iSAM: Integrative Systems Analysis of the Shoot Apical Meristem

Morphogenesis is the process by which organisms are built up from cells during development. Living organisms and their component organs have defined and recognisable shapes and forms, and this requires the coordinated actions of many cells. However, despite extensive focus on the cellular components, we still do not understand how such complex structures and patterns are produced. The goal of this project is to understand the morphogenetic events leading to growth and organ production in the shoot apical meristem (SAM) of higher plants, in an iterative process of analysis, model building, biological testing and refinement. The SAM is a population of dividing, undifferentiated cells that generates the leaves and other organs of plants in highly ordered patterns at shoot tips throughout the life of the plant. The SAM is a complex self-maintaining and stable structure, housing at its centre a population of stem cells and initiating organs on its periphery. The SAM produces the cells that comprise all aboveground plant tissues, and defines the number, type and position of lateral organs. SAMs are thus the basis of plant architecture and determinants of major agronomic traits. In view of its importance, the SAM has been extensively studied and a wealth of information is available concerning its molecular and cellular components. Nevertheless, we do not understand how these components assemble into the multicellular structures that have specific shapes and growth dynamics. It is this question we wish to address. We will do this through building multi-level computer models of SAM function, based on biological observation of living SAMs and measurements of key parameters, including responses to plant hormones that both define the growth and division of individual cells and coordinate the overall behaviour of the SAM structure. The outcome of the project will be a greatly increased understanding of the cellular basis of morphogenesis in the important SAM system. It will generate many relevant new data that will be organised in a database. This will underpin the first complete spatialised cellular model of SAM growth in the form of a growing virtual tissue, in which cells mechanically interact and respond according to a small network programme determining responses based on quantitative data. This model will be used for predictive experimentation allowing specific questions regarding the maintenance, organogenesis and morphogenesis of the SAM system to be addressed. This proposal links four leading research teams in UK, France and Finland, with a previous track record of several relevant joint collaborations, and bringing synergistic expertise and technologies in imaging, modelling, plant hormones and cell division to address this important systems problem.

The shoot apical meristem (SAM) of higher plants is a typical example of a complex system, where individual entities, the cells, interact by exchanging signals. It is the overall structure of the interaction network that feeds back on the 'machineries' of individual cells, thereby controlling local growth through the modulation of proliferation rates. Added up, the local cell proliferation rates, patterned by the signalling networks, lead to specific shape changes, which are the emergent properties of the system. To understand the SAM, we will use a complex systems approach. We will focus on the interaction networks, concentrating on two established essential signals, the plant hormones auxin and cytokinin. These integrate stem cell maintenance, organ initiation and meristem organisation through their effects on the component cells. We will provide a detailed spatial description, or map, of these signalling components in the SAM and a quantified link between these signals and cell proliferation rates in different parts of the meristem, based on novel image collection and analysis techniques already developed by the partners that allow data to be captured for the whole SAM structure. These detailed, multidimensional data will be integrated in a specially designed database and then serve as direct input into new predictive mathematical models for morphogenesis and gene regulation that will then be further tested through rounds of experimental perturbation and analysis. The required tools allowing domain-specific inducible gene targeting of hormone and cell regulators have already been developed by the partners, partly in previous collaborations. By iterating an experimental-theoretical loop, we will continuously refine our models toward a three-dimensional (3D) 'virtual shoot apex' with cellular resolution. This virtual shoot apex will integrate our descriptive data with a causal understanding based on our experimentally refined mechanical and regulatory model

Plants grow and develop by producing new leaves or flowers (organs) at the shoot tip from a small dome of cells called the shoot apical meristem (SAM). The SAM is a complex self-maintaining structure that initiates these new organs on its periphery, and also maintains itself and a population of stem cells within it for the lifetime of the plant. The SAM is thus the source of all above-ground plant tissues. Since it defines the number, type and position of organs, it is the basis of plant architecture and a major determinant of agronomic productivity. The SAM is also responsible for developmental adaptation to the environment. As the ultimate origin of most harvested crops and indeed of all agricultural production, a fuller understanding of SAM function is essential to develop better adapted and higher yielding plant varieties. Although primarily aimed at increasing basic understanding, project outputs will provide key underpinning knowledge for companies interested in crop improvement and breeding, since rate of growth and organ production may limit crop productivity, particularly under stress conditions. Models of SAM function may improve predictability in engineering of plant growth and architecture, and the project could also produce new genetic methods to achieve this. A greater understanding of SAM initiation and development is also key to plant micro-propagation, an industry worth $15Bn globally, whose high costs limit broader application. In addition, global trade in ornamentals is worth $8Bn dollars, and UK hardy plant production about £750M, but macro-propagation of many ornamental perennials is slow. Since many important garden ornamentals are rather recalcitrant to micro-propagation, as are endangered species for which it may provide a route to survival, a greater understanding of hormonal circuits underpinning shoot function could lead to improved techniques and opportunities for this industry, and for species survival. A particular need in UK and European industry and government is for trained personnel whose expertise and practical experience spans disciplinary boundaries, particularly the biological and more technical sciences such as computational analysis and modelling needed in systems approaches. This project will not only build expertise in the applicant's lab, but also provide excellent training in interdisciplinary working, helping to contribute to the highly skilled, flexible and interactive personnel needed for the goal of building the 'Knowledge Based BioEconomy' and its sustaining infrastructure. The applicant has a strong track record of engagement with industry, both in research and commercialisation. He currently has an Industrial CASE award and a fully funded studentship with Bayer CropScience, and in the past ten years has held 12 research grants involving commercial partners, 5 of which were fully industry funded and worth £1.25M. He has also held 5 CASE studentships, 3 with Bayer CropScience. The applicant has also been author of 11 commercially licensed patents, and established a successful spin-out company (Lumora Ltd) based on work arising from BBSRC funding and currently employing 7 R&D staff. He was Academic Director 2004-8 of the Master's in Bioscience Enterprise course jointly with the Judge Business School, Cambridge, involving regular contact with the biotech and funding community. He has personal contacts in most European multinational biotech companies, andnumerous smaller companies. The applicant is thus experienced and well placed to commercialise or publicise as appropriate the outcomes of the research. His lab is also actively involved in wider public engagement activities, including organising an exhibition and workshop exploring plant form and diversity by lab member Dr Walter Dewitte, and presentations to Members of Parliament. Cardiff University also has a strategic partnership with Wales Techniquest to promote science, technology, engineering and maths with young people.