Specifying Vascular Pattern in Newly Emerged Roots
Lead Research Organisation:
University of Nottingham
Department Name: Sch of Biosciences
Abstract
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.
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.
Technical Summary
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.
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.
Planned Impact
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.
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.
People |
ORCID iD |
Anthony Bishopp (Principal Investigator) | |
Leah Band (Co-Investigator) |
Publications

Kümpers BM
(2015)
Plant grafting: making the right connections.
in Current biology : CB

Kümpers BMC
(2022)
Dual expression and anatomy lines allow simultaneous visualization of gene expression and anatomy.
in Plant physiology

Mellor N
(2017)
Theoretical approaches to understanding root vascular patterning: a consensus between recent models.
in Journal of experimental botany

Mellor N
(2014)
The innermost secrets of root development
in Science

Mellor N
(2019)
A core mechanism for specifying root vascular patterning can replicate the anatomical variation seen in diverse plant species.
in Development (Cambridge, England)

Miyashima S
(2019)
Mobile PEAR transcription factors integrate positional cues to prime cambial growth.
in Nature

Muraro D
(2014)
Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots.
in Proceedings of the National Academy of Sciences of the United States of America

Schaller GE
(2015)
The yin-yang of hormones: cytokinin and auxin interactions in plant development.
in The Plant cell

Vaughan-Hirsch J
(2018)
North, East, South, West: mapping vascular tissues onto the Arabidopsis root.
in Current opinion in plant biology
Description | We have developed many of the methodologies required to achieve the original research questions. Briefly, this involved generating new 3D templates of roots in which mathematical models could be run. It also involved developing a new system for the observation of multiple flourescent markers in plants. We have used this to investigate how vascular patterning occurs in plants. Our simulations have suggested that using a 1D growing template produces more reliable results and allows us to address similar questions, so we have developed this in parallel. This has allowed us to understand how the vasculature is patterned in a variety of species, and provide a mechanism to observations from 100 years ago that the number of xylem poles are correlated to the size of the vascular cylinder. This has been now accepted in Development. |
Exploitation Route | We will make all components of our multiple marker system available to the community. This is currently being written up. Mathematical models made public. |
Sectors | Agriculture Food and Drink |
Description | Leverhulme Trust Research Project |
Amount | £175,000 (GBP) |
Funding ID | RPG-2018-403 |
Organisation | The Leverhulme Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 05/2019 |
End | 05/2021 |
Description | Royal Society Enhancement Award |
Amount | £96,000 (GBP) |
Funding ID | RGF\EA\180308 |
Organisation | The Royal Society |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 08/2018 |
End | 08/2022 |
Title | New destination plasmids for observation of multiple fluorescent markers in roots |
Description | We have created a set of multiple markers that highlight specific tissues in plants and couple GFP with a red plasma membrane marker. This is built around the greengate cloning system, and involved the creation of bespoke destination vectors as well as individual entry clones. |
Type Of Material | Biological samples |
Year Produced | 2018 |
Provided To Others? | No |
Impact | This is fantastic for creating live movies of gene expression via light sheet microscopy. We aim to submit a publication with this information within the next 6 months. |
Description | Investigating vascular pattern in Arabidopsis |
Organisation | University of Cambridge |
Department | The Sainsbury Laboratory |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have collaborated with Prof. Helariutta's lab on modelling the process of vascular patterning via the EPM/PEAR proteins. |
Collaborator Contribution | We provided a conceptual framework to help interpret the data in Prof. Helariutta's recent Nature paper. |
Impact | 1 Multidisciplinary paper published in Nature (see publications). Our input involved mathematical modelling of biological processes. |
Start Year | 2014 |
Description | Cub scout Science badge |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | I ran 3 events with the 2nd East Leake Cub Scouts doing different Science experiments to help them gain their Science Investigator badge. I tried to link my work to this project. |
Year(s) Of Engagement Activity | 2019 |
Description | Hosting a Work experience student |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | My group hosted a 16 year old student as part of his work experience. He was very enthusiastic about the work, and said that it has influenced his choices for A level. In particular he was inspired by the combination of maths/modelling with biology, and he has selected to do both maths and computer science. |
Year(s) Of Engagement Activity | 2019 |