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Research @ Centre for Plant Integrative Biology

Summer 2009 - Getting to the root of crop development

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In the first of a new series, taking a look at BBSRC-funded research across a department or institution, Susannah Lydon from the Centre for Plant Integrative Biology at the University of Nottingham reports on how a systems approach to answering some fundamental plant science questions could have a real impact on crop improvement.

Food security is an increasingly pressing issue that requires all sectors involved in the process of breeding and growing crops to raise their game, both in order to increase productivity and meet the challenges relating to climate change. Adopting a systems approach to the underpinning biology of plant growth and development could accelerate the rate at which improvements to crops can be made.

The Centre for Plant Integrative Biology (CPIB) is using such an approach – combining the skills of mathematicians, computer scientists, engineers and plant biologists – to produce a ‘virtual plant root’.

Understanding the root is vital because it is the organ through which plants obtain water and nutrients. Just as the ‘green revolution’ in the 1960s saw great gains in crop yields through improvements to crop plant traits above the ground, so improvements to roots, such as breeding crops with roots that exploit more of the upper layer of topsoil, could result in a much-needed second green revolution.

CPIB Director, Professor Charlie Hodgman, says "Our approach is a prime example of how a modern interdisciplinary research team can have an impact on real world problems".

CPIB researchers are modelling root growth and development across the physical scales, from the sub-cellular to whole-organ level, using the model plant Arabidopsis thaliana. The resulting ‘virtual root’ will simulate hormone-regulated root growth, providing researchers with a vital tool for investigating and manipulating root development and architecture in crop species.

Modelling early root development

Prof. Mike Holdsworth is leading a team of researchers to understand how cells elongate in the root as it emerges from the seed, integrating hormone signalling networks with mechanical properties of the elongating cells. Finite element modelling – an engineering technique – is being used to simulate the cell wall of an elongating root cell as a fibre-reinforced viscous material.

Mapping the action of hormones

Plant hormones such as auxin and gibberellins represent key regulators of root growth. Determining exactly where and when these hormones act is critical to understanding their mechanisms of action. Several CPIB research associates are using a systems approach involving mathematical models combined with experimental approaches to map which tissues within the root are the site of action of different plant hormones. For example, such systems approaches have revealed that auxin accumulates in elongating epidermal cells where it causes root curvature.

Another approach being coordinated by Dr Ranjan Swarup is to create a protein atlas of the Arabidopsis root, using antibodies raised against several hundred key proteins that regulate root growth. The antibodies will be deposited in NASC, the European Arabidopsis Stock Centre, which is also based at the Sutton Bonington Campus, for distribution to the international scientific community.

Understanding the genetics of root architecture

Recent work by Marie Curie Research Fellow Dr Benjamin Péret and colleagues has identified key genes that control lateral root emergence. This work is being used to build mathematical models of the regulatory network for lateral root emergence to examine how the root system is able to elaborate its architecture.

Integrating research

A vital part of CPIB’s remit is to integrate models at different physical scales. This requires the coupling of models of cell growth, hormone transport and genetic regulation. One of the CPIB mathematicians is using ‘multiscale asymptotic’ methods to study the movement of the plant hormone auxin in an elongating root. Meanwhile, a computational approach using ‘P-systems’, a computational modelling framework inspired by the structure and functioning of biological cells, is also being employed to develop a tissue-level model of plant hormone transport and signalling.

In addition to CPIB’s focus on modelling the root, the Centre’s multidisciplinary approaches will soon be applied to another key area of underpinning plant biology: multiscale modelling of seed germination, as part of a Europe-wide systems biology programme on plant genomics, ERANET PG.

CPIB has close collaborations with various external research groups. Work in conjunction with Dr Steve Thomas and Prof. Peter Hedden at Rothamsted Research has produced a transcriptomic dataset showing the primary response of Arabidopsis roots to treatment with the hormone gibberellic acid. Analysis of cell wall components has been undertaken in collaboration with Prof. Paul Knox (University of Leeds) and Prof. William Willats (University of Copenhagen). Ongoing work with Prof. Mike Burrell at the University of Sheffield is looking to locate and measure metabolites in root tissues without having to extract them. On the modelling side, CPIB is working with Dr Stefan Kepinski (University of Leeds) to develop mathematical models of auxin signalling.

Back to reality

The CPIB core project involves studying Arabidopsis seedlings grown in artificial agar media, but a collaboration with Dr Sacha Mooney at Nottingham is allowing roots to be imaged in their proper environment: soil. Microscale X-ray Computed Tomography (Micro-CT) is allowing researchers to visualise live roots growing in structured soil as it exists in the field, moving root research ever closer to crop species in realistic environments. Malcolm Bennett, a new BBSRC Professorial Fellow, is employing Micro-CT to study Arabidopsis root architecture in soil. The aim is to identify genes that regulate key traits such as root depth, angle and density which can be employed as molecular markers in crop breeding programmes.

CPIB is already feeding directly into crop development research: expertise in biomolecular network inference and analysis is helping to understand the processes of tomato ripening, in collaboration with Syngenta and others, which will assist in the development of novel tomato varieties with, for example, enhanced health benefits. Work to develop new varieties is also in progress in wheat, with a focus on ‘vernalisation’ – the process by which many plants acquire the ability to flower through exposure to a prolonged period of cold – in collaboration with Dr Chungui Lu (University of Nottingham/Nottingham Trent University). Dr Lu is also investigating nitrogen-use efficiency in rice. CPIB scientists are also modelling lateral root development in barley and other cereals.

Spreading the word

The Centre also undertakes outreach activities to promote and initiate new collaborations between plant and crop scientists and modellers. In September, CPIB will be hosting a biological modelling summer school for postdoctoral researchers and PhD students. Organised in conjunction with GARNet (the UK Arabidopsis network) STEMN (Spatio-temporal modelling network on plant systems) and SIGNET (the Cell Signalling Network), the aim is to introduce modelling and quantitative approaches to biology, as well as to encourage experimental design that generates data suitable for modelling.

The third Mathematics in the Plant Sciences Study Group will take place at CPIB in December. Co-organised with GARNet, these workshops give biologists the opportunity to present well-defined problems to an assembled body of mathematicians, computer scientists and engineers, who then spend the next four days modelling the biological problem. These meetings have resulted in new collaborations, publications (including a patent) and successful grant applications, and are an invaluable means of bridging the gaps between experimental and theoretical disciplines.

Modelling roots for efficient nutrient uptake

Nathan Mellor, a PhD student in the Interdisciplinary Doctoral Training Centre associated with CPIB, is developing mathematical models to explain the genetic control of lateral root emergence. Lateral roots are responsive to the mineral resources in soils and enable the plant to use them efficiently, so understanding how they develop has important implications for food security.

Using data on gene expression and transport of the hormone auxin, Nathan has developed a preliminary model using ordinary differential equations. This initial model has a single layer of cortical cells within the root (as in Arabidopsis), and will form the basis of more sophisticated models for cereal species such as barley, which have up to 15 cortical layers. Nathan’s ultimate aim is to produce a multi-cell model of lateral root development in cereal species.

CIPB, based at the University of Nottingham’s Sutton Bonington Campus, is a £9.2M, 5-year project, which began in 2007. It is one of 6 Centres for Integrative Systems Biology currently funded by BBSRC and Engineering and Physical Sciences Research Council.

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