Recent advances in cattle functional genomics and their application to beef quality

Combined Use of Univariate and Multivariate Approaches to Detect Selection Signatures Associated with Milk or Meat Production in Cattle

OBJECTIVES

The aim of this study was to investigate the genomic structure of the cattle breeds selected for meat and milk production and to identify selection signatures between them.

METHODS

A total of 391 animals genotyped at 41,258 SNPs and belonging to nine breeds were considered: Angus (N = 62), Charolais (46), Hereford (31), Limousin (44), and Piedmontese (24), clustered in the Meat group, and Brown Swiss (42), Holstein (63), Jersey (49), and Montbéliarde (30), clustered in the Milk group. The population stratification was analyzed by principal component analysis (PCA), whereas selection signatures were identified by univariate (Wright fixation index, FST) and multivariate (canonical discriminant analysis, CDA) approaches. Markers with FST values larger than three standard deviations from the chromosomal mean were considered interesting. Attention was focused on markers selected by both techniques.

RESULTS

A total of 10 SNPs located on seven different chromosomes (7, 10, 14, 16, 17, 18, and 24) were identified. Close to these SNPs (±250 kb), 165 QTL and 51 genes were found. The QTL were grouped in 45 different terms, of which three were significant (Bonferroni correction < 0.05): milk fat content, tenderness score, and length of productive life. Moreover, genes mainly associated with milk production, immunity and environmental adaptation, and reproduction were mapped close to the common SNPs.

CONCLUSIONS

The results of the present study suggest that the combined use of univariate and multivariate approaches can help to better identify selection signatures due to directional selection.

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.

Association study between SNP markers located in meat quality candidate genes with intramuscular fat content in an endangered dual-purpose cattle population

The aim of this study was to associate single nucleotide polymorphisms (SNP) of the bovine calcium-activated neutral protease µ-calpain, calpastatin, diacylglycerol-O-acyltransferase, adipose fatty acid binding protein, retinoic acid receptor-related orphan receptor C (RORC), and thyroglobulin (TG) gene with intramuscular fat content (IMF). Therefore, 542 animals of the cattle breed "Rotes Höhenvieh" (RHV) were phenotyped for IMF. Genotyping of the animals was performed using polymerase chain reaction-restriction fragment length polymorphism tests for six SNP from candidate genes for meat quality traits. In addition, we calculated allele substitution and dominance effects on IMF. A subgroup of animals (n = 44, reduced dataset) with extraordinary high IMF was analyzed separately. The mean IMF content was 2.5% (SD: 2.8) but ranged from 0.02% to 23.9%, underlining the breeds' potential for quality meat production. Allele and genotype frequencies for all SNP were similar in the complete and reduced dataset. Association analyses in the complete dataset revealed the strongest effects of RORC on IMF (P = 0.075). The log-transformed least-squares mean for IMF of genotype g.3290GG was 0.45 ± 0.16, 0.26 ± 0.14 for genotype g.3290GT, and 0.32 ± 0.14 for genotype g.3290TT. In the reduced dataset, we found a significant effect (P < 0.05) of the g.422C>T-SNP of TG on IMF, with highest IMF for genotype CT (0.91 ± 0.17), lowest IMF for genotype TT (0.37 ± 0.25), and medium IMF for genotype CC (0.59 ± 0.16; log-transformed values). Compared to the complete dataset, allele substitution effects increased in the reduced dataset for most of the SNP, possibly due to the selective genotyping strategy, with focus on animals with highest IMF implying strong phenotypic IMF contrast. Dominance effects were small in both datasets, related to the high heritability of IMF. Results indicated RHV breed particularities regarding the effects of meat quality genes on IMF. An explanation might be the breeding history of RHV with focus on adaptation and resilience in harsh outdoor systems. Consequently, it is imperative to develop breed-specific selection strategies. Allele substitution and dominance effects were in a similar direction in both datasets, suggesting the same breeding approaches for different RHV strains in different regions. Nevertheless, a selective genotyping approach (reduced dataset), contributed to more pronounced genotype effect differences on IMF and dominance values.

Associations between gene polymorphisms and selected meat traits in cattle - A review

Maintaining a high level of beef consumption requires paying attention not only to quantitative traits but also to the quality and dietary properties of meat. Growing consumer demands do not leave producers many options for how animals are selected for breeding and animal keeping. Meat and carcass fatness quality traits, which are influenced by multiple genes, are economically important in beef cattle breeding programs. The recent availability of genome sequencing methods and many previously identified molecular markers offer new opportunities for animal breeding, including the use of molecular information in selection programs. Many gene polymorphisms have thus far been analyzed and evaluated as potential candidates for molecular markers of meat quality traits. Knowledge of these markers can be further applied to breeding programs through marker-assisted selection. In this literature review, we discuss the most promising and well-described candidates and their associations with selected beef production traits.

Transcriptomic profile of semitendinosus muscle of bulls of different breed and performance

The aim of the study was to compare the transcriptomic profiles of fully differentiated skeletal muscle derived from bulls belonging to different breeds of varying performance. Microarray analyses were performed to determine the differences in the expression profiles of genes between semitendinosus muscles of 15-month-old beef-breed bulls (Limousin—LIM and Hereford—HER) and dairy-breed bulls (Holstein Friesian—HF). These analyses allowed for the identification of those genes the expression of which is similar and characteristic of fully differentiated muscle in beef breeds, but differs in skeletal muscle of a typical dairy breed. The analysis revealed 463 transcripts showing similar expression in the semitendinosus muscle of beef breeds (LIM/HER), in comparison with the dairy breed (HF). Among the identified genes, 227 were upregulated and 236 were downregulated in beef breeds. The ontological analyses revealed that the largest group of genes similarly expressed in LIM and HER was involved in the processes of protein metabolism and development of muscle organ. In beef breeds, some genes involved in protein synthesis and proteolysis showed an upregulation, including ctsd, ctsf, fhl2, fhl3, fst, sirt1, and trim63, whereas some were downregulated, including bmpr1a, bmpr2, mstn, smad2, hspa8, gsk3β, and tgfβ2. The expression of the chosen genes was confirmed by RT-qPCR technique. Thus, it can be assumed that the identified genes involved in the regulation of growth and development of muscle tissue and the processes of protein metabolism in the examined cattle breeds may be responsible for the greater gain of muscle mass in beef-breed bulls.

Genome-wide association study identified genomic regions and putative candidate genes affecting meat color traits in Nellore cattle

Single and multiple-trait GWAS were conducted to detect genomic regions and candidate genes associated with meat color traits (L*, lightness; a*, redness; b*, yellowness) in Nellore cattle. Phenotypic records of 5000 animals, and 3794 genotypes for 614,274 SNPs were used. The BLUPF90 family programs were used through single step GWAS approach. The top 10 genomic regions from single-trait GWAS explained 13.64%, 15.12% and 13% of genetic variance of L*, a* and b*, which harbored 129, 70, and 84 candidate genes, respectively. Regarding multiple-trait GWAS, the top 10 SNP windows explained 17.46%, 18.98% and 13.74% of genetic variance of L*, a* and b*, and harbored 124, 86, and 82 candidate genes, respectively. Pleiotropic effects were evidenced by the overlapping regions detected on BTA 15 and 26 associated with L* and a* (genetic correlation of -0.53), and on BTA 18 associated with a* and b* (genetic correlation of 0.60). Similar genomic regions located on BTA 2, 5, 6, and 18 were detected through single and multi-trait GWAS. Overlapped regions harbored a total of 30 functional candidate genes involved in mitochondrial activity, structural integrity of muscles, lipid oxidation, anaerobic metabolism, and muscular pH.

Using Genetic Panels to Predict Tenderness in Beef Cattle

Genetic panel use as a selection tool has grown in popularity in the beef industry. The objective of the study was to determine whether beef cattle genetically selected for tenderness generated a tender product. Igenity® (IT) panel results were provided by a cattle producer for 52 steers, which were harvested at a commercial harvest facility. Boneless strip loins (Institutional Meat Purchase Specifications #180; United States Department of Agriculture [USDA] Choice, n = 32; USDA Prime n = 20) were collected from the left side of each carcass and transported to the University of Idaho Meat Science Laboratory. Four steaks were cut from each subprimal and assigned to aging periods of 7, 14, and 21 d for Warner-Bratzler Shear Force (WBSF) analysis or 21 d for consumer sensory analysis. Carcasses were assigned to tenderness groups based on their IT tenderness indexes (Low IT, 3 – 6, n = 30; High IT, 7 – 10, n = 22). Data were analyzed using the mixed model procedure of SAS version 9.4 (SAS Institute Inc., Cary, NC). An interaction was observed between tenderness group and USDA quality grade (P = 0.015) when analyzing WBSF. All of the cattle had less than 4.14 kg of WBSF; however, USDA Prime steers that were in the High IT tenderness group produced more tender steaks than High IT USDA Choice, Low IT USDA Prime, and Low IT USDA Choice steers. Consumers were not able to detect tenderness differences between IT tenderness groups (P = 0.11) or USDA quality grades (P = 0.11), but they found USDA Prime steaks to be more acceptable (P = 0.01), juicier (P = 0.01), and more flavorful (P = 0.02) than USDA Choice steaks. In conclusion, regardless of tenderness group, USDA Prime steaks were preferred by consumers over USDA Choice steaks in terms of flavor, juiciness, and acceptability.

Aggregation of Omic Data and Secretome Prediction Enable the Discovery of Candidate Plasma Biomarkers for Beef Tenderness

Beef quality is a complex phenotype that can be evaluated only after animal slaughtering. Previous research has investigated the potential of genetic markers or muscle-derived proteins to assess beef tenderness. Thus, the use of low-invasive biomarkers in living animals is an issue for the beef sector. We hypothesized that publicly available data may help us discovering candidate plasma biomarkers. Thanks to a review of the literature, we built a corpus of articles on beef tenderness. Following data collection, aggregation, and computational reconstruction of the muscle secretome, the putative plasma proteins were searched by comparison with a bovine plasma proteome atlas and submitted to mining of biological information. Of the 44 publications included in the study, 469 unique gene names were extracted for aggregation. Seventy-one proteins putatively released in the plasma were revealed. Among them 13 proteins were predicted to be secreted in plasma, 44 proteins as hypothetically secreted in plasma, and 14 additional candidate proteins were detected thanks to network analysis. Among these 71 proteins, 24 were included in tenderness quantitative trait loci. The in-silico workflow enabled the discovery of candidate plasma biomarkers for beef tenderness from reconstruction of the secretome, to be examined in the cattle plasma proteome.

In silico disease model: from simple networks to complex diseases

In this chapter we consider in silico modeling of diseases starting from some simple to some complex (and mathematical) concepts. Examples and applications of in silico modeling for some important categories of diseases (such as for cancers, infectious diseases, and neuronal diseases) are also given.

Gene and protein expression of myosin heavy chain in Nellore cattle comparing growth or meat tenderness traits

The objective was to investigate gene and protein expression of myosin heavy chain (MyHC) in Nellore cattle slaughtered at different weights (BW) or degrees of meat tenderness. Ninety animals with initial BW 370 ± 37 kg, 24 months of age, were slaughtered after 95 days on feed. We evaluated shear force (SF), myofibrillar fragmentation index, ribeye area, backfat thickness, marbling, color, and cooking losses. Subsequently, 24 animals were selected and divided into four contrasting groups, in which light (BW = 504.58 ± 32.36 kg) versus heavy animals (BW = 604.83 ± 42.97 kg) and animals with tender (SF = 3.88 ± 0.57 kg) versus tough meat (SF = 7.95 ± 1.04 kg) were compared. The MYH7, MYH2 and MYH1 genes were analyzed by real-time PCR. The MyHC isoforms (MyHC-I, MyHC-IIa, and MyHC-IIx) were quantified by SDS-PAGE electrophoresis. We found lower expression of MYH2 and MYH1 genes in heavy compared to light animals and a higher amount of MyHC-I isoform in the tough meat group compared to the tender meat group. Protein expression of MyHC-IIa was higher in the tender meat group. A negative correlation was found of this protein and SF (tenderness), suggesting MyHC-IIa as a biomarker of meat quality.

Feeding strategies alter gene expression of the calpain system and meat quality in the longissimus muscle of Braford steers

Objective

The aim of the present study was to determine the effect of supplementing pasture-finished steers with corn silage on the expression level of the calpain system proteins and beef tenderization.

Methods

Thirty Braford steers grazing on summer pasture were used for the study. For 120 days fifteen animals were supplemented with corn silage at 1% of body weight per head per day (Suppl) whereas the remaining 15 steers only received pasture (Contr). Carcass and meat traits were evaluated and compared between groups. Gene expression and activities of proteases (calpain 1 and calpain 2) and inhibitor (calpastatin) were measured using real-time polymerase chain reaction and casein zymography.

Results

Carcass and meat traits were significantly different between feeding systems. Supplemented steers showed higher hot carcass weight (p<0.01), fat content (p = 0.02), and Warner-Bratzler shear force (p = 0.03). Furthermore, the control group showed higher protease:inhibitor ratios, at mRNA (p = 0.01) and protein levels (p<0.10). Warner-Bratzler shear force and mRNA calpains:calpastatin ratio were associated in both feeding systems (p<0.01).

Conclusion

Based on the results obtained in the study, beef tenderness differences among finishing strategies could be modulated through differential expression of the calpain system proteins.

Early differential gene expression in beef Longissimus thoracis muscles from carcasses with normal (<5.8) and high (>5.9) ultimate pH

The objective of this study was to investigate early postmortem (0.5 h) gene expression in beef Longissimus thoracis (LT) muscles from carcasses with NORMAL (<5.8) and HIGH (>5.9) ultimate pH (pH_u). A total of 53 transcripts were differentially expressed (P-value <.05): 40 showed up-regulation and 13 showed down-regulation in HIGH pH_u carcasses. Four up-regulated (PDK4, GADD45B, MAOA, METTL21C) genes were confirmed (P < .05) by q-PCR. HIGH pH_u samples resulted with lower values in glycolytic potential and AMP-activated protein kinase activity compared to NORMAL at 0.5 and 24 h postmortem (P < .05). Functional pathway analysis showed that calcium transport and GADD45 signaling pathways are associated with the development of HIGH pH meat. Genes involved in stress-related signaling, such as GADD45B, METTL21C and MAOA were overexpressed. These genes are involved in stress signaling that might be affecting Ca²⁺ transport and oxidative metabolism pathways in HIGH pH muscles.

NeuroMuscleDB: a Database of Genes Associated with Muscle Development, Neuromuscular Diseases, Ageing, and Neurodegeneration

Skeletal muscle is a highly complex, heterogeneous tissue that serves a multitude of biological functions in living organisms. With the advent of methods, such as microarrays, transcriptome analysis, and proteomics, studies have been performed at the genome level to gain insight of changes in the expression profiles of genes during different stages of muscle development and of associated diseases. In the present study, a database was conceived for the straightforward retrieval of information on genes involved in skeletal muscle formation, neuromuscular diseases (NMDs), ageing, and neurodegenerative disorders (NDs). The resulting database named NeuroMuscleDB ( http://yu-mbl-muscledb.com/NeuroMuscleDB ) is the result of a wide literature survey, database searches, and data curation. NeuroMuscleDB contains information of genes in Homo sapiens, Mus musculus, and Bos Taurus, and their promoter sequences and specified roles at different stages of muscle development and in associated myopathies. The database contains information on ~ 1102 genes, 6030 mRNAs, and 5687 proteins, and embedded analytical tools that can be used to perform tasks related to gene sequence usage. The authors believe NeuroMuscleDB provides a platform for obtaining desired information on genes related to myogenesis and their associations with various diseases (NMDs, ageing, and NDs). NeuroMuscleDB is freely available on the web at http://yu-mbl-muscledb.com/NeuroMuscleDB and supports all major browsers.

Analysis of Longissimus thoracis Protein Expression Associated with Variation in Carcass Quality Grade and Marbling of Beef Cattle Raised in the Pacific Northwestern United States

Longissimus thoracis (LD) samples from 500 cattle were screened for protein expression differences relative to carcass quality grade. The LD of the top 5% (low prime and high choice, HQ) and bottom 5% (low select, LQ) carcasses were analyzed using two-dimensional difference gel electrophoresis and Western blot. Following initial screening, 11 candidate proteins were selected for Western blot analyses. Differentially expressed proteins were clustered into four groups: (1) heat shock proteins and oxidative protection, (2) sarcomeric proteins (muscle maturity and fiber type), (3) metabolism and energetics, and (4) miscellaneous proteins. Proteins from groups 1 and 2 were greater in HQ carcasses. Alternatively, increased quantities of proteins from group 3 were observed in LQ carcasses. Proteomic differences provide insights into pathways contributing to carcass quality grade. A deeper understanding of the physiological pathways involved in carcass quality grade development may allow producers to employ production practices that improve quality grade.

Biomarkers: Non-destructive Method for Predicting Meat Tenderization

Meat tenderness is the primary and most important quality attribute for the consumers worldwide. Tenderness is the process of breakdown of collagen tissue in meat to make it palatable. The earlier methods of tenderness evaluation like taste panels and shear force methods are destructive, time consuming and ill suited as they requires removing a piece of steak from the carcass for performing the test. Therefore, a non-destructive method for predicting the tenderness would be more desirable. The development of a meat quality grading and guarantee system through muscle profiling research can help to meet this demand. Biomarkers have the ability to identify if an exposure has occurred. Biomarkers of the meat quality are of prime importance for meat industry, which has ability to satisfy consumers' expectations. The biomarkers so far identified have been then sorted and grouped according to their common biological functions. All of them refer to a series of biological pathways including glycolytic and oxidative energy production, cell detoxification, protease inhibition and production of Heat Shock Proteins. On this basis, a detailed analysis of these metabolic pathways helps in identifying tenderization of meat having some domains of interest. It was, therefore, stressed forward that biomarkers can be used to determine meat tenderness. This review article summarizes the uses of several biomarkers for predicting the meat tenderness.

Adaptive traits of indigenous cattle breeds: The Mediterranean Baladi as a case study

Generally taken, breeds of Bos taurus ancestry are considered more productive, in comparison with Bos indicus derived breeds that present enhanced hardiness and disease resistance, low nutritional requirements and higher capability of feed utilization. While breeds of B. taurus have been mostly selected for intensive production systems, indigenous cattle, developed mostly from indicine and African taurines, flourish in extensive habitats. Worldwide demographic and economic processes face animal production with new challenges - the increasing demand for animal food products. Intensification of animal husbandry is thus a desired goal in stricken parts of the world. An introduction of productive traits to indigenous breeds might serve to generate improved biological and economic efficiencies. For this to succeed, the genetic merit of traits like efficiency of feed utilization and product quality should be revealed, encouraging the conservation initiatives of indigenous cattle populations, many of which are already extinct and endangered. Moreover, to overcome potential genetic homogeneity, controlled breeding practices should be undertaken. The Baladi cattle are a native local breed found throughout the Mediterranean basin. Purebred Baladi animals are rapidly vanishing, as more European breeds are being introduced or used for backcrosses leading to improved production. The superiority of Baladi over large-framed cattle, in feedlot and on Mediterranean pasture, with respect to adaptability and efficiency, is highlighted in the current review.

Inverse relationships between biomarkers and beef tenderness according to contractile and metabolic properties of the muscle

Previous proteomic analyses established a list of proteins biomarkers of beef tenderness. The present study quantified the relative abundance of 21 of these proteins by dot-blot technique in the Longissimus thoracis and Semitendinosus muscles of 71 young bulls from three breeds: Aberdeen Angus (AA), Limousin (LI), and Blond d'Aquitaine (BA). For both muscles overall tenderness was estimated by sensory analysis; shear force was measured with a Warner-Bratzler instrument, and an index combining sensory and mechanical measurements was calculated. Multiple regressions based on relative abundances of these proteins were used to propose equations of prediction of the three evaluations of tenderness. Hsp70-1B appeared to be a good biomarker of low tenderness in the three breeds and in the two muscles. Proteins such as lactate dehydrogenase-B, myosin heavy chain IIx, and small heat shock proteins (Hsp27, Hsp20, and αB-crystallin) were related to tenderness but inversely according to the muscle and breed. The results demonstrate that prediction of tenderness must take into account muscle characteristics and animal type.

Heat shock and structural proteins associated with meat tenderness in Nellore beef cattle, a Bos indicus breed

Nellore beef cattle, a Bos indicus (Zebu) breed, is well adapted to tropical conditions and has allowed Brazil to become one of the largest producers of red meat. Nevertheless, B. indicus breeds are reported to have less tender meat than Bos taurus. This study was designed to identify genes associated with meat tenderness and thus provides important information for breeding programs. A group of 138 animals was evaluated for longissimus thoracis muscle shear force (SF). Animals with the highest and lowest SF values (six animals each) were then selected for protein abundance studies. Samples were subjected to two-dimensional gel electrophoresis (2-DE) followed by peptide sequencing through mass spectrometry (MS) to identify differentially expressed proteins associated with SF values. Seventeen differentially expressed spots were observed (p<0.05) between the two groups. The 13 proteins identified included structural proteins (alpha actin-1, MLC1, MLC3, MLC2F and tropomyosin), related to cell organization (HSPB1 and HSP70), metabolism (beta-LG, ACBD6 and Complex III subunit I) and some uncharacterized proteins. Results confirm the existence of differentially expressed proteins associated with SF, which can lead to a better understanding of mechanisms involved in meat tenderness.

Identification and association of polymorphisms in CAPN1 and CAPN3 candidate genes related to performance and meat quality traits in chickens

Meat quality is an important feature for the poultry industry and is associated with consumer satisfaction. The calpain 1 (CAPN1) gene is related to the tenderness process of meat post- mortem, and the calpain 3 (CAPN3) gene plays an important role in myofibrillar organization and growth. The objective of the present study was to identify polymorphisms in these genes and to determine the association between these polymorphisms and traits of economic interest in poultry. Eleven animals (F₁) from an experimental poultry population at Embrapa Swine and Poultry were used to identify the polymorphisms. Four single nucleotide polymorphisms (SNPs) were found in the CAPN1 gene, and one SNP was found in the CAPN3 gene. A polymorphism from each gene was selected for genotyping in 152 chickens from the Embrapa F₂ experimental population and 311 chickens from a commercial population. Polymorphism g.2554T>C (CAPN1) was associated with body weight at 35 to 42 days, thigh weight, breast weight, carcass weight, and meat lightness content. SNP g.15486C>T (CAPN3) was associated with thigh yield, thawing-cooking loss, and shear force. Results suggest the possibility of using molecular markers in CAPN1 and CAPN3 genes as a tool for performance and meat quality traits in poultry breeding programs.

Endocrine and metabolic regulation of muscle growth and body composition in cattle

Muscle metabolism (in interaction with other organs and tissues, including adipose tissue) plays an important role in the control of growth and body composition. Muscle ontogenesis has been described in different genotypes of cattle for myofibres, connective tissue and intramuscular depots. The ontogenesis or the action of putatively important factors controlling muscle development (IGF-II expression, IGF receptors, growth hormone (GH) receptor, myostatin, basic fibroblast growth factor, transforming growth factor-β1, insulin and thyroid hormones) has also been studied on bovine foetal muscle samples and satellite cells. The glucose/insulin axis has been specifically studied in both the bovine adipose tissue and heart. Clearly, cattle, like sheep, are mature species at birth based on their muscle characteristics compared to other mammalian or farm animal species. The different myoblast generations have been well characterised in cattle, including the second generation which is liable to be affected by foetal undernutrition at least in sheep. Interesting genotypes, for example, double-muscled genotype, have been characterised by an altered metabolic and endocrine status associated with a reduced fat mass, specific muscle traits and different foetal characteristics. Finally, the recent development of genomics in cattle has allowed the identification of novel genes controlling muscle development during foetal and postnatal life. Generally, a high muscle growth potential is associated with a reduced fat mass and a switch of muscle fibres towards the glycolytic type. The possibility and the practical consequences of manipulating muscle growth and, hence, body composition by nutritional and hormonal factors are discussed for bovines based on our current biological knowledge.

The GENOTEND chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction

Background

Previous research programmes have described muscle biochemical traits and gene expression levels associated with beef tenderness. One of our results concerning the DNAJA1 gene (an Hsp40) was patented. This study aims to confirm the relationships previously identified between two gene families (heat shock proteins and energy metabolism) and beef quality.

Results

We developed an Agilent chip with specific probes for bovine muscular genes. More than 3000 genes involved in muscle biology or meat quality were selected from genetic, proteomic or transcriptomic studies, or from scientific publications. As far as possible, several probes were used for each gene (e.g. 17 probes for DNAJA1). RNA from Longissimus thoracis muscle samples was hybridised on the chips. Muscles samples were from four groups of Charolais cattle: two groups of young bulls and two groups of steers slaughtered in two different years. Principal component analysis, simple correlation of gene expression levels with tenderness scores, and then multiple regression analysis provided the means to detect the genes within two families (heat shock proteins and energy metabolism) which were the most associated with beef tenderness. For the 25 Charolais young bulls slaughtered in year 1, expression levels of DNAJA1 and other genes of the HSP family were related to the initial or overall beef tenderness. Similarly, expression levels of genes involved in fat or energy metabolism were related with the initial or overall beef tenderness but in the year 1 and year 2 groups of young bulls only. Generally, the genes individually correlated with tenderness are not consistent across genders and years indicating the strong influence of rearing conditions on muscle characteristics related to beef quality. However, a group of HSP genes, which explained about 40% of the variability in tenderness in the group of 25 young bulls slaughtered in year 1 (considered as the reference group), was validated in the groups of 30 Charolais young bulls slaughtered in year 2, and in the 21 Charolais steers slaughtered in year 1, but not in the group of 19 steers slaughtered in year 2 which differ from the reference group by two factors (gender and year). When the first three groups of animals were analysed together, this subset of genes explained a 4-fold higher proportion of the variability in tenderness than muscle biochemical traits.

Conclusion

This study underlined the relevance of the GENOTEND chip to identify markers of beef quality, mainly by confirming previous results and by detecting other genes of the heat shock family as potential markers of beef quality. However, it was not always possible to extrapolate the relevance of these markers to all animal groups which differ by several factors (such as gender or environmental conditions of production) from the initial population of reference in which these markers were identified.

Leptin in farm animals: where are we and where can we go?

Fat affects meat quality, value and production efficiency as well as providing energy reserves for pregnancy and lactation in farm livestock. Leptin, the adipocyte product of the obese (ob) gene, was quickly seen as a predictor of body fat content in animals approaching slaughter and an aid to assessing reproductive readiness in females. Its participation in inflammation and immune responses that help animals survive infection and trauma has clear additional relevance to meat and milk production. Furthermore, almost a decade of discoveries of nucleotide polymorphisms in the leptin and leptin receptor genes has suggested useful applications relating to feed intake regulation, the efficiency of feed use, the composition of growth, the timing of puberty, mammogenesis and mammary gland function and fertility in cattle, pigs and poultry. The current review attempts to summarise where research has taken us in each of these aspects and speculates on where future research might lead.

Chianina beef tenderness investigated through integrated Omics

In the present study we performed an integrated proteomics, interactomics and metabolomics analysis of Longissimus dorsi tender and tough meat samples from Chianina beef cattle. Results were statistically handled as to obtain Pearson's correlation coefficients of the results from Omics investigation in relation to canonical tenderness-related parameters, including Warner Bratzler shear force, myofibrillar degradation (at 48 h and 10 days after slaughter), sarcomere length and total collagen content. As a result, we could observe that the tender meat group was characterized by higher levels of glycolytic enzymes, which were over-phosphorylated and produced accumulation of glycolytic intermediates. Oxidative stress promoted meat tenderness and elicited heat shock protein responses, which in turn triggered apoptosis-like cascades along with PARP fragmentation. Phosphorylation was found to be a key process in post mortem muscle conversion to meat, as it was shown not only to modulate glycolytic enzyme activities, but also mediate the stability of structural proteins at the Z-disk. On the other hand, phosphorylation of HSPs has been supposed to alter their functions through changing their affinity for target interactors. Analogies and breed-specific differences are highlighted throughout the text via a direct comparison of the present results against the ones obtained in a parallel study on Maremmana Longissimus dorsi. It emerges that, while the main cornerstones and the final outcome are maintained, post mortem metabolism in tender and tough meat yielding individuals is subtly modulated via specific higher levels of enzymes and amino acidic residue phosphorylation in a breed-specific fashion, and whether calcium homeostasis dysregulation was a key factor in Maremmana, higher early post mortem phosphocreatine levels in the Chianina tender group could favor a slower and prolonged glycolytic rate, prolonging the extent of the minimum hanging period necessary to obtain tender meat from this breed by a few days.

Cattle genomics and its implications for future nutritional strategies for dairy cattle

The recently sequenced cattle (Bos taurus) genome unraveled the unique genomic features of the species and provided the molecular basis for applying a systemic approach to systematically link genomic information to metabolic traits. Comparative analysis has identified a variety of evolutionary adaptive features in the cattle genome, such as an expansion of the gene families related to the rumen function, large number of chromosomal rearrangements affecting regulation of genes for lactation, and chromosomal rearrangements that are associated with segmental duplications and copy number variations. Metabolic reconstruction of the cattle genome has revealed that core metabolic pathways are highly conserved among mammals although five metabolic genes are deleted or highly diverged and seven metabolic genes are present in duplicate in the cattle genome compared to their human counter parts. The evolutionary loss and gain of metabolic genes in the cattle genome may reflect metabolic adaptations of cattle. Metabolic reconstruction also provides a platform for better understanding of metabolic regulation in cattle and ruminants. A substantial body of transcriptomics data from dairy and beef cattle under different nutritional management and across different stages of growth and lactation are already available and will aid in linking the genome with metabolism and nutritional physiology of cattle. Application of cattle genomics has great potential for future development of nutritional strategies to improve efficiency and sustainability of beef and milk production. One of the biggest challenges is to integrate genomic and phenotypic data and interpret them in a biological and practical platform. Systems biology, a holistic and systemic approach, will be very useful in overcoming this challenge.

Identification of candidate genes related to bovine marbling using protein-protein interaction networks

Complex traits are determined by the combined effects of many loci and are affected by gene networks or biological pathways. Systems biology approaches have an important role in the identification of candidate genes related to complex diseases or traits at the system level. The present study systemically analyzed genes associated with bovine marbling score and identified their relationships. The candidate nodes were obtained using MedScan text-mining tools and linked by protein-protein interaction (PPI) from the Human Protein Reference Database (HPRD). To determine key node of marbling, the degree and betweenness centrality (BC) were used. The hub nodes and biological pathways of our network are consistent with the previous reports about marbling traits, and also suggest unknown candidate genes associated with intramuscular fat. Five nodes were identified as hub genes, which was consistent with the network analysis using quantitative reverse-transcription PCR (qRT-PCR). Key nodes of the PPI network have positive roles (PPARγ, C/EBPα, and RUNX1T1) and negative roles (RXRA, CAMK2A) in the development of intramuscular fat by several adipogenesis-related pathways. This study provides genetic information for identifying candidate genes for the marbling trait in bovine.

Perception in France of the Australian system for the prediction of beef quality (Meat Standards Australia) with perspectives for the European beef sector

Australia has developed the Meat Standards Australia (MSA) grading scheme to predict beef quality for consumers. This system is comprehensive, accurate and scientifically supported. It is based on the development and the use of a research database with a large amount of data, including the use of a large-scale consumer testing system with cuts cooked in different ways as well as information on the corresponding animals, carcasses and cuts. The system is also based on statistical analyses carried out on this database to identify the critical control points of beef palatability which is indicated for individual muscles and for a specific cooking method and aging time. Experts involved in the French beef industry were questioned about their knowledge and views on the application of the MSA system. They recognised many qualities of the MSA system and it was judged as original, relevant and sufficiently mature in its application, and favouring scientifically based prediction of beef quality rather than replying on tradition and perceptions of quality. It was also thought to be credible, flexible and open ended. However, it was still considered to possess some weak points. Thus, while its development in Australia at the farmer and abattoir level has been impressive in a relatively short time, the final delivery of precise quality grades to consumers is still lacking at retail due to only partial implementation of the system. Its adaptability to France would be difficult due to the complexity of the French beef industry and market. But, the program is uniquely innovative and deserves consideration. It will facilitate awareness and induce much needed changes to underpin the preservation and the development of the beef sector in France and eventually in Europe.

Future research priorities for animal production in a changing world

This paper reports the outcomes from an International Workshop on ‘Animal Production in a Changing World’ held in Clermont-Ferrand (INRA-Theix, France) on 9–10 September 2009 in which 35 participants from 15 different countries participated. The main objective was to discuss the main challenges within the livestock sector: its environmental impact and role in global climate change; balancing the need for increased production of animal products coupled with a lower footprint and addressing societal needs in terms of product quality for the consumer. Five key lectures presented the main drivers of animal agriculture: population growth, environmental impact, mitigation and adaptation options, efficiency of production and quality of animal products. The key lectures highlighted the synergies between research needs and strategies dedicated to improving food quality and safety and those devoted to decreasing the environmental impact of ruminant livestock production. After the lectures two discussion groups were set up to discuss the main research priorities in relation to reducing environmental footprint and improving product quality. The main remarks from the group working on product quality were that the existing knowledge is not fully applied, the priorities with regards to quality differ between developing and developed countries and that, as one component in assessing food quality, an environmental index needs to be established taking into account carbon footprint, water and energy use. The discussion within the group working on environmental issues highlighted the importance of focusing on whole life cycle analysis in the mitigation area, while the adaptation strategy should be based on selection for profitable animals under different production systems. In summary, a fundamental shift in designing our production systems is required to help ensure present needs for animal products are met without compromising future generations.

Genetic and environmental effects on meat quality

In order for livestock industries to consistently produce high quality meat, there must be an understanding of the factors that cause quality to vary, as well as the contribution of genetics. A brief overview of meat tenderness is presented to understand how genotype and environment may interact to influence this trait. Essentially, meat tenderness is determined from the contribution of connective tissue, sarcomere length determined pre-rigor and rate of proteolysis during ageing, as well as contributions from intramuscular fat and post-mortem energy metabolism. The influence of mutations in myostatin, the callipyge gene, the Carwell or rib eye muscle gene as well as the calpain system on meat tenderness is presented. Specific examples of interactions between the production or processing environment and genetics are presented for both sheep and cattle. The day-to-day variation in tenderness is evident across experiments and this variation needs to be controlled in order to consistently produce tender meat.