Molecular insights into quality and authentication of sheep meat from proteomics and metabolomics

Meat quality differences and protein molecular mechanisms affecting meat flavor in different breeds of Tibetan sheep analyzed by 4D label-free quantitative proteomics

To evaluate the meat quality of the new breed of Panou sheep, the longissimus dorsi (LD) muscles of 1.5-year-old Panou sheep and the local breed of Oula sheep were selected for comparative analysis in terms of meat quality, and the molecular mechanisms influencing flavor were investigated using 4D label-free proteomics technology. The results revealed that the fiber density, tenderness, and brightness of the Panou sheep meat were lower than those of the Oula sheep, and the composition of amino acids and flavor substances made it possible to determine that the Panou sheep meat has a high-quality and distinctive flavor. Proteomic analysis indicated that the metabolic pathways that may be associated with meat flavor are amino acid catabolism and sugar metabolism. This study explored the role of proteins in the regulation of meat flavor in Tibetan sheep, which provides a reference for the identification of meat products and subsequent breed improvement.

Effect of different Lys/Met ratios in a low-protein diet on the meat quality of Tibetan sheep: A transcriptomics- and metabolomics-based analysis

This study integrated the the effects of dietary Lys/Met ratio in a low protein diet on the meat quality in Tibetan sheep. A total of 90 weaned Tibetan sheep, 2 months old with initial weight of 15.37 ± 0.92 kg were randomly divided into 3 treatments, which were supplemented with Lys/Met ratio at 3 (LP-H), 2 (LP-M), and 1 (LP-L) in the basal diet (10 % crude protein), respectively. After slaughter (150 days of age), the growth performances and meat quality of longissimus dorsi muscle were evaluated. The LP-L group showed significantly higher final body weight compared to the LP-M group (P < 0.05). Serum albumin and total protein levels were significantly higher in the LP-L group than in the LP-H group (P < 0.05). Furthermore, meat from the LP-L group had significantly higher protein, calcium, and vitamin E content compared to the LP-M group (P < 0.05). Transcriptomic analysis revealed 3,479 differentially expressed genes enriched in pathways related to muscle growth, energy metabolism, and signaling transduction. Metabolomic analysis identified 771 differential metabolites, significantly enriched in ABC transporters, beta-alanine metabolism, and taste transduction pathways. Integrated analysis highlighted the upregulation of the ABCD4 gene and L-valine metabolite in the LP-L group, contributing to improved phenotypic traits. These findings provide molecular insights into the regulatory mechanisms underlying the effects of dietary Lys/Met ratios on Tibetan sheep meat quality and offer a basis for developing nutritional strategies to enhance premium meat production.

Accurate lamb origin identification and molecular differentiation analysis using rapid evaporative ionization mass spectrometry

Rapid and accurate methods for tracing and identifying the origin of lamb are crucial for ensuring food authenticity and quality. This study developed a precise traceability method to determine the origin of lamb by integrating rapid evaporative ionization mass spectrometry (REIMS) with multivariate statistical analysis. Lamb samples from Xilin Gol, Ordos, and Hulun Buir ranches were identified by REIMS fingerprinting within 1 min. The discrimination model based on lipid molecular features achieved the highest recognition accuracy of 99.14% compared to models based on small-molecule metabolites (91.59%), fatty acids (98.52%), and full-spectrum molecules (98.49%). Furthermore, differential analyses were conducted to assess lamb meat from different origins and feeding methods (grazing versus feedlot) using REIMS fingerprints. Lamb products from the Xilin Gol ranch exhibited significantly lower glycerophosphate (PA) content compared to lambs from other regions, while grazing resulted in significantly lower PA content in lamb meat compared to those fed in feedlots. Additionally, meat from grazed lambs had significantly higher unsaturated fatty acid content, providing molecular evidence for its superior nutritional quality and distinct flavor profile compared to the lambs from feedlot systems. REIMS is a promising tool for rapid discrimination of lamb meat from different origins and feeding systems with high accuracy, offering valuable technical support for lamb origin traceability and quality assessment.

4D DIA proteomic analysis of gender and age influences on meat quality and flavor in Hetian white sheep

To investigate the impact of age and gender on mutton flavor and quality, we analyzed mutton from 12-month-old and 6-month-old rams and ewes. The results indicated that 12 months Hetian white sheep exhibited higher levels of amino acids, protein, free fatty acids, and reducing sugars compared to 6-months. Additionally, amino acid, protein, and reducing sugar levels were higher in ewes than 12 months rams. Proteomic analysis revealed that proteins related to fatty acid metabolism, intramuscular fat (IMF), and mitochondrial function were more abundant in ram. The upregulation proteins involved in amino acid metabolism in ewes highlights its richer flavor profile compared to ram. Proteins associated with muscle development and mitochondrial activity were more highly expressed in the 12-month-old samples compared to those from 6-month-old sheep. ECI1, highly expressed in rams, is linked to IMF content. We hypothesize that ECI1 may serve as a potential protein marker for mutton quality.

Impact of Slaughter Weight on Flavor Metabolites in Longissimus Dorsi Muscle of Tianfu Finishing Pigs

In order to investigate the flavor compounds in the muscles of Tianfu finishing (TF) pigs with different slaughter weight (SW), 12 TF pigs were selected for the experiment. The volatile metabolic profiles of meat specimens from the longissimus dorsi (LD) muscle of TF pigs with different SW were studied by untargeted liquid chromatography-mass spectrometry. Our data revealed that the three types of TF pork showed significantly different profiles of hydrocarbons, alcohols, esters, heterocyclic compounds, and others, which could underpin the nuances of their flavors. A total of 118 differentially expressed metabolites (DEMs) were identified (2 upregulated DEMs and 116 downregulated DEMs). Among the volatile flavor compounds, hydrocarbons, alcohols, ester, and heterocyclic compound in the three groups accounted for 26.71%, 13.01%, 13.01%, and 13.70%, respectively, and their contents decreased with increasing SW. The contents of alcohols, aldehydes, and hydrocarbons in the 150-kg group was significantly higher than those in the 125-kg and 100-kg groups (p < 0.05). Taken together, raising SW to 125 kg, or more, decreased the flavor of TF pork and had no benefits to pork quality attributes. Our results provided insights into the molecular basis for sensory variations among different SW of TF pork.

Foodomics as a Tool for Evaluating Food Authenticity and Safety from Field to Table: A Review

The globalization of the food industry chain and the increasing complexity of the food supply chain present significant challenges for food authenticity and raw material processing. Food authenticity identification now extends beyond mere adulteration recognition to include quality evaluation, label compliance, traceability determination, and other quality-related aspects. Consequently, the development of high-throughput, accurate, and rapid analytical techniques is essential to meet these diversified needs. Foodomics, an innovative technology emerging from advancements in food science, enables both a qualitative judgment and a quantitative analysis of food authenticity and safety. This review also addresses crucial aspects of fully processing food, such as verifying the origin, processing techniques, label authenticity, and detecting adulterants, by summarizing the omics technologies of proteomics, lipidomics, flavoromics, metabolomics, genomics, and their analytical methodologies, recent developments, and limitations. Additionally, we analyze the advantages and application prospects of multi-omics strategies. This review offers a comprehensive perspective on the food chain, food safety, and food processing from field to table through omics approaches, thereby promoting the stable and sustained development of the food industry.

Gene expression profiles in specific skeletal muscles and meat quality characteristics of sheep and goats

Lamb meat is highly valued across various cultures and regions due to its unique flavor and nutritional benefits. As the primary component of edible meat, skeletal muscle holds significant economic value and research importance. However, previous studies have largely focused on a limited array of muscle groups, overlooking the differences between various types. Therefore, a comprehensive transcriptomic and meat quality analysis of the skeletal muscles of sheep and goats is essential to improve meat production traits. In this study, we performed RNA sequencing and assessed meat quality in 10 different skeletal muscles from 2-year-old Liangshan Black sheep and Meigu Black goats. We generated 803.16 Gb of high-quality bulk RNA sequencing data with six biological replicates for each muscle. This dataset provides a deeper understanding of the gene expression profiles and meat quality characteristics of different muscle tissues in sheep and goats, laying the foundation for broader comparative research.

Untargeted metabolomics reveals the alteration of metabolites during the stewing process of Lueyang black-bone chicken meat

Introduction

Black-bone chicken meat is rich in nutritional substances and bioactive compounds. Stewing is a traditional and healthy cooking style for black-bone chicken meat. However, the alteration of metabolites in chicken meat during stewing is still unknown.

Methods

A comprehensive analysis of Lueyang black-bone chicken meat metabolites was performed in fresh chicken meat (FM), short-term heat-pretreated meat (PM), fully cooked meat (CM) and chicken soup (CS) via untargeted metabolomics.

Results

By comparison, 200, 992 and 891 significantly differentially metabolites (DMs) were identified in the PM vs. FM, CM vs. FM and CS vs. FM comparisons, respectively. These DMs mainly included amino acids, peptides, carbohydrates and lipids. During the heating process, the abundances of Ser, Ala, Tyr, niacinamide, galactose, guanosine 3'-monophosphate and inosine 5'-monophosphate in chicken meat significantly decreased and were partially dissolved in the soup. Due to the hydrolysis of phospholipids, the relative contents of unsaturated lipids, especially a range of lysophosphatidylcholines, lysophosphatidylethanolamines, arachidonic acid and derivatives, increased in fully cooked meat.

Discussion

Pretreatment had little impact on the changes in metabolites in chicken meat. During stewing, the dissolved amino acids, carbohydrates and nucleic acids could enhance the taste quality of chicken soup, and the high abundance of unsaturated lipids could promote the nutritional quality of black-bone chicken meat. In summary, these data provide helpful information for nutritional quality studies on the metabolite profiles of black-bone chicken meat.

A review of genetic resources and trends of omics applications in donkey research: focus on China

Omics methodologies, such as genomics, transcriptomics, proteomics, metabolomics, lipidomics and microbiomics, have revolutionized biological research by allowing comprehensive molecular analysis in livestock animals. However, despite being widely used in various animal species, research on donkeys has been notably scarce. China, renowned for its rich history in donkey husbandry, plays a pivotal role in their conservation and utilization. China boasts 24 distinct donkey breeds, necessitating conservation efforts, especially for smaller breeds facing extinction threats. So far, omics approaches have been employed in studies of donkey milk and meat, shedding light on their composition and quality. Similarly, omics methods have been utilized to explore the molecular basis associated with donkey growth, meat production, and quality traits. Omics analysis has also unraveled the critical role of donkey microbiota in health and nutrition, with gut microbiome studies revealing associations with factors such as pregnancy, age, transportation stress, and altitude. Furthermore, omics applications have addressed donkey health issues, including infectious diseases and reproductive problems. In addition, these applications have also provided insights into the improvement of donkey reproductive efficiency research. In conclusion, omics methodologies are essential for advancing knowledge about donkeys, their genetic diversity, and their applications across various domains. However, omics research in donkeys is still in its infancy, and there is a need for continued research to enhance donkey breeding, production, and welfare in China and beyond.

Changes in meat quality, metabolites and microorganisms of mutton during cold chain storage

During the cold chain storage process, changes in metabolites and microorganisms are highly likely to lead to changes in meat quality. To elucidate the changes in the composition of metabolites and microbiota during cold chain storage of mutton, this study utilized untargeted metabolome and 5R 16S rRNA sequencing analyses to investigate the changes in the longissimus dorsi under different cold chain temperatures (4 °C and -20 °C). With the extension of cold chain storage time, the meat color darkened and the content of C18:2n-6, C20:3n-6, and C23:0 were significantly increased in mutton. In this study, nine metabolites, including 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine, alanylphenylala-nine, indole-3-acrylic acid and the others, were significantly altered during cold chain storage. The abundance of the dominant microorganisms, including Brachymonas, Aeromonas, Corynebacterium and Steroidobacter, was significantly altered. Furthermore, a high correlation was observed between the different metabolites and microorganisms. These findings provide an in-depth understanding of the effects of different cold chain storage temperatures and times on the quality of mutton.

Assessment of comprehensive PAH index in roasted Tan lamb by two-dimensional correlation spectroscopy combined with hyperspectral imaging

Thermally processed meat may contain harmful compounds, including polycyclic aromatic hydrocarbons (PAHs). This study constructed, for the first time, the comprehensive PAH index (CPI) concentration (phenanthrene [26.47%], acenaphthene [21.83%], pyrene [18.64%], fluoranthene [17.11%], fluorene [8.49%], and anthracene [7.46%]). A visible near-infrared (Vis-NIR) hyperspectral image (HSI) system was employed to detect CPI in 150 roasted Tan lamb samples. Furthermore, two-dimensional correlation spectra were used to identify spectral features and reveal the order of chemical bond changes under the characteristic peaks at 579-737-631-449 nm. The results indicated that competitive adaptive reweighted sampling-multiple linear regression quantitative prediction model worked the best with calibration set coefficient of determination of 0.9161, calibration set coefficient of root mean square error of 2.3426 µg/kg, R-squared prediction of 0.8469, and root mean square error of prediction of 2.4119 µg/kg. Finally, PAH content distributions were visualized using the best prediction model. This study aimed to propose a feasible method for CPI in roasted Tan lamb detection based on Vis-NIR HSI coupled with multivariate analysis methods.

MS based foodomics: An edge tool integrated metabolomics and proteomics for food science

Foodomics has become a popular methodology in food science studies. Mass spectrometry (MS) based metabolomics and proteomics analysis played indispensable roles in foodomics research. So far, several methodologies have been developed to detect the metabolites and proteins in diets and consumers, including sample preparation, MS data acquisition, annotation and interpretation. Moreover, multiomics analysis integrated metabolomics and proteomics have received considerable attentions in the field of food safety and nutrition, because of more comprehensive and deeply. In this context, we intended to review the emerging strategies and their applications in MS-based foodomics, as well as future challenges and trends. The principle and application of multiomics were also discussed, such as the optimization of data acquisition, development of analysis algorithm and exploration of systems biology.

Foetal programming in sheep: Reproductive and productive implications

The aim of this study was to evaluate the effects of pregnant ewe nutrition on the performance of offspring in terms of meat, wool production, and reproduction. Foetal programming in sheep has focused on several aspects related to foetal growth, postnatal production, behaviour, and immunological performance. Currently, significant efforts are being made to understand the endocrine, metabolic, and epigenetic mechanisms involved in offspring development. Current studies have not only evaluated the foetal period, despite the pre-conception parental nutrition has demonstrated an effect on the foetal, embryonic, and pre-implantation periods and can generate permanent effects in the foetal and postnatal phases. The performance of offspring is the result of interactions between the genome, epigenome, and environmental interventions during conception. Several factors influence the expression of phenotypic characteristics in progenies; however, this study focused on presenting data on the effect of pregnant ewe nutrition alone on foetal growth and the productive aspects of their offspring.

Genome-wide association analysis explores the genetic loci of amino acid content in duck's breast muscle

BACKGROUND

Amino acids are the basic components of protein and an important index to evaluate meat quality. With the rapid development of genomics, candidate regions and genes affecting amino acid content in livestock and poultry have been gradually revealed. Hence, genome-wide association study (GWAS) can be used to screen candidate loci associated with amino acid content in duck meat.

RESULT

In the current study, the content of 16 amino acids was detected in 358 duck breast muscles. The proportion of Glu to the total amino acid content was relatively high, and the proportion was 0.14. However, the proportion of Met content was relatively low, at just 0.03. By comparative analysis, significant differences were found between males and females in 3 amino acids, including Ser, Met, and Phe. In addition, 12 SNPs were significantly correlated with Pro content by GWAS analysis, and these SNPs were annotated by 7 protein-coding genes; 8 significant SNPs were associated with Tyr content, and these SNPs were annotated by 6 protein-coding genes. At the same time, linkage disequilibrium (LD) analysis was performed on these regions with significant signals. The results showed that three SNPs in the 55-56 Mbp region of chromosome 3 were highly correlated with the leader SNP (chr3:55526954) that affected Pro content (r2 > 0.6). Similarly, LD analysis showed that there were three SNPs in the 21.2-21.6 Mbp region of chromosome 13, which were highly correlated with leader SNP (chr13:21421661) (r2 > 0.6). Moreover, Through functional enrichment analysis of all candidate genes. The results of GO enrichment analysis showed that several significant GO items were associated with amino acid transport function, including amino acid transmembrane transport and glutamine transport. The results further indicate that these candidate genes are closely associated with amino acid transport. Among them, key candidate genes include SLC38A1. For KEGG enrichment analysis, CACNA2D3 and CACNA1D genes were covered by significant pathways.

CONCLUSION

In this study, GWAS analysis found a total of 28 significant SNPs affecting amino acid content. Through gene annotation, a total of 20 candidate genes were screened. In addition, Through LD analysis and enrichment analysis, we considered that SERAC1, CACNA2D3 and SLC38A1 genes are important candidate genes affecting amino acid content in duck breast muscle.

Unraveling proteome changes of Sunit lamb meat in different feeding regimes and its relationship to flavor analyzed by TMT-labeled quantitative proteomic

In order to explore the molecular mechanism of the effect of feeding regimes on lamb flavor, biceps femoris muscle samples from pasture-fed groups (PF) and concentrate-fed groups (CF) were chosen, and tandem mass tag (TMT) labeling combined with mass spectrometry (MS) was performed to find associations between flavor indicators and proteome profiles. The content and composition of amino acids and volatile flavor substances were better in the PF compared to the CF, with higher levels of some beneficial flavor components such as Arg, Pro Pentanal, Heptanal, Octanal, 1-octen-3-ol and 2,3-Octanedione. About 82 differentially abundant proteins (DAPs) were identified. The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that the pathways that may be associated with lamb flavor are focused on amino acid anabolism. These results provide a basis for further understanding of the molecular mechanisms of proteins in meat flavor regulation.

Insights into the influence of diet and genetics on feed efficiency and meat production in sheep

Feed costs and carcass yields affect the profitability and sustainability of sheep production. Therefore, it is crucial to select animals with a higher feed efficiency and high-quality meat production. This study focuses on the impact of dietary and genetic factors on production traits such as feed efficiency, carcass quality, and meat quality. Diets promote optimal sheep growth and development and provide sufficient protein can lead to higher-quality meat. However, establishing an optimized production system requires careful consideration and balance of dietary parameters. This includes ensuring adequate protein intake and feeding diets with higher intestinal absorption rates to enhance nutrient absorption in the gut. The study identifies specific genes, such as Callipyge, Calpastatin, and Myostatin, and the presence of causal mutations in these genes, as factors influencing animal growth rates, feed efficiency, and meat fatty acid profiles. Additionally, variants of other reported genes, including PIGY, UCP1, MEF2B, TNNC2, FABP4, SCD, FASN, ADCY8, ME1, CA1, GLIS1, IL1RAPL1, SOX5, SOX6, and IGF1, show potential as markers for sheep selection. A meta-analysis of reported heritability estimates reveals that residual feed intake (0.27 ± 0.07), hot carcass weight (0.26 ± 0.05), dressing percentage (0.23 ± 0.05), and intramuscular fat content (0.45 ± 0.04) are moderately to highly heritable traits. This suggests that these traits are less influenced by environmental factors and could be improved through genetic selection. Additionally, positive genetic correlations exist between body weight and hot carcass weight (0.91 ± 0.06), dressing percentage (0.35 ± 0.15), and shear force (0.27 ± 0.24), indicating that selecting for higher body weight could lead to favorable changes in carcass quality, and meat quality.

Pan-Omics in Sheep: Unveiling Genetic Landscapes

Multi-omics-integrated analysis, known as panomics, represents an advanced methodology that harnesses various high-throughput technologies encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Sheep, playing a pivotal role in agricultural sectors due to their substantial economic importance, have witnessed remarkable advancements in genetic breeding through the amalgamation of multiomics analyses, particularly with the evolution of high-throughput technologies. This integrative approach has established a robust theoretical foundation, enabling a deeper understanding of sheep genetics and fostering improvements in breeding strategies. The comprehensive insights obtained through this approach shed light on diverse facets of sheep development, including growth, reproduction, disease resistance, and the quality of livestock products. This review primarily focuses on the application of principal omics analysis technologies in sheep, emphasizing correlation studies between multiomics data and specific traits such as meat quality, wool characteristics, and reproductive features. Additionally, this paper anticipates forthcoming trends and potential developments in this field.

Integrating proteomics and metabolomics to elucidate the molecular network regulating of inosine monophosphate-specific deposition in Jingyuan chicken

Inosine monophosphate (IMP) plays a significant role in meat taste, yet the molecular mechanisms controlling IMP deposition in muscle tissues still require elucidation. The present study systematically and comprehensively explores the molecular network governing IMP deposition in different regions of Jingyuan chicken muscle. Two muscle groups, the breast and leg, were examined as test materials. Using nontargeted metabolomic sequencing, we screened and identified 20 metabolites that regulate IMP-specific deposition. We maintained regular author and institution formatting, used clear, objective, and value-neutral language, and avoided biased or emotional language. We followed a consistent footnote style and formatting features and used precise word choice with technical terms where appropriate. Out of these, 5 were identified as significant contributors to the regulation of IMP deposition. We explained technical term abbreviations when first used and ensured a logical flow of information with causal connections between statements. The results indicate that PGM1, a key enzyme involved in synthesis, is higher in the breast muscle compared to the leg muscle, which may provide an explanation for the increased deposition of IMP in the breast muscle. We aimed for a clear structure with logical progression, avoided filler words, and ensured grammatical correctness. The activity of key enzymes (PKM2, AK1, AMPD1) involved in this process was higher in the breast muscle than in the leg muscle. In the case of IMP degradation metabolism, the activity of its participating enzyme (PurH) was lower in the breast muscle than in the leg muscle. These findings suggest that the increased deposition of IMP in Jingyuan chickens' breast muscle may result from elevated metabolism and reduced catabolism of key metabolites. In summary, a metaomic strategy was utilized to assess the molecular network regulation mechanism of IMP-specific deposition in various segments of Jingyuan chicken. These findings provide insight into genetic improvement and molecular breeding of meat quality traits for top-notch broilers.