Pig Feed Efficiency: A systems integrative biology approach

An unprecedented increase in the global demand for food is predicted between now and 2050. Without major advances in production, food shortages will become more frequent across the globe, including developed parts of the world. It is therefore essential that we ensure sufficient food is available, in other words to establish "global food security". The world population currently stands at 7 billion but is predicted to increase to 9 billion by 2050. This is a major threat to food security, but there are also other exacerbating pressures. There is a need to reduce greenhouse gas emissions to reduce global warming and climate change, while land and crops are being increasingly used to produce alternative energy sources to fossil fuels (coal, gas and oil). This leads to competition for land, water, energy and the sources of food themselves. To produce more food requires either more land (which isn't available) or an improvement in the efficiency of production. Increases in personal wealth in developing countries is predicted to increase the demand for meat and animal products, which consumers associate with a higher quality diet and social status. However, meat requires significantly more resource to produce than other foods. Meat producing animals, such as pigs and poultry, commonly require grain-based feeds which will become an increasingly limited resource, due to competition from human diets and the biofuels industry. These pressures make it important to reduce the quantity of feed required per unit meat produced, thereby improving "feed efficiency". To do this, use of technologies will be required including those not currently deemed acceptable to the consumer (in the EU at least), although threats to food security may change consumers values and ethical stances.

For efficient production of meat, the goal is to maximize the deposition of nutrients (particularly protein) into skeletal muscle and repartition nutrients (particularly those for energy) away from fat. The liver is critical as it processes nutrients and plays a major role in coordinating whole body protein and energy metabolism. Animal growth promoters are used legally in some countries (Australia, Brazil and USA), but not the EU, and have the effect of increasing lean while decreasing body fat. The objective of this project is to gain a fundamental understanding of the mechanisms by which these agents affect these tissues. Pigs will be given either a beta agonist (BA) or growth hormone (GH), and compared to a control group over a time course (28 days) during which these agents are known to increase feed efficiency. Skeletal muscle, liver and fat tissues will be collected at 5 fixed time points (1, 3, 7, 14 and 28 days). Three of these time points will be subsequently selected for more "in-depth" measurements, based on the growth data and expression of some key genes. Using a technique called "deep sequencing" all the genes expressed in these 3 tissues at these 3 timepoints will be identified along with other genetic material called microRNA, which is involved in determining which proteins are produced. Deep sequencing produces a large quantity of information, which will identify the genes and microRNAs produced by these pig tissues; information which by itself will enhance our understanding. Secondly, by comparison between the treatment groups, those genes and microRNAs influenced by the growth promoters will be identified. Finally, the relationships and interactions (so called networks) between the expressed genes and tissues will be identified, to determine common processes influenced by these growth promoters. The expectation is that specific "key" genes and processes (i.e. networks) will be identified in these tissues, which could be manipulated in the future to enhance the efficiency of animal growth.

Global Food Security is becoming an increasingly important issue. The increasing competition for land and crops for human consumption with their use for animal feed and biofuels industries, mean strategies to improve animal feed efficiency are urgently needed. This will require use of new or existing technologies, including those currently deemed unacceptable by consumers (in the EU at least). Animal growth promoters (beta-agonists (BA) and growth hormone (GH)), currently used commercially in some countries (Australia, Brazil and USA), improve feed efficiency, increase lean and decrease fat deposition. This project will determine the time course (1, 3, 7, 14 and 28 days) for the effects of Ractopamine (BA) and Reporcin (GH) on finisher pigs, including their effects on muscle, fat and liver transcriptomes using deep sequencing (HiSeq Illumina sequencing platform) and subsequent pathway and network analysis (e.g. IPA, SolCyc, ANN). This will generate a large quantity of sequence information, which will be used to identify the genes and microRNAs expressed in these pig tissues. Then, by comparison between the treatment groups, those genes and microRNAs involved in the growth response, together with the key pathways, gene networks and interactions between genes and tissues will be identified. Verification of key mRNA and microRNAs will be carried out by qRT-PCR (Roche Lightcycler 480), using SYBR green and Taqman small RNA detection probes (Applied Biosystems). The expectation is that specific "key" nodes within the networks will be identified, which could be manipulated in the future to enhance the efficiency of animal growth.

The proposed pig time course trial will be the most comprehensive study ever performed to investigate the mechanisms for how these growth promoters work. It is extremely costly and therefore very unlikely to be repeated anywhere else in the world. The fact Pfizer have chosen to fund this work at Nottingham is testimony to the calibre of the staff and facilities available. The results and subsequent publications are therefore likely to have a high impact and to be highly cited in years to come, thereby benefiting both academic and industry scientists. Ultimately, the main benefit will be an academic one with the studies leading to a comprehensive understanding of how tissues interact to regulate growth and metabolism, information which may then be developed into a better understanding of other species, including man.

In addition, the deep sequencing data will be made freely available via online databases, which will be accessible by other researchers and therefore provide a complementary resource to the pig genome project which is still on-going. Hence a wide variety of pig researchers will benefit in terms of both published information and tissue transcriptome sequence data, but the information may also be translated for the benefit of human medicine (e.g. use of pigs as models for human health).

The overall aim is that this comprehensive in-depth study into the changes in tissue transcriptome at different times following administration of these potent growth promoters, will identify key networks and nodes that can then be targeted for drug development to enhance pig growth and feed efficiency. Our industrial partners, Pfizer, will benefit from this important step in the drug discovery process, but will then need to invest further in terms of patents and further studies before any resulting product would reach the market and be commercially available for use. However, were this to eventually reach fruition, we would all benefit via a small but significant improvement in food security.