Deliverables Associations between markers and traits Scientific results description The most important result of this project deals with the identification of genes underlying meat quality traits in beef cattle. This result provides a detailed description of the associations found between candidate genes and meat quality traits. For this purpose, we have analysed a total of 440 bulls belonging to 15 European breeds fed similar diets across all countries, for which measurements of meat quality parameters have been performed to a total of 108 traits were measured on the live animal (weight, body measures) or after slaughter (carcass parameters, fatty acid profiles, tenderization of the meat, colour, weight losses, pH and other instrumental texture measurements, enzymatic activity and fiber type and sensory analysis. Simultaneously, a search was undergone to identify markers on candidate genes. A total of 391 SNPs (Single Nucleotide Polymorphisms) markers were genotyped after being validated for the 434 bulls and their available sires and dams to a total of 977 animals. A nuclear family design was designed to be able to use a TDT (Transmission Disequilibrium Test) (Sun et al., 1999) which allows to discard spurious associations and also a linear model accounting for breed effects that does not use information from the parents, and a composed principal component method (CPC) (Mangin et al., 1998) was used to build a multivariate test at each marker respecting the breed structure of the data by adopting a stratified permutation procedure. Suggestive results were found with the TDT, linear model and CPC. A total of 20 genes appeared to be associated with different phenotypes in the pairwise tests with lowest p-values. Some genes appeared to be involved with different traits. In conclusion, 12 genes turned out to be associated with a particular fatty acid, one of them with the EPA (Eicosapentaenoic acid) muscle content. Four genes were associated with live measures and thought to be involved with growth rate and fattening. Nine were associated with measures as meat colour, weight losses and other instrumental texture measurements and five with carcass measures. As it is possible to license some of this information, specific results are not available for the public domain. Dissemination and use potential The results presented here are important in terms of exploitation as they show associations of particular genes with some traits of economic importance. There is a considerable interest in the beef industry to be able to select animals by using their genotypes for some genes shown to be partially responsible for a specific trait. At present, classical selection methods are difficult to apply in meat quality traits due to the lack of recording in these traits and to the high variability shown for these quality traits attributable both to genetic factors and to the production system. The use of polymorphism at the gene level is therefore seen as a progress which could make the selection of sires possible for meat quality based solely on the molecular information. However, at this stage, only a few published or patented DNA markers are available for genetic tests, marketed by genomics companies for improving beef meat quality. This limited molecular information shows also another problem which is its value in European beef cattle since some publications have demonstrated different results in particular populations. The identification of genes associated with some measures on meat quality is therefore a good new, although the markers used will not be in most cases the causal mutation explaining different phenotypes but will be in close linkage disequilibrium with it, sufficient to select individuals for meat quality improvement based on molecular information alone. These markers will allow the improvement of beef breeds through selection by increasing the frequency of the alleles which have shown to be favorable to commercial criteria based on consumer preference and on health purposes. As in the last years, the beef meat industry has showed a decline produced by several causes as product quality, the BSE problem and an overall lack of confidence, giving the industry the possibility of selecting beef animals for producing healthy, tasty meat will provide the producers a commercial advantage which should be taken into account and will raise the demand. The genes found in this project to be associated with different meat quality traits are presently being further investigated and will be of use in the short-term. Their benefits are difficult to quantify as it will be necessary to incorporate the gene information in a routine pipeline together with paternity testing and genotyping of some major genes which is at the moment not as common as it should in most European breeds. However, it is foreseen that some of the genes, particularly those affecting traits as fatty acid content, tenderness or juiciness will have a certain importance in the next years. Meat Quality variations Meat quality indicators of 15 European Beef Breeds. The measurement of some meat quality parameters have been shown as breed specific. This is of importance to all members in the supply chain, since it suggests that different strategies may be necessary when measuring meat quality of different breeds. It has been shown that the calpain system and its relationship with shear force measurements differ between breeds. The dairy beeds showed higher values for all components of the calpain system, in contrast to the double muscled Piemontese breed, which had low calpastatin activity. Overall, calpastatin showed a poor correlation with 10 day aged meat shear froce measurements. However, the relationship was breed dependent and 36% of shear force could be explained by the calpastatin activity in the Pirenaica breed. Principal component analysis of metabolic measurements on the same animals showed that measures of fatness and discriminated some breeds eg Aberdeen Angus and Highland and leaness others Limousin and Piamontesa. These variable were defined by myosin heavy chain type MHC1 and MHC11A as opposed to MHC 11X. COX and CS activities associated with breeds adapted to hardy local conditions: the extensive grazing breeds (eg Casina, Avilena) have higher CS and COX activities as do some dual purpose breeds (Red Cattle, Jersey, Simmental and Holstein). In contrast specialised beef breeds with high muscle mass, e.g. South Devon, Charolais, Marchigiana and Piamontesa have low CS and COX activities. Eating quality measurements by trained sensory panels in UK and Spain showed a similar stratification of breed. The most tender being Pirenaica, Avilena and Piamontesa, and the least tender group being the Marchigiana and Simmental, and to a lesser extent the Highland. The colour of the lean muscle also showed breed differences, Avilena, Casina and Pirenaica were redder than South Devon, Aberdeen Angus and Highland, with other breeds intermediate. These various parameters could be used eg by retailers to define difference in beef quality and may be used in selection programmes to change the characteristics of beef to meet consumer preferences, or to provide a defined, quantifiable choice. The meat characteristics, together with genetic information could also be used to provide a method of verifying beef origin. Single Nucleotide Polymorphisms A list of candidate genes was identified based on their likely involvement in muscle development or composition. Several sources of information were used in an integrative approach that incorporated the knowledge from genomic studies, cellular and developmental biology and muscle science. A total of 525 candidate genes were identified and sufficient sequence information was available to design primers for 365 of these candidate genes to carry out resequencing to look for polymorphisms. The primers designed for 365 candidate genes allowed 917 separate PCR fragments to be analysed. A total of 729 SNPs were identified in 208 genes (3.5 SNPs per gene), against a target of identifying 700 SNPs. Analysis of the length of sequence vs number of SNPs provides and estimated that one SNP occurs on average every 410 bp., however the density of SNPs is not uniform, with some genes showing much greater genetic variation than others. These fragments ranged in size from 123 bp to 1747 bp with an average of 2.5 fragments per gene. Polymorphisms were discovered in 316 fragments from 208 different genes. The number of SNP identified per fragment ranged from 1 to 16 (2.22 on average). The number of SNPs per gene ranged from 1 to 27, but in addition 98 genes did not show any polymorphism. The polymorphisms identified in these candidate genes can be used to investigating the role of the genes in controlling variation in meat quality and growth traits and in eg muscle biology. The markers could also be used for tracking animal products. The markers will be made publicly available so they can be used in further research programmes. Searching for OpenAIRE data... There was an error trying to search data from OpenAIRE No results available
