Rewiring the Plant Transcriptome for Improved Environmental Stress Tolerance

Plants need to detect and respond to a wide variety of environmental challenges. Activation of plant environmental stress responses represents a significant cost to the plant requiring resource reallocation away from growth and reproduction, processes critical to crop yield. Understanding these interactions are key to ensuring sufficient and stable food production as the human population grows and climate change increases environmental uncertainty. We do know that plant-environmental interactions are governed by complex networks that allow plants to adapt and respond to external stresses. However we do not have a detailed map of these networks and only know of a few key control components in these networks. For this fellowship I propose a novel approach that will allow me to build a detailed comprehensive map of a plant defence network governing environmental stress responses against pathogens. Here I also propose a novel approach that will facilitate the analysis of this plant defence response networks to identify key control points. Identifying key control points will aid the development of crops with enhanced stress tolerance. To this end I propose an experimental approach that change the way these key network points function by rewiring the connections between them. By screening large number of different network rewiring events we can begin to test how well we understand the structure of these defence networks, while at the same time identify specific rewiring events that improve plant tolerance to environmental stress.

This will be achieved through three objectives:
1. Construct a Comprehensive Network Model of Plant Defence Regulation
2. Develop a Method to Identify and Select Key Network Components for Network rewiring
3. Experimentally Rewire the Plant Defence Network and Screen for Rewired Networks that Improve Stress Tolerance

This proposal will serve to answer many fundamental questions about how the plant stress response networks function. Additionally, the experimental approach emulates natural processes of network evolution in plants. Therefore this research will also provide new understanding for how plant stress networks have evolved. I will conduct this fellowship at Silwood Park, Imperial College London as an Independent Research Fellow. My work will contribute to a new Grand Challenges in Ecosystems and the Environment initiative and help tackle a major initiative challenge of addressing Food security in a changing world. Network rewiring will contribute to improving our understanding of how to counteract environmental stress such as pathogen infection in agricultural crops. This can be used to direct crop breeding efforts to develop useful stress resistant traits in crops, but also offers a strategy to synthetically evolve crops to be more tolerant to different environmental stresses when lack of suitable breeding stock is available.

Beneficiaries Include:

Academics studying plant stress, systems biology, network theory, genetic rewiring and the evolution of transcriptome networks.

Companies and organisations developing new plant protection products.

The knowledge gained from this study will contribute to the fundamental knowledge in the academic disciplines listed above. This proposal will provide a solution to further integrate diverse omics data sets into coherent network models that will provide improved understanding of the regulation of complex biological processes in plants, in particular those governing plant stress. However this approach can also be used to construct networks for all other eukaryotes for which their is suitable data.

The theoretical novelty of this approach involves using large scale omics data to guide transcriptome network rewiring. Many systems approaches use simple gene knockout or constitutive expression strategies to assess the relevance to key regulators. Network rewiring will provide additional information regarding the importance of temporal and spatial control of expression of key regulators. This proposal will pave the way for future studies using this novel network perturbation approach in plants. This will in turn facilitate further study of regulatory networks in plants and other complex organisms. Also this synthetic network rewiring approach is essentially recapitulating proposed mechanisms for neo and sub-functionalization following gene duplication during natural organism evolution. This fellowship will thus contribute new knowledge to this area of evolutionary research.

Also, this work will help uncover the techniques to successfully translate fundamental plant knowledge including systems biology information into relevant plant protection strategies that can be used in the field. Companies interested in developing plant protection products will be able to use the output of this research to design new crop protection strategies. A major impact of this work will be in plant protection for agriculture. Harvest loss due to crop pests can reach 40%. This represents a serious threat to global food security which could escalate in response to climate change. This network rewiring approach will provide a framework for the development of crop cultivars capable of naturally defending themselves against pathogens. This will in turn allow for the development of more sustainable farming practices providing more food on less land, relieving pressure on ecosystems thus helping conserve global biodiversity.