Identification of key genes and functional enrichment pathways involved in fat deposition in Xinyang buffalo by WGCNA.

The Xinyang buffalo is a valuable and endangered domestic heritage resource in the Dabie Mountain region in China. With the increasing mechanization of agriculture, the Xinyang buffalo, mainly used for labor, faces unprecedented challenges. One of the feasible approaches to conserve and expand the species is to transfer Xinyang buffalo from service-use to meat-use, but the main hindrance to this transformation is the inferior meat quality of Xinyang buffalo, which is not popular with consumers. Based on the above, this study was conducted to evaluate the growth performance (n = 120) and slaughter performance (n = 3) of Xinyang buffalo and to measure the amino acid levels of the eye muscle (EM), and assess the meat quality. Later, transcriptome sequencing was performed on the subcutaneous fat of the back at six (n = 3) and 30 months of age (n = 3), together with the excavation of candidate genes associated with fat deposition using the weighted co-expression network analysis (WGCNA) method. The results showed that the slaughter rate of Xinyang buffalo was 43.09%, net meat percentage was 33.04%, the ocular area was 59.16 ± 7.58, the backfat thickness was 1.03 ± 0.16, and meat bone ratio was 3.29. The total amino acid contents were 0.63 g per gram of beef, which contained 0.05 g of essential amino acids, and the three most abundant amino acids were Ser (447.17 mg/g), Asp (29.8 mg/g), and Pro (27.24 mg/g). The WGCNA results showed that six phenotypes measured were significantly correlated with the turquoise module (r > 0.97, P < 0.001), and the genes in these modules were significantly enriched in the pathways related to substance metabolism and energy metabolisms, such as metabolic pathways, citrate cycle, and fatty acid metabolism. Meanwhile, six key candidate genes (FH, MECR, GPI, PANK3, ATP6V1A, PHYH) were identified, which were associated with growth and development, fat deposition, and intra-muscular amino acid levels (P < 0.05). In short, this study provides another feasible way to preserve buffalo and enriches the theory of its molecular genetic breeding.

Visual Image Analysis for a new classification method of bovine carcasses according to EU legislation criteria.

In the European Community, conformation and fat cover of bovine carcasses is assessed using the SEUROP grading system. In this study we pursued the development of an application software (App) based on Visual Image Analysis, useful for SEUROP and Fat Cover grading of bovine carcasses using a smartphone. The App was trained using 500 bovine carcasses. Carcass conformation and Fat Cover classes were assessed in parallel by expert evaluators and by App. Overall, a high correspondence was found between the measurements of carcasses parameters by operators and by the App, as high as 84.2% for SEUROP and 86.4% for the Fat Cover. In the 15.8% of samples with discordant SEUROP evaluation, and in the 13.6% of samples with discordant Fat Cover evaluation, the operators' and App measurements deviated by only one class. All values also aligned with the requirements expected by the current legislation for the use of automated and/or semi-automated systems able to determine the market value of carcasses.

Ageing as a method to increase bloom depth and improve retail colour in beef graded AUS-MEAT colour 4.

Meat colour is an important attribute for consumer acceptance but there is an interval between colour grading and retail display. This experiment investigates the effect of time post-slaughter (5, 14 and 40 days) on colour and bloom depth (after 1 and 24 h) for beef carcasses graded AUS-MEAT colour 4 (MC 4). Sixteen carcasses were selected at grading, 8 carcasses were graded MC 4 and 8 as compliant colour (AUS-MEAT score 2 or 3). At 5 days post-slaughter, compliant loins had greater overall bloom depth and were more red than MC 4 loins. Bloom depth (24 h) increased with ageing time but reached maximum bloom at 14 days for both treatments. After ageing for 14 and 40 days, the bloom depth of MC 4 loin was no different to the 5 day aged compliant loins after 24 h on display. Colour at grading may not be a reliable measure of retail colour considering the changes post slaughter.

Quality and Safety of Fresh Beef in Retail: A Review.

ABSTRACT: This study aimed to review the scientific literature on the quality and safety of beef sold in retail, methodologies used for quality evaluation, and proposed interventions for the sector. Bibliographical research was performed to identify scientific articles using the electronic databases Ovid, PubMed, Scielo, LILACS, Scopus, and Embase. Thirty-three articles were included in the review. Given the different dimensions of the studies, the results were organized into three categories, according to the following approaches: food, environment, and handlers; consumers and selection criteria; and intervention strategies for the retail sector. The applied methodological strategies revealed inadequate conditions and neglect in several processing and operation stages that are fundamental to the maintenance of quality standards. The results confirm a worrying scenario and the presence of risks to consumers. Based on the studies evaluated, it is necessary to emphasize consumer concern about the importance of the integrated information chain-all stages involved in the production process and meat distribution for retail meat stores. The reported conditions from different studies indicate the need for interventions with a view to prevention of health risks, continued training of food handlers, and transformation of evidenced realities. In this context, it is possible to point out the predominance of diagnostic studies, in contrast with interventional studies focused on the training and qualification of food handlers.

Long-range linkage disequilibrium in French beef cattle breeds.

BACKGROUND: Linkage disequilibrium (LD) is a key parameter to study the history of populations and to identify and fine map quantitative trait loci (QTL) and it has been studied for many years in animal populations. The advent of new genotyping technologies has allowed whole-genome LD studies in most cattle populations. However, to date, long-range LD (LRLD) between distant variants on the genome has not been investigated in detail in cattle. Here, we present the first comprehensive study of LRLD in French beef cattle by analysing data on 672 Charolais (CHA), 462 Limousine (LIM) and 326 Blonde d'Aquitaine (BLA) individuals that were genotyped on the Illumina BovineHD Beadchip. Furthermore, whole-genome LD and haplotype block structure were analysed in these three breeds. RESULTS: We computed linkage disequilibrium (r2) values for 5.9, 5.6 and 6.0 billion pairs of SNPs on the 29 autosomes of CHA, LIM and BLA, respectively. Mean r2 values drop to less than 0.1 for distances between SNPs greater than 120 kb. However, for the first time, we detected the existence of LRLD in the three main French beef breeds. In total, 598, 266, and 795 LRLD events (r2 ≥ 0.6) were detected in CHA, LIM and BLA, respectively. Each breed had predominantly population-specific LRLD interactions, although shared LRLD events occurred in a number of regions (55 LRLD events were shared between two breeds and nine between the three breeds). Examples of possible functional gene interactions and QTL co-location were observed with some of these LRLD events, which suggests epistatic selection. CONCLUSIONS: We identified long-range linkage disequilibrium for the first time in French beef cattle populations. Epistatic selection may be the main source of the observed LRLD events, but other forces may also be involved. LRLD information should be accounted for in genome-wide association studies.

Effects of Green Tea Powder, Pomegranate Peel Powder, Epicatechin and Punicalagin Additives on Antimicrobial, Antioxidant Potential and Quality Properties of Raw Meatballs.

Alternative technologies, which have been developed in order to meet the consumers' demand for nourishing and healthy meat and meat products, are followed by the food industry. In the present study, it was determined, using the HPLC method, that green tea contains a high level of epicatechin (EP) under optimal conditions and that pomegranate peel contains a high level of punicalagin (PN). Green tea, pomegranate peel, EP and PN were added to meatballs at different concentrations in eight groups. The antioxidant capacities of extracts were measured. The antimicrobial activity was examined for 72 h using three different food pathogens. The highest level of antimicrobial activity was achieved in the 1% punicalagin group, whereas the minimum inhibition concentration (L. monocytogenes, S. typhimurium) was found to be 1.87 mg/mL. A statistically significant decrease was found in FFA, POV and TBARS levels of meatballs on different days of storage (p < 0.05). When compared to the control group, the bioactive compounds preserved the microbiological and chemical properties of meatballs during storage at +4 °C (14 days). It was concluded that the extracts with high EP and PN concentrations can be used as bio-preservative agents for meat and meat products.

Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection.

BACKGROUND: While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. RESULTS: We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. CONCLUSIONS: In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle.

Water holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = - 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = - 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein-protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

iTRAQ-mediated analysis of the relationship between proteomic changes and yak longissimus lumborum tenderness over the course of postmortem storage.

To identify differentially expressed proteins associated with energy metabolism and tenderness during the postmortem aging of yak longissimus lumborum muscle samples, we collected tissue samples from yaks raised at different altitudes. At 12 h post-slaughter, we identified 290 differentially expressed proteins (DEPs) in these samples, whereas 436 such DEPs were detected after 72 h. Identified DEPs were clustered into four main functional categories: cell structural proteins, glycogen metabolic proteins, energy reserve metabolic proteins, and cellular polysaccharide metabolic proteins. Further bioinformatics analysis revealed that these proteins were associated with carbon metabolism, glycolysis, and the biosynthesis of amino acids. Our functional insights regarding these identified proteins contribute to a more detailed molecular understanding of the processes of energy metabolism in yak muscle tissue, and represent a valuable resource for future investigations.

Consumers' perception and purchase behaviour of meat in China.

China has experienced significant economic growth in recent decades, and this has accounted for an increase in meat consumption. Therefore, it is important to understand the underlying factors of consumers' perception and purchasing behaviour of lamb meat in China. This study adopts a conceptual framework, which includes expectations, perception, and purchase behaviour of red meat among Chinese consumers. A total of 31 questions were included in a self-administered questionnaire through an online platform, with 601 meat consumers who participated in this study. Results showed that Australian and New Zealand meat were perceived as having positive quality characteristics (e.g. natural, reliable) followed by Chinese local meat. Partial Least Squares Path Modelling (PLS-PM) further identified that the key drivers that influenced meat purchase were seasonality, purchase location, and consumer experience particularly in cooking methods used. Purchase point for Chinese consumers were equally weighed with butchers, supermarket, and traditional market as being the most common purchase locations. Unexpectedly, Chinese consumers were found to consume less meat in summer and more during winter. Purchase drivers included meat safety certification and the perceived health benefits of meat.

At-home methods for tenderizing meat using blade tenderization, lime juice and pineapple puree.

We evaluated at-home methods to tenderize flank steaks. Steaks sourced from a commercial beef processor were aged 28 d postmortem, prior to treatment application. Individual steaks were cut into four sampling portions and treated via blade tenderization (BT), and marination with lime juice (LJ) and/or pineapple puree (PP). Blade tenderization (2×) was conducted parallel and perpendicular to muscle fiber direction; LJ and PP were added at 25% of sample weight. Tenderness was assessed via Warner-Bratzler Shear Force (WBSF) and data was analyzed via mixed models. Neither the three-way interaction (P = 0.64), the BT x PP interaction (P = 0.19), nor LJ (P = 0.35) treatment altered WBSF. Blade tenderization x LJ (P = 0.09) and LJ x PP (P = 0.07) tended to alter WBSF. Blade tenderization (P = 0.03) and pineapple puree (P < 0.01) reduced WBSF by 2.40 and 4.50 N, respectively. WBSF was reduced by 7.3 to 24% via treatment combinations of LJ, BT, or PP.

Partial least squares and machine learning for the prediction of intramuscular fat content of lamb loin.

Given the paucity of lamb carcase grading tools, there is a distinct need for the development of rapid, non-destructive grading tools for Australian lamb carcases, particularly fat content given its importance to meat and eating quality. The aim of the current study was to determine the potential for Near Infrared (NIR) spectroscopy to predict IMF using Partial Least Squares (PLS) and machine learning analysis methods. As such, 299 lamb loins were measured using a NIR fibre optic device, a sample was excised for Soxhlet determination of IMF content and prediction models were created using either PLS or machine learning analyses methods. IMF prediction model outcomes were similar between analysis methods with an R2 = 0.6 and RMSE = 0.84 and R2 = 0.65 and RMSE = 0.72, respectively. This study highlighted that spectra from one slaughter varied greatly from the two succeeding slaughters and wavelengths selected between studies are not consistent.

Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits.

BACKGROUND: Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles. RESULTS: Whereas a relatively small number of molecular phenotypes were significantly heritable (h2 > 0, P < 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR < 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly (P < 0.05) larger than expected by chance. The identified eQTL were significantly (P < 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For example, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles. CONCLUSIONS: We detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.

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.

Eating quality of the longissimus thoracis muscle in beef cattle - Contributing factors to the underlying variability and associations with performance traits.

The objective was to determine the factors associated with meat tenderness, juiciness, flavour and chewiness in 4791 growing crossbred cattle. Meat quality of bulls was inferior to that of both steers and heifers with little difference between the latter two genders. Angus, Hereford and Belgian Blues had the most tender meat with the Simmental being the toughest albeit the difference was, on average, only 5%. Moderate to strong correlations (r ≥ |0.43|) existed among tenderness, juiciness and flavour although some of the correlations differed by animal gender. Correlations between chewiness and tenderness in the different genders varied from -0.81 to -0.74 while the correlations between chewiness and the other sensory traits varied from -0.54 to -0.09. The (partial) correlations between each of the four sensory metrics and all of carcass weight, carcass conformation and carcass fat score were ≤|0.09| with most not being different from zero. Correlations between the sensory traits with growth rate, muscle depth, feed intake and efficiency were all ≤|0.08| and mostly not different from zero.

Multiplex PCR and 12S rRNA gene sequencing for detection of meat adulteration: A case study in the Egyptian markets.

Recently, DNA-based methods have proved to be accurate, fast and sensitive for meat authentication. According to the European Union, the food safety standards require accurate and detailed composition information of the meat products. Therefore, an accurate, fast and cost-effective identification methodology is needed. In this study, multiplex PCR coupled with 12S rDNA sequencing was employed for the detection of meat adulteration in two red meat products (frozen beef liver and cold cut samples, respectively) in Egypt. Multiplex PCR allowed the identification of ruminant, poultry, pork, and donkey residuals in processed red meat products (cold cuts) in a single step PCR reaction. Preliminary uniplex PCR was performed to evaluate primers specificity using DNA extracted from the positive control samples. The primers produced specific fragments for ruminant, poultry, pork, and donkey as follows: 271, 183, 531 and 145 bp, respectively. Multiplex PCR revealed that none of the samples was contaminated by porcine or donkey residuals, but 62.5% of all tested processed beef samples contained poultry contaminants. The sensitivity of this method was 0.01 ng/µL for beef, poultry and donkey and 0.1 ng/µL for pig. Another promising finding is the identification of all frozen beef liver samples as a cattle species (Bos taurus) through PCR-sequencing of a short fragment of 12S rRNA gene. Finally, we recommend the employment of multiplex PCR and PCR-sequencing of 12S rDNA for quality control in routine analysis of processed and frozen meat products.

Genomic sequencing analysis reveals copy number variations and their associations with economically important traits in beef cattle.

Copy number variation (CNV) represents a major source of genetic variation, which may have potentially large effects, including alternating gene regulation and dosage, as well as contributing to gene expression and risk for normal phenotypic variability. We carried out a comprehensive analysis of CNV based on whole genome sequencing in Chinese Simmental beef cattle. Totally, we found 9313 deletion and 234 duplication events, covering 147.5 Mb autosomal regions. Within them, 257 deletion events of high frequency overlapped with 193 known RefGenes. Among these genes, we observed several genes were related to economically important traits, like residual feed intake, immune responding, pregnancy rate and muscle differentiation. Using a locus-based analysis, we identified 11 deletions and 1 duplication, which were significantly associated with three traits including carcass weight, tenderloin and longissimus muscle area. Our sequencing-based study provided important insights into investigating the association of CNVs with important traits in beef cattle.

Prediction of consumer palatability in beef using visual marbling scores and chemical intramuscular fat percentage.

With development of objective technologies that can predict chemical intramuscular fat percentage (IMF%), there is a need to understand the relationships between existing marbling traits, IMF% and eating quality. This study utilised historical carcass data (n = 9641 observations) from the Meat Standards Australia (MSA) industry research dataset and included MSA grading data, chemical IMF% data and weighted composite eating quality scores (MQ4). Several analyses were performed to assess the prediction of MQ4 by MSA marbling, M. longissimus thoracis et lumborum (striploin) IMF% and cut specific IMF%. Results demonstrated that there was similar precision between chemical IMF% (R2 = 0.32, RSE = 11.8) and MSA marbling (R2 = 0.28, RSE = 11.9) in the prediction of grilled 14 day aged striploin MQ4, with similar results across other cut by cook by days aged combinations. These results support the development of objective technologies that predict chemical IMF% in parallel with MSA marbling for carcass grading and the prediction of eating quality.

Genetic parameters associated with meat quality of Nellore cattle at different anatomical points of longissimus: Brazilian standards.

The present study estimated genetic parameters and evaluated the genetic and phenotypic correlations between meat quality characteristics of Nellore cattle evaluated at different anatomical points of the longissimus. Data from 1329 Nellore young bulls were used to evaluate, in the 5th and 12th ribs, marbling score (MAR), shear force (SF), cooking weight losses (CWL) and intramuscular fat (IMF). In addition, the subcutaneous fat thickness was measured at the 12th rib (SFT12) and between the last lumbar and the first sacral vertebrae (SFTLR), in the separation of loin and round. Results yielded moderate heritability coefficients for evaluated characteristics, except CWL. High genetic correlations (0.61) were found between measurements of SFT12 and SFTLR. MAR, IMF and SF were evaluated at the 5th and 12th rib. Meat quality and subcutaneous fat thickness measured at different anatomical points of the longissimus are genetically correlated and can be used in genetic selection programs to improve meat quality characteristics in Nellore cattle.