Improving the traits that underlie meat quality is a major challenge in the beef industry. The objective of this paper was to detect QTL linked to sensory meat quality traits in 3 French beef cattle breeds. We genotyped 1,059, 1,219, and 947 young bulls and their sires belonging to the Charolais, Limousin, and Blonde d'Aquitaine breeds, respectively, using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). After estimating relevant genetic parameters using VCE software, we performed a linkage disequilibrium and linkage analysis on 4 meat traits: intramuscular fat content, muscle lightness, shear force, and tenderness score. Heritability coefficients largely ranged between 0.10 and 0.24; however, they reached a maximum of 0.44 and 0.50 for intramuscular fat content and tenderness score, respectively, in the Charolais breed. The 2 meat texture traits, shear force and tenderness score, were strongly genetically correlated (-0.91 in the Charolais and Limousin breed and -0.86 in the Blonde d'Aquitaine breed), indicating that they are 2 different measures of approximately the same trait. The genetic correlation between tenderness and intramuscular fat content differed across breeds. Using a significance threshold of 5 × 10(-4) for QTL detection, we found more than 200 significant positions across the 29 autosomal chromosomes for the 4 traits in the Charolais and Blonde d'Aquitaine breeds; in contrast, there were only 78 significant positions in the Limousin breed. Few QTL were common across breeds. We detected QTL for intramuscular fat content located near the myostatin gene in the Charolais and Blonde d'Aquitaine breeds. No mutation in this gene has been reported for the Blonde d'Aquitaine breed; therefore, it suggests that an unknown mutation could be segregating in this breed. We confirmed that, in certain breeds, markers in the calpastatin and calpain 1 gene regions affect tenderness. We also found new QTL as several QTL on chromosome 3 that are significantly associated with meat tenderness in the Blonde d'Aquitaine breed. Overall, these results greatly contribute to the goal of building a panel of markers that can be used to select animals of high meat quality.

Consumers demand healthy and palatable meat, both factors being affected by fat composition. However, red meat has relatively high concentration of saturated fatty acids and low concentration of the beneficial polyunsaturated fatty acids. To select animals prone to produce particular fat types, it is necessary to identify the genes influencing muscle lipid composition. This paper describes an association study in which a large panel of candidate genes involved in adipogenesis, lipid metabolism and energy homoeostasis was tested for effects on fat composition in 15 European cattle breeds. Sixteen genes were found to have significant effects on different lipid traits, and among these, CFL1 and MYOZ1 were found to have large effects on the ratio of 18:2/18:3, CRI1 on the amount of neutral adrenic acid (22:4 n-6), MMP1 on docosahexaenoic acid (22:6 n-3) and conjugated linoleic acid, PLTP on the ratio of n-6:n-3 and IGF2R on flavour. Several genes - ALDH2, CHRNE, CRHR2, DGAT1, IGFBP3, NEB, SOCS2, SUSP1, TCF12 and FOXO1 - also were found to be associated with both lipid and organoleptic traits although with smaller effect. The results presented here help in understanding the genetic and biochemical background underlying variations in fatty acid composition and flavour in beef.

Variations in meat quality traits are under complex genetic control and improvement has been hampered by the difficulty in their measurement. Several QTL have been reported for different meat quality related traits, but few genes have been described which explain large amounts of the phenotypic variation. The use of single nucleotide polymorphism (SNP) marker panels with predictive value for carcass traits have been evaluated for cattle and SNP are commercially available even though their predictive accuracy may be low in different breeds. To identify new molecular markers for meat quality, an association study was performed in 15 breeds of cattle using 389 SNP belonging to 206 candidate genes known to be involved in muscle development, metabolism and structure. Fifty-four SNP belonging to 20 different genes were found associated with different growth, carcass and meat quality traits. Some of them were novel associations and other were replications of known associations. Among the former, the gene-network associated with the calpain/calpastatin system was shown to be associated with meat texture, although small effects are found for the examined polymorphisms. Novel associations also included SNP in AANAT which was associated with collagen (P=0.006), CAST with fatty acid muscle composition (P=0.00003), CYP1A1 with juiciness (P=0.0005), DGAT2 with physical traits (P=0.0009) and lipid content (P=0.01) in muscle, MADH3 with the myofibrilar fragmentation index (MFI) (P=0.01), NEB with weight (P=0.00009), PCSK1 with juiciness (P=0.002), PLOD3 with carcass performance (P=0.0009) and fatty acids (P=0.04), and PGAM2 and VIM with post-mortem maturation (P=0.00008 and 0.000005, respectively). These data provide a starting point to investigate the complex gene-networks underlying economically important traits which are of importance to the beef industry for the improvement of production efficiency and meat quality.

The objectives of the study were to evaluate allelic frequencies and to test the association of polymorphisms in the calpastatin (CAST) and mu-calpain (CAPN1) genes with meat tenderness in 3 French beef breeds. A total of 1,114 Charolais, 1,254 Limousin, and 981 Blonde d'Aquitaine purebred young bulls were genotyped for 3 SNP in the CAST gene and 4 SNP in the CAPN1 gene. Two of these markers, 1 in each gene, can be found in Australian or American commercial genetic tests. Others have previously been reported in American studies or are newly evidenced SNP. The quantitative traits studied were Warner-Bratzler shear force and a tenderness score evaluated by trained sensory panels. All the SNP were informative in the 3 breeds. Associations of individual markers or haplotypes with traits were analyzed. The results differed in the 3 breeds. The G allele of a CAST marker (position 97574679 on Btau4.0) was found to exert a significant effect on the shear force (+0.18 phenotypic SD; RSD) and tenderness score (-0.22 RSD) in the Blonde d'Aquitaine breed. In the same breed, this marker was associated with another CAST SNP (position 97576054 on Btau4.0) such that the GA haplotype appeared to be associated with tougher meat. Two CAPN1 markers (positions 45221250 and 45241089 on Btau4.0) had a significant effect on both traits in the Charolais breed (from |0.11| to |0.25| RSD). In the same breed, these markers were associated with another CAPN1 SNP (position 45219395 on Btau4.0) such that the ACA and AGG haplotypes appeared to be associated with a tender meat and a tougher meat, respectively. Consequently, the present results indicate that the effects of the markers studied are breed-specific and cannot be extended to all Bos taurus breeds. Further studies are also required to identify other more appropriate markers for French beef breeds.

The availability of genetic tests to detect different mutations in the myostatin gene allows the identification of heterozygous animals and would warrant the superiority of these animals for slaughter performance if this superiority is confirmed. Thus, 2 mutations of this gene, Q204X and nt821, were studied in 3 French beef breeds in the program Qualvigène. This work was done with 1,114 Charolais, 1,254 Limousin, and 981 Blonde d'Aquitaine young bulls from, respectively, 48, 36, and 30 sires and slaughtered from 2004 to 2006. In addition to the usual carcass traits recorded at slaughter (e.g., carcass yield, muscle score), carcass composition was estimated by weighing internal fat and dissecting the 6th rib. The muscle characteristic traits analyzed were lipid and collagen contents, muscle fiber section area, and pH. Regarding meat quality, sensory qualities of meat samples were evaluated by a taste panel, and Warner-Bratzler shear force was measured. Deoxyribonucleic acid was extracted from the blood samples of all calves, the blood samples of 78% of the dams, and the blood or semen samples of all the sires. Genotypes were determined for 2 disruptive mutations, Q204X and nt821. Analyses were conducted by breed. The superiority of carcass traits of calves carrying one copy of the mutated allele (Q204X or nt821) over noncarrier animals was approximately +1 SD in the Charolais and Limousin breeds but was not significant in the Blonde d'Aquitaine. In the Charolais breed, for which the frequency was the greatest (7%), young bulls carrying the Q204X mutation presented a carcass with less fat, less intramuscular fat and collagen contents, and a clearer and more tender meat than those of homozygous-normal cattle. The meat of these animals also had slightly less flavor. Also in the Charolais breed, 13 of 48 sires were heterozygous. For each sire, the substitution effect of the wild allele by the mutant allele was approximately +1 SD for carcass conformation and yield, showing that the estimate of the substitution effect was independent of family structure, as it ought to be for a causal mutation. These results illustrate the challenge of using genetic tests to detect animals with the genetic potential for greater grades of carcasses and meat quality.

Italian Maremmana, Turkish Grey and Hungarian Grey breeds belong to the same Podolic group of cattle, have a similar conformation and recently experienced a similar demographic reduction. The aim of this study was to assess the relationship among the analysed Podolic breeds and to verify whether their genetic state reflects their history. To do so, approximately 100 single nucleotide polymorphisms (SNPs) were genotyped on individuals belonging to these breeds and compared to genotypes of individuals of two Italian beef breeds, Marchigiana and Piemontese, which underwent different selection and migration histories. Population genetic parameters such as allelic frequencies and heterozygosity values were assessed, genetic distances calculated and assignment test performed to evaluate the possibility of recent admixture between the populations. The data show that the physical similarity among the Podolic breeds examined, and particularly between Hungarian Grey and Maremmana cattle that experienced admixture in the recent past, is mainly morphological. The assignment of individuals from genotype data was achieved using Bayesian inference, confirming that the set of chosen SNPs is able to distinguish among the breeds and that the breeds are genetically distinct. Individuals of Turkish Grey breed were clearly assigned to their breed of origin for all clustering alternatives, showing that this breed can be differentiated from the others on the basis of the allelic frequencies. Remarkably, in the Turkish Grey there were differences observed between the population of Enez district, where in situ conservation studies are practised, and that of Bandirma district of Balikesir, where ex situ conservation studies are practised out of the original raising area. In conclusion, this study demonstrates that molecular data could be used to reveal an unbiased view of past events and provide the basis for a rational exploitation of livestock, suggesting appropriate cross-breeding plans based on genetic distance or breeding strategies that include the population structure.

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.

La tendreté de la viande bovine présente une forte variabilité non maîtrisée qui est à l’origine d’une insatisfaction des consommateurs. De plus, il n’existe pas d’outils fiables et utilisables par la filière bovine pour prédire ce critère de qualité. Depuis de nombreuses années, l’implication des caractéristiques musculaires (collagène, lipides, systèmes protéolytiques, fibres) dans la tendreté a été bien étudiée. Toutefois, lorsque ces caractéristiques sont maîtrisées, il demeure encore une variabilité élevée et non expliquée. Afin d’approfondir les connaissances sur l’origine de cette variabilité, des études de génomique fonctionnelle ont été conduites durant les 10 dernières années. Ces approches permettent de rechercher sans a priori des gènes ou des protéines dont l’expression varie en fonction de la tendreté de la viande. Ces études ont permis d’établir une liste de marqueurs biologiques de la tendreté dont l’analyse phénotypique pourra venir compléter les analyses génétiques de recherche de polymorphismes.

Beef tenderness exhibits a high and uncontrolled variability which is one reason for the consumer's dissatisfaction. Moreover, the beef industry does not have predictive tools to measure meat tenderness. During the last few years, the impact of muscular characteristics such as collagen, lipids, proteolytic systems and fibres on meat tenderness has been studied. however, there is still an uncontrolled highly variable meat tenderness even when these muscular characteristics are under control. In order to understand this variability, some genomic studies have been conducted during the last 10 years. They allow the screening, without a priori, of genes and proteins whose expression is variable with meat tenderness. These studies have established a list of tenderness biomarkers whose phenotypic analyses can complete the polymorphism analyses. This article summarises the current knowledge concerning the phenotypic approach, and will be followed by a second article which will present the genetic approach of beef tenderness markers.

A large number of putative single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project. However, few of these have been validated and many will turn out to be sequencing artefacts or have low minor allele frequencies. In addition, there is little information available on SNPs within coding regions, which are likely to be responsible for phenotypic variation. Therefore, additional SNP discovery is necessary to identify and validate polymorphisms both in specific genes and genome-wide. Sequence-tagged sites within 286 genes were resequenced from a panel of animals representing a wide range of European cattle breeds. For 80 genes, no polymorphisms were identified, and 672 putative SNPs were identified within 206 genes. Fifteen European cattle breeds (436 individuals plus available parents) were genotyped with these putative SNPs, and 389 SNPs were confirmed to have minor allele frequencies above 10%. The genes containing SNPs were localized on chromosomes by radiation hybrid mapping and on the bovine genome sequence by Blast. Flanking microsatellite loci were identified, to facilitate the alignment of the genes containing the SNPs in relation to mapped quantitative trait loci. Of the 672 putative SNPs discovered in this work, only 11 were found among the validated SNPs and 100 were found among the approximately 2.3 million putative SNPs currently in dbSNP. The genes studied in this work could be considered as candidates for traits associated with beef production and the SNPs reported will help to assess the role of the genes in the genetic control of muscle development and meat quality. The allele frequency data presented allows the general utility of the SNPs to be assessed.

Genomics has brought with it a true biological revolution and has a great number of potential applications in all areas of life sciences. Thanks to the simultaneous analysis of vast numbers of genes, proteins and metabolites, genomics opens up new perspectives for a host of research programs in the genetic and physiological control of beef quality especially tenderness. Indeed, tenderness is a complex trait which depends on interplay between a great number of interacting genes associated with connective tissue, the contractile and metabolic characteristics of muscle fibres as well as proteolysis during aging. The completed bovine genome sequence and the availability of high-throughput genotyping chips help the discovery of genetic markers for beef quality and the development of marker-assisted selection and of "genomic selection". Meanwhile, transcriptomics and proteomics have favoured the study of muscle development and of muscle hypertrophy as well as the discovery of new biological markers of beef quality. The development of metabolomics is in progress. Thanks to the development of genomics, the new challenge is now to develop high-throughput pheno-typing as well as modelling approaches to better predict beef quality from the different genomic markers so far identified.

The effectiveness of single nucleotide polymorphisms (SNPs) for the assignment of cattle to their source breeds was investigated by analysing a panel of 90 SNPs assayed on 24 European breeds. Breed assignment was performed by comparing the Bayesian and frequentist methods implemented in the STRUCTURE 2.2 and GENECLASS 2 software programs. The use of SNPs for the reallocation of known individuals to their breeds of origin and the assignment of unknown individuals was tested. In the reallocation tests, the methods implemented in STRUCTURE 2.2 performed better than those in GENECLASS 2, with 96% vs. 85% correct assignments respectively. In contrast, the methods implemented in GENECLASS 2 showed a greater correct assignment rate in allocating animals treated as unknowns to a reference dataset (62% vs. 51% and 80% vs. 65% in field tests 1 and 2 respectively). These results demonstrate that SNPs are suitable for the assignment of individuals to reference breeds. The results also indicate that STRUCTURE 2.2 and GENECLASS 2 can be complementary tools to assess breed integrity and assignment. Our findings also stress the importance of a high-quality reference dataset in allocation studies.

The use of SNPs in combination with Bayesian statistics for the geographic traceability of cattle was evaluated using a dataset comprising 24 breeds from Italy, France, Spain, Denmark, the Netherlands, Switzerland and UK genotyped with 90 polymorphic markers. The percentage of correct assignment of the individuals to their Country of origin was 90%, with an average assignment probability of 93% and an average specificity of 92%. The higher value was observed for UK breeds (97% of correct assignment) while Swiss animals were the most difficult to allocate (77% of correct assignment). Tracing of Protected Geographic Indication (PGI) products, the approach correctly assigned 100% of Guaranteed Pure Highland Beef; 97% of "Vitellone dell'Appennino Centrale" breeds; 84% of Ternera de Navarra, and 80% of Boeuf de Chalosse. Methods to verify Products of Designated Origin (PDO) and Protected Geographic Indication (PGI) products will help to protect regional foods and promote the economic growth of marginal rural areas by encouraging the production of high quality niche market foods.

Genomics has brought about in its wake a true biological revolution and can be applied to all areas of life sciences. Having sequenced the genomes of several different species, genomics techniques now allow us to study polymorphisms and the gene expression of proteins, enhancing our understanding of the biological functions of genes. The combined know-how of physicists and computer scientists, as well as of geneticists and physiologists is required to identify how genes control the dynamics of cell functions. Naturally enough, it is in the sphere of human medicine that the applications of genomics look most promising. Preventive and customized medicine, adapted to the genetic potential and to the way of life of each individual, will in all probability see the light of clay in the foreseeable future. in farm animals, there is no doubt that sequencing the bovine genome will give rise to new concepts and new molecular tools which will accelerate studies in bovine genomics. Comparing the bovine genome with that of other species, including humans, is also a potential source of huge progress for both human health and ruminant husbandry in general.

The current study presents the results of a preliminary haplotype association analysis at the bovine PRKAG3 locus with meat quality traits in the Chianina breed. No significant association was shown between haploid haplotypes (or diplotypes) and phenotypical traits after applying a Bonferroni correction for multiple comparison. Nonetheless, data from Longissimus dorsi muscle suggest the presence of a statistically non-significant trend toward an influence of the PRKAG3 haploid haplotypes on meat colour (a*) and water holding capacity (M/T) traits, as confirmed also by diplotype-based association analysis. A less clear set of results was observed for the Triceps brachii and Semitendinosus muscles.

Traceability of meat has become a key aspect of food-quality assurance and a priority for EU countries, to meet consumer demand for comprehensive and integrated food safety policies. In this context, the traceability of animals and animal products at the breed level might play a key role as it would enable the certification of regional products linked to particular breeds. Technologies based on DNA analysis have the potential to achieve this goal bypassing the large scale and systematic biological sampling necessary for individual fingerprinting.The objective of this work was to test the power of a SNP panel to trace PGI “Vitellone Bianco dell’Appennino Centrale”, a product linked to three breeds: Chianina, Marchigiana and Romagnola.A total of 180 unrelated animals belonging to PGI-allowed breeds (Chianina n=22; Romagnola n=22; and Marchigiana n=22) and PGI-not allowed breeds (Piemontese n=22, Maremmana n=24, Italian Red Pied n=24, Italian Brown n=22, Italian Friesian n=22) were sampled and genotyped with a panel of 130 SNP in 90 independent genes.Individual genotypes were assigned to breed by Bayesian based clustering approach. In particular the SNP data were analysed by the Rannala and Mountain approach implemented in the software Geneclass 2 (file:///C:/Software/GeneClass2/Help/index.htm).The SNP-based molecular approach in combination with Bayesian assignment algorithms allowed an overall correct assignment of more than 95% of individuals to their breeds of origins. This percentage increase to 96% grouping the breeds allowed in a unique cluster.Sorting the SNPs by their Gst values and using the 90 showing a value higher than 0.01, we maintain the same rate of allocation success indicating that selecting SNPs for their informative content will reduce the number of markers required for a reliable traceability at breed level, reducing the laboratory effort and consequently the cost for the large scale application of the methodOur results suggest that SNP markers in combination with Bayesian algorithm can be exploited in allocation studies and are able to trace “Vitellone Bianco dell’Appennino Centrale”. The main advantages of SNP are their abundance and the potential of full automation.