipids in crisp grass carp dorsal muscle. A total of 1036 lipids were remarkably different between ordinary and crisp grass carp. The concentrations of the LPC, LPE, PG, Cer, Hex2Cer, SM, MG and MGMG were positively correlated with hardness and springiness, and the CL, TG, PMe, WE, dMePE and AcCa were negative correlation. High content of lipids involved in storage in ordinary grass carp, such as glycerophospholipids, polyunsaturated and saturated fatty acid content. In contrast, high content of membrane components in crisp grass carp, such as monounsaturated fatty acid, sphingolipid and glycerolipids content, and the distribution of PUFA in lipid molecules was related to lipid biosynthesis. This study might provide some insights into improved knowledge of the association between meat texture and lipid molecules in fish fed with faba bean.

Effect of bovine myosin heavy chain 3 on proliferation and differentiation of myoblast

The myosin heavy chain 3 (MYH3) gene is an essential gene that affects muscle development. This study aimed to discuss the expression characteristics of the MYH3 gene and its effect on the proliferation and differentiation of bovine myoblasts. Quantitative real time-PCR results display that the expression level of MYH3 was higher in muscle tissue, and the expression increased in the early stage of myoblast differentiation. Interfering with the MYH3 gene in myoblasts resulted in fewer EDU-positive cells and decreased expression of proliferation marker genes. Interference with MYH3 can also affect the differentiation process of myoblasts. Regarding phenotype, myotube differentiation in the interference group was slowed or even stopped. Interference with the expression of MYH3 could significantly reduce the expression of myogenic differentiation marker genes. The above results show that MYH3 is mainly expressed in muscle tissue and is highly expressed in the early stage of differentiation of bovine myoblasts, and interfering with the MYH3 can promote the proliferation and inhibit the differentiation of bovine myoblasts. This study provides a theoretical basis for revealing the regulatory process of bovine myoblast proliferation and differentiation and bovine molecular breeding.

Impact of sampling location and aging on the Longissimus thoracis et lumborum muscle proteome of dry-aged beef

This study aimed to explore the differences in the proteome and molecular pathways between two sampling locations (external, internal) of bovine Longissimus thoracis et lumborum (LTL) muscles at 0, 21, and 28 days of dry-aging (i.e. 3, 24, and 31 days post-mortem). It further assessed the impact of post-mortem aging on the meat proteome changes and the biological processes at interplay. Proteins related to defence response to bacterium and regulation of viral entry into host cell were identified to be more abundant on the external location before dry-aging, which may be associated to the oxidative conditions and microbial activity to which post-mortem muscle is exposed during dressing, chilling, and/or quartering of the carcasses. This highlights the relevance of sampling from interior tissues when searching for meat quality biomarkers. As dry-aging progressed, the meat proteome and related biological processes changed differently between sampling locations; proteins related to cell-cell adhesion and ATP metabolic processes pathways were revealed in the external location at 21 and 28 days, respectively. On the other hand, the impact of aging on the proteome of the interior meat samples, evidenced that muscle contraction and structure together with energy metabolism were the major pathways driving dry-aging. Additionally, aging impacted other pathways in the interior tissues, such as regulation of calcium import, neutrophil activation, and regeneration. Overall, the differences in the proteome allowed discriminating the three dry-aging times, regardless of the sampling location. Several proteins were proposed for validation as robust biomarkers to monitor the aging process (tenderization) of dry-aged beef: TTN, GRM4, EEF1A1, LDB3, CILP2, TNNT3, GAPDH, SERPINI1, and OMD.

Variation in Acetyl-CoA Carboxylase Beta Gene and Its Effect on Carcass and Meat Traits in Gannan Yaks

Acetyl-CoA carboxylase beta (ACACB) is a functional candidate gene that impacts fat deposition. In the present study, we sequenced exon 37-intron 37, exon 46-intron 46, and intron 47 of yak ACACB using hybrid pool sequencing to search for variants and genotyped the gene in 593 Gannan yaks via Kompetitive allele-specific polymerase chain (KASP) reaction to determine the effect of ACACB variants on carcass and meat quality traits. Seven single nucleotide polymorphisms were detected in three regions. Eight effective haplotypes and ten diplotypes were constructed. Among them, a missense variation g.50421 A > G was identified in exon 37 of ACACB, resulting in an amino acid shift from serine to glycine. Correlation analysis revealed that this variation was associated with the cooking loss rate and yak carcass weight (p = 0.024 and 0.012, respectively). The presence of haplotypes H5 and H6 decreased Warner-Bratzler shear force (p = 0.049 and 0.006, respectively), whereas that of haplotypes H3 and H4 increased cooking loss rate and eye muscle area (p = 0.004 and 0.034, respectively). Moreover, the presence of haplotype H8 decreased the drip loss rate (p = 0.019). The presence of one and two copies of haplotypes H1 and H8 decreased the drip loss rate (p = 0.028 and 0.004, respectively). However, haplotype H1 did not decrease hot carcass weight (p = 0.011), whereas H3 increased the cooking loss rate (p = 0.007). The presence of one and two copies of haplotype H6 decreased Warner-Bratzler shear force (p = 0.014). The findings of the present study suggest that genetic variations in ACACB can be a preferable biomarker for improving yak meat quality.

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.

Effect of postmortem pH on the physical, biochemical, and sensory characteristics of bovine longissimus thoracis et lumborum muscle

From a large feeding trial study consisting of 299 bulls and steers, 15 carcasses exhibited stress-related syndromes manifested by atypical color and pH which were then selected for subsequent analysis. Samples of longissimus thoracis et lumborum muscle with postmortem pH in the range of 5.5-6.9 were subjected to a 14-day aging period at 2°C. Sensory panel tenderness, connective tissue, juiciness, and flavor intensity of high pH (6.4-6.9) meat were significantly different (p < .05) from samples of intermediate pH (6.0-6.1) as well as normal pH (5.5). Muscles at pH 6.0-6.1 were the toughest samples. This was confirmed by Warner-Bratzler shear force (WBSF), residual force, and myofibril fragmentation index. Palatability attributes of normal pH (5.5) samples were significantly different (p < .05) from dark-cutting beef in terms of tenderness and flavor and at the high pH extreme. The increase in WBSF at pH 6.0-6.1, lack of extensive degradation of muscle proteins, and the decreased sarcomere length resulted in tougher meat than low or high pH muscles. Sodium dodecyl-sulfate polyacrylamide gel electrophoresis of meat at the high pH extreme (6.7-6.9) revealed that the breakdown of troponin-T to 30 kD was complete while at intermediate pH (6.0-6.1) was incomplete. In addition, the appearance of a 'doublet' on high-molecular-weight resolution gels may also account for the greater tenderness experienced by sensory panelists.

"The Yak"-A remarkable animal living in a harsh environment: An overview of its feeding, growth, production performance, and contribution to food security

Yaks play an important role in the livelihood of the people of the Qinghai-Tibet Plateau (QTP) and contribute significantly to the economy of the different countries in the region. Yaks are commonly raised at high altitudes of ~ 3,000-5,400 m above sea level. They provide many important products, namely, milk, meat, fur, and manure, as well as social status, etc. Yaks were domesticated from wild yaks and are present in the remote mountains of the QTP region. In the summer season, when a higher quantity of pasture is available in the mountain region, yaks use their long tongues to graze the pasture and spend ~ 30-80% of their daytime grazing. The remaining time is spent walking, resting, and doing other activities. In the winter season, due to heavy snowfall in the mountains, pasture is scarce, and yaks face feeding issues due to pasture scarcity. Hence, the normal body weight of yaks is affected and growth retardation occurs, which consequently affects their production performance. In this review article, we have discussed the domestication of yaks, the feeding pattern of yaks, the difference between the normal and growth-retarded yaks, and also their microbial community and their influences. In addition, blood biochemistry, the compositions of the yaks' milk and meat, and reproduction are reported herein. Evidence suggested that yaks play an important role in the daily life of the people living on the QTP, who consume milk, meat, fur, use manure for fuel and land fertilizer purposes, and use the animals for transportation. Yaks' close association with the people's well-being and livelihood has been significant.

Effect of Lipids in Yak Muscle under Different Feeding Systems on Meat Quality Based on Untargeted Lipidomics

Simple Summary

With the development of living standards, consumers are paying more and more attention to meat quality and flavor. When consumers choose meat, they directly pay attention to meat quality and flavor, so the meat quality and flavor directly decide meat price and sales volume. Better meat quality and flavor are the crucial factors that increase the additional value of meat. Because of its special nutritional value and taste, yak meat is popular with consumers. The intramuscular lipids can greatly affect the meat quality and flavor, but there is no report on the effect of lipids in yak muscle on the meat quality and flavor. In this study, we studied the characterization of lipids in yak muscle under different feeding systems and further explored the key lipids affecting yak meat quality and flavor. This study can provide new insight into the improvement of yak meat quality and flavor.

Abstract

The effect of lipids on yak meat quality and volatile flavor compounds in yak meat under graze feeding (GF) and stall feeding (SF) was explored using untargeted lipidomics based on liquid chromatography–mass spectrometry (LC-MS) in this study. First, the volatile flavor compounds in longissimus dorsi (LD) of SF and GF yaks were detected by gas chromatography–mass spectrometry (GC-MS). In total 49 and 39 volatile flavor substances were detected in the LD of GF and SF yaks, respectively. The contents of pelargonic aldehyde, 3-hydroxy-2-butanone and 1-octen-3-ol in the LD of both GF and SF yaks were the highest among all detected volatile flavor compounds, and the leading volatile flavor substances in yak LD were aldehydes, alcohols and ketones. In total, 596 lipids were simultaneously identified in the LD of SF and GF yaks, and the leading lipids in the LD of both GF and SF yaks were sphingolipids (SPs), glycerolipids (GLs) and glycerophospholipids (GPs). Seventy-five significantly different lipids (SDLs) between GF and SF yaks were identified in the LD. The high content of TG(16:1/18:1/18:1), TG(16:0/17:1/18:1) and TG(16:0/16:1/18:1), PE(18:0/22:4) and PC(18:2/18:0) can improve the a* (redness) and tenderness of yak muscle. The changes in volatile flavor compounds in yak muscle were mainly caused by TG(18:1/18:1/18:2), TG(18:0/18:1/18:1), TG(16:0/17:1/18:1), TG(16:0/16:1/18:1), PC(18:2/18:0), TG(16:1/18:1/18:1), PI(18:0/20:4), TG(16:1/16:1-/18:1) and TG(17:0/18:1/18:1). The above results provide a theoretical basis for improving yak meat quality from the perspective of intramuscular lipids.

Meat Quality and Muscle Tissue Proteome of Crossbred Bulls Finished under Feedlot Using Wet Distiller Grains By-Product

Wet distiller grains (WDG) are a corn by-product rich in protein and fiber that can be used in feedlot diets. This study evaluated F1 Angus-Nellore bulls fed on a control diet vs. WDG (n = 25/treatment). After a period of 129 days on these feeds, the animals were slaughtered and Longissimus thoracis samples were collected for both a meat quality evaluation and gel-based proteomic analyses. A greater ribeye area (99.47 cm²) and higher carcass weight (333.6 kg) (p < 0.05) were observed in the WDG-finished cattle compared to the control (80.7 cm²; 306.3 kg). Furthermore, there were differences (p < 0.05) in the intramuscular fat between the WDG and control animals (IMF = 2.77 vs. 4.19%), which led to a significant decrease (p < 0.05) in saturated fatty acids (FA). However, no differences (p > 0.10) were observed in terms of tenderness, evaluated using Warner–Bratzler shear force (WBSF). The proteomic and bioinformatic analyses revealed substantial changes in the biological processes, molecular functions, and cellular components of the WDG-finished cattle compared to the control. Proteins related to a myriad of interconnected pathways, such as contractile and structural pathways, energy metabolism, oxidative stress and cell redox homeostasis, and transport and signaling. In this experiment, the use of WDG supplementation influenced the protein expression of several proteins, some of which are known biomarkers of beef quality (tenderness and color), as well as the protein–protein interactions that can act as the origins of increases in muscle growth and reductions in IMF deposition. However, despite the effects on the proteome, the tenderness, evaluated by WBSF, and fatty acid profile were not compromised by WDG supplementation.

Metabolic, proteomic and microbial changes postmortem and during beef aging

The purpose of this review is to provide an overview of the current knowledge about proteomic and metabolic changes in beef, the microbiological alteration postmortem and during aging, and observe the influence on beef quality parameters, such as tenderness, taste and flavor. This review will also focus on the different aging types (wet- and dry-aging), the aging or postmortem time of beef and their effect on the proteome and metabolome of beef. The Ca2+ homeostasis and adenosine 5'-triphosphate breakdown are the main reactions in the pre-rigor phase. After rigor mortis, the enzymatic degradation of connective tissues and breakdown of energy metabolism dominate molecular changes in beef. Important metabolic processes leading to the formation of saccharides, nucleotides, organic acids (e.g. lactic acid), creatine and fatty acids are considered in this context as possible flavor precursors or formers of beef flavor and taste. Flavor precursors are substrates for lipid oxidation, Strecker degradation and Maillard reaction during cooking or roasting. The findings presented should serve as a basis for a better understanding of beef aging and its molecular effects and are intended to contribute to meeting the challenges of improving beef quality.

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.

Integrative Analysis of Nanopore and Illumina Sequencing Reveals Alternative Splicing Complexity in Pig Longissimus Dorsi Muscle

Alternative splicing (AS) is a key step in the post-transcriptional regulation of gene expression that can affect intramuscular fat (IMF). In this study, longissimus dorsi muscles from 30 pigs in high- and low- IMF groups were used to perform Oxford Nanopore Technologies (ONT) full-length sequencing and Illumina strand-specific RNA-seq. A total of 43,688 full-length transcripts were identified, with 4,322 novel genes and 30,795 novel transcripts. Using AStalavista, a total of 14,728 AS events were detected in the longissimus dorsi muscle. About 17.79% of the genes produced splicing isoforms, in which exon skipping was the most frequent AS event. By analyzing the expression differences of mRNAs and splicing isoforms, we found that differentially expressed mRNAs with splicing isoforms could participate in skeletal muscle development and fatty acid metabolism, which might determine muscle-related traits. SERBP1, MYL1, TNNT3, and TNNT1 were identified with multiple splicing isoforms, with significant differences in expression. AS events occurring in IFI6 and GADD45G may cause significant differences in gene expression. Other AS events, such as ONT.15153.3, may regulate the function of ART1 by regulating the expression of different transcripts. Moreover, co-expression and protein-protein interaction (PPI) analysis indicated that several genes (MRPL27, AAR2, PYGM, PSMD4, SCNM1, and HNRNPDL) may be related to intramuscular fat. The splicing isoforms investigated in our research provide a reference for the study of alternative splicing regulation of intramuscular fat deposition.

Integrated analysis of expression profiles with meat quality traits in cattle

MicroRNAs (miRNAs) play a vital role in improving meat quality by binding to messenger RNAs (mRNAs). We performed an integrated analysis of miRNA and mRNA expression profiling between bulls and steers based on the differences in meat quality traits. Fat and fatty acids are the major phenotypic indices of meat quality traits to estimate between-group variance. In the present study, 90 differentially expressed mRNAs (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Eighty-three potential DEG targets and 18 DEMs were used to structure a negative interaction network, and 75 matching target genes were shown in this network. Twenty-six target genes were designated as intersection genes, screened from 18 DEMs, and overlapped with the DEGs. Seventeen of these genes enriched to 19 terms involved in lipid metabolism. Subsequently, 13 DEGs and nine DEMs were validated using quantitative real-time PCR, and seven critical genes were selected to explore the influence of fat and fatty acids through hub genes and predict functional association. A dual-luciferase reporter and Western blot assays confirmed a predicted miRNA target (bta-miR-409a and PLIN5). These findings provide substantial evidence for molecular genetic controls and interaction among genes in cattle.

Kohonen Artificial Neural Network and Multivariate Analysis in the Identification of Proteome Changes during Early and Long Aging of Bovine Longissimus dorsi Muscle Using SWATH Mass Spectrometry

To study proteomic changes involved in tenderization of Longissimus dorsi, Charolais heifers and bulls muscles were sampled after early and long aging (12 or 26 days). Sensory evaluation and instrumental tenderness measurement were performed. Proteins were analyzed by gel-free proteomics. By pattern recognition (principal component analysis and Kohonen's self-organizing maps) and classification (partial least squares-discriminant analysis) tools, 58 and 86 dysregulated proteins were detected after 12 and 26 days of aging, respectively. Tenderness was positively correlated mainly with metabolic enzymes (PYGM, PGAM2, TPI1, PGK1, and PFKM) and negatively with keratins. Downregulation in hemoglobin subunits and carbonic anhydrase 3 levels was relevant after 12 days of aging, while mimecan and collagen chains levels were reduced after 26 days of aging. Bioinformatics indicated that aging involves a prevalence of metabolic pathways after late and long periods. These findings provide a deeper understanding of changes involved in aging of beef and indicate a powerful method for future proteomics studies.

Fat Deposition in the Muscle of Female and Male Yak and the Correlation of Yak Meat Quality with Fat

This study aimed to explore the differences in fat deposition between female (FYs) and male yaks (MYs). Compared with MYs, the tenderness, L*, marbling, absolute content of fat, and most fatty acids (FAs) of longissimus dorsi (LD) in FYs were higher or better (p < 0.05), whereas the relative content of polyunsaturated fatty acids (PUFAs) and n-3 PUFAs were lower (p < 0.01). The absolute content of fat, C18:0, cis-C18:2, cis-C18:1, and C24:0 were positively correlated with L*_{45 min}, b*_{24 h}, tenderness, and marbling score of LD in FYs and MYs (p < 0.05), respectively. LPL, FATP2, ELOVL6, HADH, HACD, and PLINS genes play a crucial role in improving the marbling score and tenderness of yak meat. The results of gene expression and protein synthesis showed the effect of gender to FA biosynthesis, FA transport, lipolysis, and FA oxidation in the adipose tissue of yak was realized by the expressions of ME1, SCD, ACSL5, LPL, FABP1, PLIN4, and PLIN2 in peroxisome proliferators-activated receptor (PPAR) signaling. This study established a theoretical basis for the improvement of the meat quality of yak and molecular breeding.

Dark-cutting beef: A brief review and an integromics meta-analysis at the proteome level to decipher the underlying pathways

Comprehensive characterization of the post-mortem muscle proteome defines a fundamental goal in meat proteomics. During the last decade, proteomics tools have been applied in the field of foodomics to help decipher factors underpinning meat quality variations and to enlighten us, through data-driven methods, on the underlying mechanisms leading to meat quality defects such as dark-cutting meat known also as dark, firm and dry (DFD) meat. In cattle, several proteomics studies have focused on the extent to which changes in the post-mortem muscle proteome relate to dark-cutting beef development. The present data-mining study firstly reviews proteomics studies which investigated dark-cutting beef, and secondly, gathers the protein biomarkers that differ between dark-cutting versus beef with normal-pH in a unique repertoire. A list of 130 proteins from eight eligible studies was curated and mined through bioinformatics for Gene Ontology annotations, molecular pathways enrichments, secretome analysis and biological pathways comparisons to normal beef color from a previous meta-analysis. The major biological pathways underpinning dark-cutting beef at the proteome level have been described and deeply discussed in this integromics study.

Relationship Between Meat Quality, Carcass Characteristics, and Protein Abundance of HSPβ1, HSPA, and DJ1 in Beef Longissimus thoracis Pre-Rigor or After 14 Days’ Aging

This study evaluated associations of heat shock proteins (HSP) and an oxidative stress protein, protein deglycase (DJ1), with beef quality and tenderness. Samples from the longissimus thoracis (N = 99) were collected pre-rigor (day 0) and after 14-d aging. Warner-Bratzler shear force (WBSF), myofibrillar fragmentation index (MFI), and a trained sensory panel were used to determine meat quality. Protein abundance of DJ1 and 2 HSP—HSPβ1 and HSPA—were assessed. Regression analyses demonstrated that DJ1 abundance after 14 d of aging is a predictor of WBSF (P &lt; 0.001), MFI (P = 0.02), and sensory panel tenderness (P &lt; 0.001). Abundance of HSPβ1 after 14 d of aging is also a predictor of MFI (P = 0.03). Additionally, abundance of both HSPβ1 and DJ1 pre-rigor are predictors of juiciness (P &lt; 0.05). Abundance of HSPβ1 pre-rigor was correlated with WBSF (R = 0.67), sensory panel tenderness (R = −0.44), juiciness (R = −0.30), and umami (R = −0.20). Abundance of DJ1 pre-rigor was also correlated with WBSF (R = 0.72), sensory panel tenderness (R = −0.44), juiciness (R = − 0.24), and umami (R = −0.31). After 14-d aging, HSP β 1 abundance was cor- related with WBSF (R = 0.66), sensory panel tenderness (R = −0.34), juiciness (R = −0.34), umami (R = −0.33), and brown/ roasted (R = −0.30). Abundance of DJ1 after 14-d aging was also correlated with WBSF (R = 0.68), sensory panel tenderness (R = −0.41), juiciness (R = −0.21), and umami (R = −0.28). These results demonstrate that abundance of HSPβ1 and DJ1 both pre-rigor and after 14 d of aging are correlated with meat tenderness and end-product quality as assessed by a trained sensory panel. Regression analyses further reveal that abundance of DJ1 and HSPβ1 after 14 d of aging is causative in development of beef tenderness and juiciness, respectively. Taken together, these results suggest that abundance of DJ1 is a predictor of tenderness, whereas abundance of HSPβ1 is related to meat quality but cannot be used to predict tenderness.

A Proteomic Study for the Discovery of Beef Tenderness Biomarkers and Prediction of Warner-Bratzler Shear Force Measured on Longissimus thoracis Muscles of Young Limousin-Sired Bulls

Beef tenderness is of central importance in determining consumers’ overall liking. To better understand the underlying mechanisms of tenderness and be able to predict it, this study aimed to apply a proteomics approach on the Longissimus thoracis (LT) muscle of young Limousin-sired bulls to identify candidate protein biomarkers. A total of 34 proteins showed differential abundance between the tender and tough groups. These proteins belong to biological pathways related to muscle structure, energy metabolism, heat shock proteins, response to oxidative stress, and apoptosis. Twenty-three putative protein biomarkers or their isoforms had previously been identified as beef tenderness biomarkers, while eleven were novel. Using regression analysis to predict shear force values, MYOZ3 (Myozenin 3), BIN1 (Bridging Integrator-1), and OGN (Mimecan) were the major proteins retained in the regression model, together explaining 79% of the variability. The results of this study confirmed the existing knowledge but also offered new insights enriching the previous biomarkers of tenderness proposed for Longissimus muscle.

Quantitative proteomic analysis of beef tenderness of Piemontese young bulls by SWATH-MS

Quantitative proteomic approach is a suitable way to tackle the beef tenderness. Ten aged-beef samples from Longissimus thoracis of Piemontese breed classified as tender (n = 5) and tough (n = 5) meat were evaluated using SWATH-MS and bioinformatic tools for the identification of the proteins and pathways most influencing tenderness variability. Between the two textural groups, proteomic changes were mainly caused by 43 differentially abundant proteins (DAPs) arranged in reference patterns as displayed by the heat map analysis. Most of these DAPs were associated with energy metabolism. From the functional proteomic analysis, two clusters of proteins, including ACO2, MDH1, MDH2 and CS in one cluster and FBP2, PFKL, LDHA, TPI1 and GAPDH/S in the other cluster, suggest gluconeogenesis, glycolysis and citrate cycle as key pathways for Piemontese breed beef tenderness. These findings contribute to a deeper insight into molecular pathways related to beef tenderness.

Insights on meat quality from combining traditional studies and proteomics

Following a century of major discoveries on the mechanisms determining meat colour and tenderness using traditional scientific methods, further research into complex and interactive factors contributing to variations in meat quality is increasingly being based on data-driven "omics" approaches such as proteomics. Using two recent meta-analyses of proteomics studies on beef colour and tenderness, this review examines how knowledge of the mechanisms and factors underlying variations in these meat qualities can be both confirmed and extended by data-driven approaches. While proteomics seems to overlook some sources of variations in beef toughness, it highlights the role of post-mortem energy metabolism in setting the conditions for development of meat colour and tenderness, and also points to the complex interplay of energy metabolism, calcium regulation and mitochondrial metabolism. In using proteomics as a future tool for explaining variations in meat quality, the need for confirmation by further hypothesis-driven experimental studies of post-hoc explanations of why certain proteins are biomarkers of beef quality in data-driven studies is emphasised.

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.