Specifying Vascular Pattern in Newly Emerged Roots

All plants and animals start life as a single cell. This cell and the subsequent daughter cells then divide to form a multicellular organism. These divisions do not occur at random. They follow a precisely coordinated developmental programme to generate a specific shape or form. Individual cells are instructed to undertake specific cell identities and these various cell types are arranged in specific patterns to create tissues, organs and ultimately an entire organism.

In this project we will investigate the genetic mechanisms that generate the positional information upon which a cellular pattern can be superimposed, and specifically on the information is generated to position vascular tissues form within newly formed roots. This project will improve our understanding about how organisms form, but it will also give us detailed insights into vascular development. Plants generate sugars in the leaves and extract water and minerals through their roots. However, it is the vascular tissues (the xylem and phloem) that allow these substances to be transported throughout the plant. These vascular tissues must be arranged in precise patterns to provide a continuous network linking organs within the plant and we will uncover how that pattern is determined.

In order to do this, we will generate a series of tools that will allow not only aid our understanding of vascular patterning, but also of many other aspects of root growth. In this project a biologist and mathematician will work together to build a computer programme that can simulate the way that a group of genes behave as a root grows. This will allow us to rapidly test what happens as we change the genetic make up of our computer programme. Using this computational approach we can rapidly test many different patterning mechanisms, allowing us to focus the time consuming experimental analysis on the most important genes. We will make this programme freely available so that other researchers can adapt it to study other types of roots or other processes within the roots.

This project will take a single patterning event (the establishment of vascular tissues) and provide an integrated solution demonstrating how the required positional information is generated. Previous research into vascular development has focused on mature roots where the cellular pattern has already been elucidated. This project will focus on newly emerging organs (lateral roots) and determine how vascular pattern is generated anew.

This project will fuse our existing knowledge of root vascular pattern into an experimentally verified three-dimensional mathematical model showing the dynamics of vascular patterning in lateral roots. This modelling will occur at a multi-scale level incorporating individual molecules, genes and genetic networks. With this data we will be able to dissect the effects that alterations in hormonal input, geometric constraints imposed by the shape of the primordia and alterations in the regulatory network have on the emerging pattern. Taken together this will allow us to understand with vascular pattern is set de-novo in newly formed organs or propagated from the pre-existing vascular tissues.

The multidisciplinary programme is broken down into 4 clearly defined objectives:

Objective 1 will develop a new framework for modelling roots and examining a minimal set of auxin transport/signalling components to position the auxin response maximum in 3D.

Objective 2 will develop a new multiplex marker system for observing the expression of up three root specific markers simultaneously.

Objective 3 will identify a minimal regulatory network that self-organize vascular pattern in the growing root.

Objective 4 will use this model to determine what (if any) additional information is required to generate vascular pattern in newly formed roots.

Who will benefit from this research?
Life science researchers
Mathematicians and computer scientists
Agronomists and plant breeders

How will they benefit from this research?
The project will generate new and innovative experimental tools, data resources and models that can be used by researchers from a wide variety of areas. For example, Life Scientists could employ similar approaches to study multi-cellular processes in other biological systems; plant breeders and agronomists will use the information generated about new regulatory signals, genes and mechanisms in breeding studies or to design new approaches to manipulate vascular pattern or auxin response in roots; and researchers in the areas of mathematics and computer sciences would adapt the multicellular models to other purposes.

Data generated during the project will be stored in accordance with UKAS guidelines and published in peer reviewed journals. All biological materials generated will be deposited at the Nottingham Arabidopsis Stock Centre (NASC); whilst models would be downloadable from the Edinburgh-based Plant Model Repository and then, following their publication, the Biomodels database at EMBL and the multiplex markers (and components) will be made available through the CPIB webpage and through appropriate databases for components such as the PlantProm database at the University of London.

The project will also help train researchers experienced with working as part of a multidisciplinary team. This multidisciplinary expertise will uniquely position them for employment in the UK Life Science and Pharmaceutical Industries.
In terms of timescales of benefits, selected data, materials and models generated would be made publically available during the period of the award. Staff would be available to enter the UK work force in 2015-17.

Engagement with end users and beneficiaries about the project:
The PI, co-I and PDRAs will disseminate their results at scientific conferences, through published journal articles and at our annual CPIB Research Showcase meeting with Industrial collaborators, such as Syngenta and Unilever. We will favour conferences that are attended by a people from a wide variety of disciplines and subject areas such as the Society of Experimental Biology meetings, as this offers us the opportunity to share are research with non-plant scientists. The PI is organizing a session on computational biology at next year's SEB meeting and it will include animal, plant and cell biologists.