Molecular Biology

Genomics and proteomics approaches for characterising and improving beef quality

Projects in this area use tools of proteomics and functional genomics with a view to understanding the function of genes and proteins. The overall aim is to identify genes and proteins and the expression levels that confer the consistently high quality beef required by both the Irish and export markets. The project objectives fall into three broad categories: phenotypic characterisation, proteomics and functional genomics. State-of-the-art techniques including development of cDNA libraries, development and analysis of cDNA microarrays, and 2-dimensional (2D) gel electrophoresis will be applied to achieve the project objectives. The plan is based on the hypothesis that meat quality is affected by differential expression of genes in response to environmental factors such as nutrition and handling. Technologies such as real time PCR and microarray analysis are being employed which will allow genes differentially expressed at the time of slaughter, in carcasses with extremes of quality traits (e.g. nutritional composition, water-holding capacity, tenderness), to be identified. Protein expression patterns will be monitored throughout the postmortem ageing period using 1-D and 2-D gel electrophoresis and associations with meat quality traits will be identified. Meat from each carcass will be characterised in terms of sensory, nutritive and technological quality. The importance of these genes and proteins in determining desirable meat quality will be assessed by analysing associations between quality traits and the expression of the identified genes and gene products.

An extensive database is now available at the Ashtown Food Research Centre containing phenotypic information for cattle exhibiting wide variation in beef quality characteristics as well as frozen tissue samples suitable for gene and protein expression analysis. Animals displaying extremes of quality will provide a valuable method for identifying gene and protein expression patterns associated with meat quality. Quality is characterized in a number of ways including palatability, nutritive and technological attributes. Information generated will provide a powerful resource to improve the basic understanding of muscle biology and will ultimately lead to an improvement in our ability to predict and optimise beef quality parameters. anne.mullen@teagasc.ie or blanaid.mee@teagasc.ie

Teagasc beef quality biotechnology initiative

The new scientific orientation towards transcriptome and proteome analysis have opened up new possibilities for discovering molecular predictors (highly regulated genes or molecular polymorphisms) that control muscle growth and meat quality traits. Meat quality is an extremely complex set of properties, identified as economically important phenotypic traits such as tenderness, nutrition and water holding capacity. A molecular biology programme has been established and is progressing to further our understanding of meat quality. Gene expression profiling of bovine muscle tissue is a powerful technique, which can be used to identify genes and gene families associated with meat quality traits. Advances in proteomics have enabled similar profiling of gene products (proteins). Genes and proteins associated with quality are ultimately determined by the interaction of genetic factors with the environment. In this project we are establishing functional genomics and proteomics technologies in the Ashtown Food Research Centre, which will allow new strides to be made towards a greater understanding of the complex interplay of gene and protein expression events involved in the transformation of muscle to high quality meat. anne.mullen@teagasc.ie or ruth.hamill@teagasc.ie

Interaction of gene expression pathways, breed and diet on the nutritive and flavour aspects of pigmeat

Although the growth and carcass composition of pigs can now be largely controlled, we still cannot define all of the factors that will ensure a consistently tender, juicy and well-flavoured product. Research is underway into determining how gene expression is affected by production systems particularly breed and diet. Palatability and technological pork quality are complex and multivariate properties of meat, which are influenced by multiple interacting factors including breed, diet, pre-slaughter handling, stunning, slaughter, hanging methods, chilling and storage conditions. One particular research focus area within the biotechnology group will be on gene expression patterns throughout the growth of the animal in conjunction with the effects of external stimuli particularly diet and breed of the pig and ultimate quality. Animals expressing extreme phenotypes (divergent in intramuscular fat content for example) will be identified and a functional genomics study carried out to identify genes associated with this trait. The aim is firstly to understand the control of genes and their pattern of expression, already known, or expected to impact pork quality. Secondly novel genes that play an important role in pork quality will be examined. These will be identified using state of the art techniques including microarray technology and quantitative real time PCR. Information generated will provide a powerful resource to improve the basic understanding of pork muscle biology and will ultimately lead to improving our ability to predict and optimise pork quality parameters. anne.mullen@teagasc.ie, deirdre.corcoran@teagasc.ie or ruth.hamill@teagasc.ie

Evaluation of DNA polymorphisms for beef quality in Irish cattle

Meat quality is a difficult trait to improve by traditional selection because it can only be assessed post-mortem. Genetic based diagnostic tools for predicting meat quality (eating, technological) during the life of the animal or post mortem would allow producers adapt their production systems to provide optimal quality. Similarly, other participants in the meat chain could adapt their processing methods and quality control measures to deliver consistently better quality meat to the consumer.

The goal of this project is to characterize the variation observed in meat quality traits in order to elucidate the underlying biological mechanisms controlling meat quality. Progress has been made world wide in identifying variations in DNA sequence (polymorphisms), which have been shown to be associated with important traits such as growth, carcass yield and quality. These polymorphisms have the potential to serve as markers of meat quality, based on the hypothesis that meat quality is affected by both allelic variants of key genes and their response to environmental factors. Due to genetic drift and recombination, a marker may be associated with a trait in one population but not another. It is important therefore to determine whether a marker that is associated with e.g. tenderness in a US population of cattle is also associated with the quality traits in the Irish herd.

To date, a number of DNA polymorphisms in candidate genes for tenderness and marbling have been screened within the AFRC animal population database, which exhibits wide variation in beef quality characteristics, to determine if an association exists between these polymorphisms and meat quality traits. anne.mullen@teagasc.ie or ruth.hamill@teagasc.ie

Identification and molecular characterisation of genes influencing Irish pork meat quality

Pork quality comprises a set of key fresh meat qualities and processing characteristics that are important for the future profitability and competitiveness of the swine industry. Since most aspects of pork quality can only be measured on the carcass or by consumer panels, they have been difficult and expensive to improve by conventional means. However, most are at least moderately heritable and several quality-related genes with a significant impact on pork meat quality have been identified. Great opportunities, therefore, exist for the use or marker-assisted selection to improve pork meat quality. The aim of the current project is to identify and characterise in detail, the genes and proteins responsible for variation in Irish pork meat quality using functional genomic and proteomic approaches, with the ultimate aim of moving one step closer to the selection of candidate gene markers in marker-assisted selection strategies. ruth.hamill@teagasc.ie or anne.mullen@teagasc.ie