Analysing how auxin dynamics control root phenotype

The hormone auxin affects many aspects of plant growth. In the plant root, auxin affects how quickly the root grows, orients the root tip to grow downwards and determines when a new root branch will grow from the main root. Therefore, auxin controls the form of the whole root system, which affects how easily roots can take-up water and nutrients from the soil and how securely roots anchor the plant in the ground.

To control the growth, bending and branching of the root, the amount of auxin within each cell varies both between different cells and over time. The plant controls the auxin distribution by positioning different proteins and channels on the cell membranes, which affect how quickly auxin can get into and out of each cell. It is hard to predict how the amount of each protein/channel on each cell membrane affects the overall auxin distribution within the root tip. In this project, we will make and test mathematical models to investigate how the proteins/channels on the cell membranes affect the auxin distribution. We will then use these models to understand how auxin controls root growth, bending and branching.

To create an accurate model of auxin transport, we will first image cell geometries and the distributions of the proteins/channels on the cell membranes. Using this information, we will write down a mathematical description of how auxin moves into and out of each cell to form a mathematical model. We will then simulate and analyse the mathematical model to predict the auxin distribution within the plant root. In order to maximise the knowledge gained, we will use a range of mathematical techniques to produce different types of model, each having different advantages and being amenable to different types of analysis. We will then carefully compare the model results with experimental data. Because auxin is very small, we are unable to measure the amount of auxin within each cell and it is hard to measure the rate of auxin transport across cell membranes. We will therefore make use of fluorescent proteins that are degraded by auxin to collect data with which to test the models. We will carry out a range of experiments to thoroughly test the models, for example, considering roots in which certain proteins are not functional, or when auxin has been supplied to the root. In the event that the model predictions and data do not agree, we will use the models to develop new hypotheses and identify which new experiment would best test these. The modelling will therefore motivate new experiments, the results of which will lead to improved models, and we will move around what is known as the 'model-experimental' loop.

The project will improve our understanding of how auxin controls the plant root system by controlling the growth, bending and branching of the root. Determining what controls auxin dynamics in the plant root will provide us with knowledge of how to manipulate plant roots. In the longer term, this knowledge will lead to the development of crops with roots that are better suited to their environmental conditions, which will significantly improve crop yields. In addition, the project will produce rigorous mathematical models which will be analysed and tested using a wide range of techniques. These models and techniques could be applied to understand other biological questions and so will also be beneficial to future research.

Strategies to manipulate root systems represent a prime target for improving crop yields. Many aspects of plant root architecture are controlled in the root tip by the hormone auxin. Auxin controls the rate of root growth, tropic responses and lateral root development. These processes depend on the auxin dynamics; thus, understanding auxin dynamics is essential to understand root development.

In this New Investigator project, we will use a systems approach to analyse auxin dynamics in the root tip, and determine how auxin dynamics affect root phenotype. Our recent models revealed the distinct roles of the PIN efflux carriers and AUX1/LAX influx carriers in creating the auxin distribution in the root tip (Band et al . Plant Cell, 2014, Band and King, J. Math. Biol. 2012); however, the predicted auxin dynamics led us to question our understanding of how auxin controls root development. In this project, we will first fully characterise the auxin dynamics in the root tip by assessing the contributions of additional key components (such as ABCB transporters, plasmodesmata and pH variations) and employing novel techniques to parameterise and test our models. We will then investigate how auxin dynamics regulate root phenotype by coupling our auxin-transport models with biomechanical models to analyse how auxin controls root growth rates, gravitropic bending and lateral root initiation. As well as significantly improving our understanding of auxin-regulated root development, the project will generate a solid knowledge base and theoretical tools which will benefit future systems-biology research.

A wide range of people will benefit from this research, including the general public, plant breeders and researchers based in industry.

In understanding how plant growth is regulated, the knowledge from this project will benefit GLOBAL FOOD SECURITY. Although crop production has significantly increased over the past 50 years, during the so-called 'Green Revolution', the Food and Agriculture Organization of the United Nations recently stated the need for global food production to increase by 70% by 2050. This aim is especially challenging given changing climates, water scarcity, competition for land and the need to reduce fertilisers to maintain healthy ecosystems. Such a complex issue has major implications throughout the world. Determining how to manipulate plant architecture is a prime target for increasing food production.

In determining how auxin regulates root phenotype, the knowledge and specific predictions generated during this project will be of commercial interest, both for large international companies and smaller plant breeders. The project will determine which genetic variations exert the most impact on root growth, gravitropism and lateral root initiation. In the longer term, I anticipate that these results would enable breeders to develop plants with root systems that are better suited to their environmental conditions, resulting in higher crop yields and enabling crops to be grown in conditions where they not currently financially viable. To maximise the impact of my research, I have recently developed a collaboration with Prof Jonathan Lynch at Penn State to create multiscale models to determine how regulation at the root tip affects the full root systems architecture. Prof Lynch works closely with plant breeders throughout the world and I envisage this collaboration will lead to the key results of this project being fully exploited in crop species, such as Maize, Rice and Brassica rapa (which have genomes that are closely related to Arabidopsis). As described in my Pathways to Impact, I will actively promote the project results to other plant breeders and agronomists.

As well as the clear academic benefit to the plant science and modelling communities, this project will generate biological insights and modelling tools that would be of wide interest for researchers in industry. By targeting appropriate conferences, we will share our results with industrial researchers and we will make data and models publicly available, as described in the Data Sharing statement.

Plant systems biology is an excellent topic to attract public interest into scientific research and inspire the next generation of scientists, showcasing both science generally and specifically highlighting how mathematics is being used to solve real-world problems. As detailed in the Pathways to Impact, we will actively bring this research to the attention of the public through outreach events and the media. Such opportunities will be identified in collaboration with the expertise of University of Nottingham's Communications Office and the School of Biosciences Outreach Officer.