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Myostatin (MSTN), a member of the TGF-β superfamily, is a negative regulator of skeletal muscle mass. We have previously shown that the cell survival/apoptosis pathway is a downstream target of MSTN loss-of-function in mice through the regulation of the expression or abundance of many survival and apoptotic factors. In this study, we used western-blot and quantitative PCR (qPCR) analyses to validate these novel downstream targets of MSTN in double-muscled (DM) cattle v. their controls including 260-day-old foetuses and adult cows from the INRA95 strain. MSTN loss-of-function in DM foetuses and DM cows resulted in a glycolytic shift of the muscles (e.g. upregulation of H-MyBP, PGM1 and SNTA1 and downregulation of H-FABP), activation of cell survival pathway through regulation of some components of the PI3K/Akt pathway (e.g. upregulation of DJ-1 and Gsk-3βser9/Gsk-3βtotal ratio and downregulation of PTEN) and upregulation of cell survival factors translationally controlled tumour protein (14-3-3E, Pink1). We also found a lower abundance of pro-apoptotic transcripts and/or proteins (Caspase-3, caspase-8, caspase-9, BID, ID2 and Daxx) and a higher expression of anti-apoptotic transcripts (Traf2 and Bcl2l2) in DM muscles. All together, these results are in favour of activation of the cell survival pathway and loss of apoptosis pathway within the muscles of DM animals. Alteration of both pathways may increase myonuclear or satellite cell survival, which is crucial for protein synthesis. This could contribute to muscle hypertrophy in DM foetuses and DM cows. [ABSTRACT FROM AUTHOR]

The objective was to compare the production and metabolic responses of 22 Montbéliarde (MONT) and 18 Holstein (HOLS) multiparous cows during the periparturient period, and during a sequential nutritional challenge (SNC), consisting of 4 successive induced short feed restrictions each separated by a refeeding period, to explore breed differences in robustness (ability to maintain lactation function during successive challenges) and resilience (ability to recover after each challenge). Cows were studied from 4 wk before expected calving until 158 ± 9 DIM (mean ± SD). Milk and ECM yields were greater in HOLS than in MONT during both the early (i.e., from calving to wk 10) and mid-lactation (i.e., from wk 18 to 22) periods, whereas BCS was greater in MONT than HOLS. During early lactation, energy balance was lower (5 vs. 16 MJ/d), plasma NEFA (270 vs 163 µM) were greater, for HOLS than MONT, respectively. Cows in third-and-greater lactation secreted more ECM, and had delayed resumption of luteal activity compared with second lactation cows. The SNC started at 87 ± 9 DIM and consisted of a sequence of 4 4-d periods of feed restriction (FR), during which feed allowance was calculated to meet 50% of individual energy requirements (FR1, FR2, FR3, FR4), each of them being followed by an ad libitum intake period. Cows were allowed 10 d of ad libitum intake between FR1 and FR2 to study the recovery and compare it with the recovery following FR4, and 3 d of ad libitum intake between FR2, FR3 and FR4 to study responses to repeated FR. Feed allowance met 59 to 67% of energy requirements during FR1 through FR4, as milk secretion decreased with successive FR. Breed differences in milk secretion persisted throughout the nutritional challenges, but were more pronounced during the first 2 FR: Uncorrected MY was greater for HOLS throughout the entire SNC, whereas ECM and plasma NEFA concentrations and milk fat yield were greater for HOLS than MONT during FR1 and FR2, but not FR3 and FR4, suggesting a reduced ability of HOLS to mobilize and transfer fatty acids into milk with successive FRs, and indicating altered robustness of HOLS to maintain high milk yield. Resilience for ECM yield did not differ between breeds. Cows were able to respond to and recover from the SNC, by decreasing milk secretion during FR, undergoing acute metabolic adaptations to support lactation, and recovering DMI during each refeeding period. Cow rankings for ECM yield were maintained consistently from early lactation throughout the SNC periods (r s = 0.59 to 0.90), suggesting that dairy potential was a major driver of responses during the SNC for both HOLS and MONT., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

In meat-producing animals, preslaughter operations ( e.g ., transportation, mixing unfamiliar animals, food and water deprivation) may be a source of stress with detrimental effects on meat quality. The objective of this work was to study the effect of emotional and physical stress by comparing the transcriptomes of two muscles (M. longissimus thoracis, LT and M. semitendinosus, ST ) in Normand cows exposed to stress ( n = 16) vs . cows handled with limited stress ( n = 16). Using a microarray, we showed that exposure to stress resulted in differentially expressed genes (DEGs) in both muscles (62 DEGs in LT and 32 DEGs in ST, of which eight were common transcription factors (TFs)). Promoter analysis of the DEGs showed that 25 cis transcriptional modules were overrepresented, of which nine were detected in both muscles. Molecular interaction networks of the DEGs targeted by the most represented cis modules helped identify common regulators and common targets involved in the response to stress. They provided elements showing that the transcriptional response to stress is likely to (i) be controlled by regulators of energy metabolism, factors involved in the response to hypoxia, and inflammatory cytokines; and (ii) initiate metabolic processes, angiogenesis, corticosteroid response, immune system processes, and satellite cell activation/quiescence. The results of this study demonstrate that exposure to stress induced a core response to stress in both muscles, including changes in the expression of TFs. These factors could relay the physiological adaptive response of cattle muscles to cope with emotional and physical stress. The study provides information to further understand the consequences of these molecular processes on meat quality and find strategies to attenuate them., Competing Interests: The authors declare that they have no competing interests., (© 2022 Cassar-Malek et al.)

Autophagy (a process of cellular self-eating) is a conserved cellular degradative process that plays important roles in maintaining homeostasis and preventing nutritional, metabolic, and infection-mediated stresses. Surprisingly, little attention has been paid to the role of this cellular function in species of agronomical interest, and the details of how autophagy functions in the development of phenotypes of agricultural interest remain largely unexplored. Here, we first provide a brief description of the main mechanisms involved in autophagy, then review our current knowledge regarding autophagy in species of agronomical interest, with particular attention to physiological functions supporting livestock animal production, and finally assess the potential of translating the acquired knowledge to improve animal development, growth and health in the context of growing social, economic and environmental challenges for agriculture. Abbreviations: AKT: AKT serine/threonine kinase; AMPK: AMP-activated protein kinase; ASC: adipose-derived stem cells; ATG: autophagy-related; BECN1: beclin 1; BNIP3: BCL2 interacting protein 3; BVDV: bovine viral diarrhea virus; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CMA: chaperone-mediated autophagy; CTSB: cathepsin B; CTSD: cathepsin D; DAP: Death-Associated Protein; ER: endoplasmic reticulum; GFP: green fluorescent protein; Gln: Glutamine; HSPA8/HSC70: heat shock protein family A (Hsp70) member 8; IF: immunofluorescence; IVP: in vitro produced; LAMP2A: lysosomal associated membrane protein 2A; LMS: lysosomal membrane stability; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MDBK: Madin-Darby bovine kidney; MSC: mesenchymal stem cells; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; NBR1: NBR1 autophagy cargo receptor; NDV: Newcastle disease virus; NECTIN4: nectin cell adhesion molecule 4; NOD1: nucleotide-binding oligomerization domain 1; OCD: osteochondritis dissecans; OEC: oviduct epithelial cells; OPTN: optineurin; PI3K: phosphoinositide-3-kinase; PPRV: peste des petits ruminants virus; RHDV: rabbit hemorrhagic disease virus; SQSTM1/p62: sequestosome 1; TEM: transmission electron microscopy.

The mutation T3811 → G3811 (TG3811) discovered in the myostatin gene of the Blonde d'Aquitaine breed is suspected of contributing to the outstanding muscularity of this breed. An experiment was designed to estimate the effect of this mutation in an F2 and back-cross Blonde d'Aquitaine × Holstein population. By genotyping all known mutations in the myostatin gene, it was ensured that the TG3811 mutation was indeed the only known mutation segregating in this population. Fifty-six calves (43 F2, 13 back-cross) were intensively fattened and slaughtered at 24.0 ± 1.4 wk of age. The effects of the mutation were estimated by comparing the calves with the [T/T] (n = 18), [T/G] (n = 30), and [G/G] (n = 8) genotypes. Highly significant substitution effects (P < 0.001), above + 1.2 phenotypic SD, were shown on carcass yield and muscularity scores. Birth weight (P < 0.001) was positively affected by the mutation (+0.8 SD) but not growth rate (P = 0.97), while carcass length (P = 0.03), and fatness (P ≤ 0.03) were negatively affected (-0.5 to -0.7 SD). The characteristics of the Triceps brachii muscle were affected by the mutation (P < 0.001), with lower ICDH activity (oxidative) and a higher proportion of myosin type 2X muscle fibers (fast twitch). The effects of the TG3811 mutation were similar to those of other known myostatin mutations, although the Blonde d'Aquitaine animals, which are predominantly [G/G] homozygous, do not exhibit extreme double muscling., (© The Author(s) 2021. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

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.

Milk contains numerous proteins including bioactive molecules that may be important in human nutrition. Thanks to improvements in proteomic methods, hundreds of proteins identified in milk are available through open data from different publications. We gathered these public data to produce an atlas reporting the cow milk proteins. We aggregated data from 20 publications reporting milk proteome and produced an atlas of 4654 unique proteins detected in milk from healthy cows. In this atlas, proteins are categorized according to four milk fractions: skimmed milk, whey, milk fat globule membranes ( MFGM ) and exosomes; and five lactation stages: colostrum period, early lactation, peak of lactation, mid-lactation and drying-off. These 9 protein lists were compared and annotated by Gene Ontology ( GO ) terms to identify the pathways they contribute to, the molecular signatures of different milk fractions and lactation stages. This data article compiles the 4654 cow milk proteins. This atlas may be used by researchers on human nutrition interested in milk protein allergy and/or digestibility in humans, and for milk processing industry. The atlas may be useful to i) find molecular signatures of physiological adaptations of dairy cows, ii) facilitate the isolation of proteins of interest, thanks to the knowledge on their presence in milk fractions and their period of secretion during lactation., (© 2020 The Authors.)

A better knowledge of the bovine milk proteome and its main drivers is a prerequisite for the modulation of bioactive proteins in milk for human nutrition, as well as for the discovery of biomarkers that are useful in husbandry and veterinary medicine. Milk composition is affected by lactation stage and reflects, in part, the energy balance of dairy cows. We aggregated the cow milk proteins reported in 20 recent proteomics publications to produce an atlas of 4654 unique proteins. A multistep assessment was applied to the milk proteome datasets according to lactation stages and milk fractions, including annotations, pathway analysis and literature mining. Fifty-nine proteins were exclusively detected in milk from early lactation. Among them, we propose six milk proteins as putative biomarkers of negative energy balance based on their implication in metabolic adaptative pathways. These proteins are PCK2, which is a gluconeogenic enzyme; ACAT1 and IVD, which are involved in ketone metabolism; SDHA and UQCRC1, which are related to mitochondrial oxidative metabolism; and LRRC59, which is linked to mammary gland cell proliferation. The cellular origin of these proteins warrants more in-depth research but may constitute part of a molecular signature for metabolic adaptations typical of early lactation.

[This corrects the article DOI: 10.1371/journal.pone.0193875.].

Despite the recent advances in transcriptomics, gene expression studies addressing cattle´s skeletal muscle adaptations in response to compensatory growth are warranted, particularly regarding lipid metabolism due to its impact in meat sensory and nutritional traits. In the present study, in comparison to ad libitum feeding, a period of feed restriction was used in order to understand the changes in bull´s lipid metabolism and gene expression of the adipogenic and lipogenic pathways after re-alimentation. Thus, 40 young Alentejana bulls were either fed ad libitum (CG group) from 9 to 18 months of age or subjected to food restriction from 9 to 15 months of age, and fed ad libitum until 24 months of age (DG group). The intramuscular fat (IMF) and total fatty acids (FA) contents were similar between groups. The major FA (>2%) contents were similar (16:0, 16:1c9, 18:1c9 and 18:2n-6) between treatments with the exception of 18:0 content that was 15% lower in DG than in CG and 20:4n-6 that tended to be greater on DG bulls. Regarding minor FA (<2%), the DG group presented greater proportions (P<0.01) of 17:1c9, 18:1t9, 18:1t10 (, 18:1c11), 18:1c13, 18:3n-6, 22:0, 22:4n-6 and 22:6n-3 and lower (P<0.05) proportions of 20:0, 18:1t16+c14, and branched chain FA (iso-15:0, anteiso-15:0, iso-16:0 and anteiso-17:0) than the CG group. Delta-9 desaturase activity indices were consistently greater (P<0.05) in DG, when compared to the CG group. Regarding microarray analysis, differentially expressed genes between CG and DG bulls were grouped in 5 main biological functions: lipid and nucleic acid metabolisms, small molecule biochemistry, molecular transport and translational modification. Discontinuous growth down-regulated the expression of ACACB (FC (fold-change) = 1.32), FABP3 (FC = 1.45), HADHA (FC = 1.41) and SLC37A4 (FC = 1.40) genes, when compared to the CG system (FDR<0.05). In contrast, in the CG bulls, the expression of ELOVL5 (FC = 1.58) and FASN (FC = 1.71) was down-regulated when compared to DG bulls. These results were confirmed to be significant (P<0.05) in the case of ELOVL5, FASN and SLC37A4, and almost significant for FABP3 by qRT-PCR analysis. The SCD1 and SCD5 gene expressions were not found to be affected by growth path. These results contribute to the still scarce knowledge about the mechanisms involved in fatty acid metabolism during compensatory growth which have decisive role on meat quality produced in Mediterranean areas.

The Blonde d'Aquitaine (BA) is a French cattle breed with enhanced muscularity, partly attributable to a MSTN mutation. The BA m. Semitendinosus has a faster muscle fibre isoform phenotype comprising a higher proportion of fast type IIX fibres compared to age-matched Charolais (CH). To better understand the molecular network of modifications in BA compared to CH muscle, we assayed the transcriptomes of the m. Semitendinosus at 110, 180, 210 and 260 days postconception (dpc). We used a combination of differential expression (DE) and regulatory impact factors (RIF) to compare and contrast muscle gene expression between the breeds. Prominently developmentally regulated genes in both breeds reflected the replacement of embryonic myosin isoforms ( MYL4 , MYH3 ) with adult isoforms ( MYH1 ) and the upregulation of mitochondrial metabolism ( CKMT2 , AGXT2L1 ) in preparation for birth. However, the transition to a fast, glycolytic muscle phenotype in the MSTN mutant BA is detectable through downregulation of various slow twitch subunits ( TNNC1 , MYH7 , TPM3 , CSRP3 ) beyond 210 dpc, and a small but consistent genome-wide reduction in mRNA encoding the mitoproteome. Across the breeds, NRIP2 is the regulatory gene possessing a network change most similar to that of MSTN ., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2017. Published by The Company of Biologists Ltd.)

Even though abundance of Hsp27 is the highest in skeletal muscle, the relationships between the expression of HspB1 (encoding Hsp27) and muscle characteristics are not fully understood. In this study, we have analysed the effect of Hsp27 inactivation on mouse development and phenotype. We generated a mouse strain devoid of Hsp27 protein by homologous recombination of the HspB1 gene. The HspB1-/- mouse was viable and fertile, showing neither apparent morphological nor anatomical alterations. We detected a gender dimorphism with marked effects in males, a lower body weight (P < 0.05) with no obvious changes in the growth rate, and a lower plasma lipids profile (cholesterol, HDL and triglycerides, 0.001 < P< 0.05). The muscle structure of the animals was examined by optical microscopy and transmission electron microscopy. Not any differences in the characteristics of muscle fibres (contractile and metabolic type, shape, perimeter, cross-sectional area) were detected except a trend for a higher proportion of small fibres. Different myosin heavy chains electrophoretic profiles were observed in the HspB1-/- mouse especially the presence of an additional isoform. Electron microscopy revealed ultrastructural abnormalities in the myofibrillar structure of the HspB1-/- mouse mutant mice (e.g. destructured myofibrils and higher gaps between myofibrils) especially in the m. Soleus. Combined with our previous data, these findings suggest that Hsp27 could directly impact the organization of muscle cytoskeleton at the molecular and ultrastructural levels.

Hsp27-encoded by HspB1- is a member of the small heat shock proteins (sHsp, 12-43 kDa (kilodalton)) family. This protein is constitutively present in a wide variety of tissues and in many cell lines. The abundance of Hsp27 is highest in skeletal muscle, indicating a crucial role for muscle physiology. The protein identified as a beef tenderness biomarker was found at a crucial hub in a functional network involved in beef tenderness. The aim of this study was to analyze the proteins impacted by the targeted invalidation of HspB1 in the Tibialis anterior muscle of the mouse . Comparative proteomics using two-dimensional gel electrophoresis revealed 22 spots that were differentially abundant between HspB1 -null mice and their controls that could be identified by mass spectrometry. Eighteen spots were more abundant in the muscle of the mutant mice, and four were less abundant. The proteins impacted by the absence of Hsp27 belonged mainly to calcium homeostasis (Srl and Calsq1), contraction (TnnT3), energy metabolism (Tpi1, Mdh1, PdhB, Ckm, Pygm, ApoA1) and the Hsp proteins family (HspA9). These data suggest a crucial role for these proteins in meat tenderization. The information gained by this study could also be helpful to predict the side effects of Hsp27 depletion in muscle development and pathologies linked to small Hsps.

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.

Thanks to genomics, we have previously identified markers of beef tenderness, and computed a bioinformatic analysis that enabled us to build an interactome in which we found Hsp27 at a crucial node. Here, we have used a network-based approach for understanding the contribution of Hsp27 to tenderness through the prediction of its interactors related to tenderness. We have revealed the direct interactors of Hsp27. The predicted partners of Hsp27 included proteins involved in different functions, e.g. members of Hsp families (Hsp20, Cryab, Hsp70a1a, and Hsp90aa1), regulators of apoptosis (Fas, Chuk, and caspase-3), translation factors (Eif4E, and Eif4G1), cytoskeletal proteins (Desmin) and antioxidants (Sod1). The abundances of 15 proteins were quantified by Western blotting in two muscles of HspB1-null mice and their controls. We observed changes in the amount of most of the Hsp27 predicted targets in mice devoid of Hsp27 mainly in the most oxidative muscle. Our study demonstrates the functional links between Hsp27 and its predicted targets. It suggests that Hsp status, apoptotic processes and protection against oxidative stress are crucial for post-mortem muscle metabolism, subsequent proteolysis, and therefore for beef tenderness.

Genetic selection in favor of muscle growth at the expense of fat should affect characteristics of muscles, and therefore beef quality. This study was conducted with two extreme groups of six animals selected among 64 Charolais young bulls ranked according to their genetic potential for muscle growth. Muscle characteristics were assessed in Rectus abdominis (RA, slow oxidative) and Semitendinosus (ST, fast glycolytic) muscles. Intramuscular fat content and proportions of myosin heavy chains I (slow) and IIA (fast oxido-glycolytic) and certain indicators of oxidative metabolism (activities of citrate synthase (CS), isocitrate dehydrogenase and cytochrome-c oxidase (COX); expression of H-fatty acid binding protein (FABP)) were higher in RA than in ST muscle. Genetic selection for muscle growth reduced intramuscular fat content and the activities of some oxidative metabolism indicators (namely CS, COX only). The positive correlation between muscle triacylglycerol content and A-FABP messenger RNA level (a marker of adipocyte differentiation) (r = 0.53, P < 0.05) suggests that A-FABP may be a good marker of the ability of bovines to deposit intramuscular fat. In conclusion, the metabolic muscle characteristics which respond to the selection process in favor of muscle growth clearly differ from the muscle characteristics which allow muscle types to be differentiated., (© 2012 The Authors. Animal Science Journal © 2012 Japanese Society of Animal Science.)

Gene expression profiles of bovine longissimus muscle as affected by dietary n-3 v. n-6 fatty acid (FA) intervention were analysed by microarray pre-screening of >3000 muscle biology/meat quality-related genes as well as subsequent quantitative RT-PCR gene expression validation of genes encoding lipogenesis-related transcription factors (CCAAT/enhancer-binding protein β, sterol regulatory element-binding transcription factor 1), key-lipogenic enzymes (acetyl-CoA carboxylase α (ACACA), fatty acid synthase (FASN), stearoyl-CoA desaturase (SCD)), lipid storage-associated proteins (adipose differentiation-related protein (ADFP)) and muscle biology-related proteins (cholinergic receptor, nicotinic, α1, farnesyl diphosphate farnesyl transferase 1, sema domain 3C (SEMA3C)). Down-regulation of ACACA (P = 0·00), FASN (P = 0·09) and SCD (P = 0·02) gene expression upon an n-3 FA intervention directly corresponded to reduced SFA, MUFA and total FA concentrations in longissimus muscle, whereas changes in ADFP (P = 0·00) and SEMA3C (P = 0·05) gene expression indicated improved muscle function via enhanced energy metabolism, vasculogenesis, innervation and mediator synthesis. The present study highlights the significance of dietary n-3 FA intervention on muscle development, maintenance and function, which are relevant for meat quality tailoring of bovine tissues and modulating animal production-relevant physiological processes.

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.

We have recently reported that maturation of the skeletal muscle is delayed in cloned calves during their first year postnatally. This delay could originate from perturbations in fetal myogenesis. The aim of this study was to evaluate the developmental characteristics of muscle in clones versus animals derived from conventional reproduction. We have characterized the anatomical and biochemical properties of the Semitendinosus muscle of clones versus controls at day 60 and day 260. We have analyzed the contractile and metabolic properties of muscle fibers by measuring the abundance of myosin heavy chain (MyHC) isoforms and activities of metabolic enzymes (LDH, PFK, COX, CS, ICDH), respectively. The spatial repartition of some components of the extracellular matrix (collagen types I, IV, VI, chondroitin-6-sulfate, decorin, and tenascin-X) was also studied. At day 60 we found lower numbers and structural organization of fibers, and a delay in the setup of the extracellular matrix. IGF-2 transcript abundance was lower in clones than in their controls. There was no difference in the expression of VEGF (a growth factor regulating vascularization and myogenesis) and its receptor. At day 260 the muscles of fetal clones have not reached the same degree of differentiation than controls as shown by their lower energy metabolisms and their MyHC pattern. These results show for the first time that disturbances in myogenesis occur early in fetal life in cloned cattle.

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.

Genomics has brought with it a true biological revolution and can be applied to all areas of life sciences. The advent of genomics is thus linked to the development of high-throughput techniques which allows the genome of organisms as a whole to be studied. The first high-throughput techniques to be developed were sequencing methods. These advances will allow new approaches to a variety of problems in biology. For instance, the emerging fields of genomic medicine in humans and genomic selection in livestock are promising. After the sequencing of genomes, genomics has shifted to the study of gene expression and function. This is called the "post-genomic area" by some authors or "functional genomics" by others. The most recent "omics" to be developed are associated with the study of the metabolism (e.g. metabolomics). Integrative "omics" approaches (e.g. nutrigenomics) are based on the association of the omics tools at different levels (DNA, RNA, proteins, metabolites) for a specific objective (here nutrition). In terms of perspectives, it is likely that methods for collecting data will outstrip our capacity to adequately analyse these data. So scientists must develop bioinformatic tools and methods to overcome this difficulty. In addition, high-throughput techniques need to be developed in physiology in order to match the increasing amount of genomic information with true biological data. Finally, there is no doubt that all these new approaches will allow important new genes and novel biological mechanisms to be discovered. Physiological models with invalidated or over-expressed genes will be precious tools to check these new biological discoveries.