How PROHEALTH investigates gene pathways
The PROHEALTH consortium came together with the aim of understanding what factors contribute to production diseases in pigs and chickens across the European Union. One very important aspect of this is to pinpoint which genes are altered when animals are diseased or when they are placed in different farm environments. Many of these changes go unnoticed until they result in poor performance and low productivity. This knowledge could be used to establish best practice, to ensure healthy animals and ultimately increase the amount of money a farm earns from its produce.
Why measure genes?
All living things contain genes which act as a blueprint for the production of proteins. These genes not only shape what the animal looks like (phenotype) but also determine every metabolic process required for the animal to function properly (genotype). In our PROHEALTH studies, we will measure the varying activity of chicken and pig genotypes which consist of around 44, 000 different genes. Increases, decreases or stability of the activity of the genes measured will be assessed in animals from across the EU which are kept in a variety of different housing conditions and on farms with different disease conditions.
Genes are made of the combination of chemicals called DNA. To enable us to measure the activity of DNA, we use a technology called ‘microarray’. Microarrays allow us to measure the whole genome of the animal much more quickly and cost effectively than older technologies that have used similar principles, such as the ‘polymerase chain reaction’ (PCR).
The microarray analysis
Microarray technology has only been available for the past 10-15 years and has not yet been used to predict animal health in a study as large as PROHEALTH. To carry out a microarray, we use spots of commercially available DNA which contain the whole pig or chicken genome, and this is then fixed to glass slides.We then extract a related chemical called RNA from our pig and chicken samples, including respiratory and intestinal tissues. RNA is required by all cells in the body to read the DNA code and to transfer this blueprint to the regions of the cell which make the specific protein, encoded by the gene via its DNA signal. To find out whether a gene is being expressed we do the reverse of this process. Firstly, the animals’ RNA from our samples is converted into a complementary DNA (cDNA) before being added to our DNA spots on the glass slides. If the same gene in the DNA spot is being expressed by the animal, then the animal cDNA from the sample will bind to the spots. The cDNA is also labelled with a fluorescent dye, enabling us to measure the extent to which this binding occurs based on the strength of the fluorescent signal, which directly reflects the amount of gene expression in the animal (see Figure 1).
What does the gene pathway tell us?
From the data we receive from the microarray, we can ascertain which gene sequences are active in any given environment or disease status experienced by the animal. These genes can then be grouped together by a computer programme, which compares them with known sequences that correspond to metabolic, immune or other pathways. Thus, sets of ‘biological markers’ of health or illness can be obtained.
What does this mean in practice?
The objective of this work by PROHEALTH, is to identify gene pathways which are associated with particular environmental, farm management or disease factors. These can be used in herd/flock surveillance to inform farmers, producers and other relevant stakeholders of any underlying issues which may influence animal health and farm productivity. It is also possible that the isolation of such biological markers may pave the way for novel treatments of production disease in pigs and poultry.