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For beef cattle research, a main objective is to control concomitantly the development of muscles and the qualities of beef cuts. Beef quality is a complex phenotype that is only detectable after slaughter and is highly variable. The beef industry is in need of tools to estimate beef quality of live cattle or online in abattoirs, with specific attention towards sensory attributes (tenderness, juiciness, flavour, and colour). Identification of relevant genetic and genomic markers is ongoing, especially for tenderness--a top priority quality attribute. In this paper, we describe the steps of an expression marker-based strategy to improve beef sensory quality, from the discovery of biomarkers that identify consistent beef and the biological functions governing beef tenderness to the integration of the knowledge into detection tests for desirable animals. These tools should soon be available for the management of sensory quality in the beef production chain for meeting market's demands and assuring good quality standards.

The knowledge of the molecular organization of living organisms evolved considerably during the last years. The methodologies associated also progressed with the development of the high-throughput sequencing (SNP array, RNAseq, etc.) and of genomic tools allowing the simultaneous analysis of hundreds or thousands of genes, proteins or metabolites. In farm animals, some proteins, mRNAs or metabolites whose abundance has been associated with meat quality traits have been detected in pig, cattle, chicken. They constitute biomarkers for the assessment and prediction of qualities of interest in each species, with potential biomarkers across species. The ongoing development of rapid methods will allow their use for decision-making and management tools in slaughterhouses, to better allocate carcasses or cuts to the appropriate markets. Besides, their application on living animals will help to improve genetic selection and to adapt a breeding system to fulfill expected quality level. The ultimate goal is to propose effective molecular tools for the management of product quality in meat production chains., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

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.

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.

Beef tenderness is a very complex and multifactorial sensorial meat quality trait, which depends partly on muscle characteristics. This tissue is very variable according to animal type (age, breed and sex) and rearing conditions. Consequently, beef tenderness exhibits a great variability. Different research programs have revealed several genes or proteins which could be good markers of beef tenderness. In order to validate the relation of these markers with beef tenderness on a large population of bovines, it is necessary to have a large-scale and trusty technique which can access different quantities of proteins related to tenderness. In this study we firstly compared Western-Blot and Dot-Blot. Secondly, we evaluated Dot-Blot technical and biological capabilities for the quantification of protein biomarkers. The results demonstrated that the Dot-Blot technique with fluorescence detection presents numerous interests. This technique allows a good reproducibility and permits the simultaneous analysis of a large number of samples. The Dot-Blot technique defined and validated in this study can be used for protein biomarkers analyses, notably to predict beef tenderness. Another major result of this study is that about 5 to 10 animals per group are required to detect large differences (>1.5) in biomarker expression between tender and tough beef, whereas much larger numbers of animals (10 to 30) are required to detect smaller differences (about 1.2 to 1.3) taking into account the biological variability of these markers.

This work investigated the metabolic basis for the variability of carcass and i.m. adiposity in cattle. Our hypothesis was that the comparison of extreme breeds for adiposity might allow for the identification of some metabolic pathways determinant for carcass and i.m. adiposity. Thus, 23- to 28-mo-old steers of 3 breeds, 2 with high [Angus or Japanese Black x Angus (J. Black cross)] and 1 with low (Limousin) i.m. and carcass adiposity, were used to measure activities or mRNA levels, or both, of enzymes involved in de novo lipogenesis [acetyl-coA carboxylase, fatty acid synthase (FAS), glucose-6-phosphate dehydrogenase (G6PDH), malic enzyme], circulating triacylglycerol (TAG) uptake (lipoprotein lipase), and fatty acid esterification (glycerol-3-phosphate dehydrogenase), as well as the mRNA level of leptin, an adiposity-related factor. In a first study, enzyme activities were assayed in the s.c. adipose tissue (AT), the oxidative rectus abdominis, and the glycolytic semitendinosus muscles from steers finished for 6 mo. Compared with Angus or J. Black cross, Limousin steers had a 27% less (P = 0.003) rib fat thickness, and 23 and 29% less (P < or = 0.02) FAS and G6PDH activities in s.c. AT. In rectus abdominis and semitendinosus, the 75% less (P < 0.001) TAG content was concomitant with 50% less (P < 0.001) G6PDH activity. In a second study, enzyme activities plus mRNA levels were assayed in an oxido-glycolytic muscle, the longissimus thoracis (LT), in the i.m. AT dissected from LT, and in s.c. AT from the same Limousin steers and from Angus steers finished for 10 mo. Compared with Angus, the 50% less (P < 0.001) rib fat thickness in Limousin contrasted with the 1.1- to 5.8-fold greater (P < or = 0.02) mRNA levels or activities, or both, of acetyl-coA carboxylase, G6PDH, lipoprotein lipase, and glycerol-3-phosphate dehydrogenase in s.c. AT. Conversely, the 90% less (P < 0.001) TAG content in Limousin LT was concomitant to the 79 and 83% less (P < or = 0.002) G6PDH activity and leptin mRNA level. Such differences could arise from a greater number of adipocytes in LT from Angus steers because no difference was found between Limousin and Angus for G6PDH activity and leptin mRNA in i.m. AT. We conclude that FAS and G6PDH in s.c. AT could be involved in differences in carcass adiposity, but this relationship disappeared when the fatness increased strongly. Leptin and G6PDH are related to the expression of marbling whatever the body condition and thus could be relevant indicators of marbling in beef cattle.

Marbling is an important criterion for beef quality grading in many countries. The purpose of the current study was to utilize the natural genetic variation to identify major metabolic indicators of marbling in cattle differing in genotypes. Rectus abdominis (RA, oxidative), semitendinosus (glycolytic), and longissimus thoracis (LT, oxido-glycolytic) muscles were taken from steers of different genotypes that expressed high [Angus, n = 16; and crossbred (Angus x Japanese Black), n = 10] or low (Limousin, n = 12) levels of marbling in their meat. Muscles from Angus and crossbred steers were characterized, as expected, by a greater triacylglycerol (TAG) content (P < 0.001) and also by greater protein contents of fatty acid-binding protein specific for heart and muscles (H-FABP; P < 0.001 for RA and P < 0.05 for LT muscle) or for adipocytes (A-FABP; P < 0.001 for RA and LT muscles). Moreover, oxidative enzyme activities (beta-hydroxyacyl-CoA dehydrogenase, citrate synthase, isocitrate dehydrogenase, cytochrome-c oxidase) were greater (P < 0.01 to 0.001) in the 3 muscles studied, whereas glycolytic enzyme activities (phosphofructokinase and lactate dehydrogenase) were lower (P < 0.001) in RA muscle in Angus and crossbred steers compared with Limousin steers. Significant correlations were observed between TAG content and H- and A-FABP protein contents, and oxidative (r > or = +0.55, P < 0.001) or glycolytic enzyme activities (r > or = -0.47, P < 0.001), when the 3 genotypes and muscles studied were considered as a whole. In addition, A-FABP protein content and some oxidative enzyme activities were significantly correlated with TAG content independently of the genotype and muscle effects. In conclusion, A-FABP protein content, as well as oxidative enzyme activities, may be used as indicators of the ability of steers from extreme genotypes to deposit intramuscular fat.

To identify new molecular markers of beef sensory quality, the transcriptomes of Longissimus thoracis muscle from 25 Charolais bull calves were analyzed using microarrays and compared between high and low meat quality groups; 215 genes were differentially expressed according to tenderness, juiciness, and/or flavor. Among these, 23 were up-regulated in the tenderest, juiciest, and tastiest meats, and 18 were highly correlated with both flavor and juiciness (e.g., PRKAG1), explaining up to 60% of their variability. Nine were down-regulated in the same meats, but only DNAJA1 [the results relating to DNAJA1 and its relationship with tenderness have been patented (Genomic marker for meat tenderness; Patent EP06300943.5, September 12, 2006)], which encodes a heat shock protein, showed a strong negative correlation with tenderness that alone explained 63% of its variability. This protein, known for its anti-apoptotic role, could be involved in meat aging. Thus, DNAJA1 could constitute a new marker of beef sensory quality.

cDNA arrays have proven to be useful tools to screen gene expression in many animal species including livestock species. A collaborative program was launched to construct a ruminant cDNA collection, representative of three tissues: Muscle, Embryo and Mammary gland, named MEM. This collection gathers clones mainly arising from 3 non-normalised cDNA libraries: a directed bovine muscle library, a 14-day-old bovine embryo library and a goat lactating mammary library. It is made up of 1896 clones (637 muscle, 882 embryo and 377 mammary cDNAs), selected after sequencing and bioinformatic analyses. Amplification products yielded from these clones as well as controls were printed onto Nylon membranes to generate macroarrays. Hybridisation with relevant cDNA targets allowed checking the location of about 50 cDNAs and the specificity of each sub-set of the repertoire. Macroarrays were hybridised with radiolabelled cDNA complex targets from five different tissues (muscle, embryo, mammary gland, adipose tissue and oocyte). Both somatic and germinal complex targets gave valid hybridisation signals with 45 to 80% of the printed probes. This specific cDNA collection now provides a powerful tool for transcriptomic studies with the ultimate objective to better understand physiological and metabolic functions in ruminants. It will be subsequently included into a forthcoming larger collection.

Abstract: Array technology has been increasingly used to monitor global gene expression patterns in various tissues and cell types. However, applications to muscle development and pathology as well as meat production in livestock species have been hampered by the lack of appropriate cDNA collections. To overcome this problem, a directed cDNA library was constructed starting from 23 muscles of meat-producing bovines to derive a collection of 3573 clones. A preliminary sequence characterization of this collection indicated that the most abundant transcripts correspond to genes encoding proteins involved in energy metabolism (COX and NADH dehydrogenase subunits) and belonging to the contractile apparatus (myosin chains and troponin isoforms). From this cDNA library, we selected a set of 435 clones representing 340 unique genes, of which 24 were novel. This collection was subsequently completed with 75 specific cDNA probes for genes of interest already studied in our laboratory. The bovine ‘muscle’ cDNA repertoire thus designed was spotted onto a nylon membrane (macroarray) in order to test its utility to further investigate the transcriptome of bovine muscles in relation to meat quality traits. It is also anticipated that this type of collection might be useful for the study of chronic myologic diseases in other mammalian species, including humans. [Copyright &y& Elsevier]