AI-based design of new plant systems
The past few years have seen the development of efficient new gene editing tools, which enable targeted manipulation of plant genomes. These CRISPR-based tools can be wielded in ways that produce modified plants that are effectively indistinguishable from those used in conventional breeding. These new genome editing technologies are powerful and allow the prospect of systematic reprogramming of plant growth. However, there is a critical need for models of whole plant growth. These are required for predicable outcomes in modified tissues and organisms after interventions at the DNA level - and required for systematic rational design of new gene-edited plant traits.
Cambridge CODE (Centre for Organismal Design and Engineering) project is a new initiative that brings together biologists, engineers, physicists, mathematicians and computer scientists to tackle the challenge of engineering of growing cellular systems - where advanced biology and artificial intelligence techniques can allow the creation of predictive multi-scale models for living systems. and used to guide genome engineering and redesign of organisms.
plantCODE: research unit in Cambridge
Cambridge has established centres of excellence for multi-scale quantitative measurement of plant growth, machine learning, artificial intelligence-based modelling of living systems and world-leading tools for bioengineering of plant systems. We are bringing these elements together as a closely integrated group of laboratories and experts, who share a sharp focus on (i) the use of an extraordinary facile model plant system for high throughput, multi-scale analysis of plant growth, (ii) use of data to feed deep learning algorithms and create dynamic executable models for growth, (iii) design and testing of gene editing approaches to rewire regulatory networks, and (iv) promotion of open tools and materials for reprogramming biology.
DNA programmed plant growth is a multi-scale process with self-organising and emergent properties. An edited genome will respond to local cell states and produce a precisely encoded genetic response. However, any programmed change is negotiated through growth and the parallel interactions of what may be millions of cell progeny during organ growth. The ability to predict the outcome of these hierarchical interactions between genome, gene regulatory networks, cellular interactions and physical and chemical constraints on growth will provide an unparalleled and revolutionary tool for engineering plant growth.
Radical changes are underway for applications of engineered plants in agriculture and industry. New technologies offer the prospects of lowered barriers to field use, increased research investment and new commercial opportunities. We aim to establish ground rules for whole-organism design in plants, and to establish a UK centre for this new, rational approach to plant breeding.