Engineering root architecture using a predictive integrative systems biology approach

Lead Research Organisation: University of Nottingham
Department Name: Sch of Biosciences

Abstract

Food security represents a major global issue. This was also a major problem in the middle of the last century when food production failed to keep pace with population growth. In this latter case, plant breeders were able to develop new high yielding dwarf varieties of rice and wheat that responded to high inputs of fertilisers. The so-called 'Green Revolution' has delivered 50 years of food security. However, western societies are increasingly demanding that agriculture becomes more sustainable, through reductions in chemical inputs; whilst in the developing world, farmers with little access to fertilisers, need crops that can grow in infertile soils. In both cases, developing crops with improved nutrient use efficiency would provide the solution. Root architecture critically influences nutrient and water uptake efficiency. For example, rooting depth impacts the efficient acquisition of soil nitrogen (and water) since nitrate leaches deep into the soil. In contrast, phosphate use efficiency could be significantly improved without increasing root depth by manipulating the angle of root growth to better explore the top soil where this macronutrient accumulates. Despite this knowledge, root architecture has not been a trait selected for by plant breeders in major cereal crops. However, the need to improve nutrient use efficiency in crops through manipulating root architecture is becoming increasingly urgent. Its impact on world agriculture would be such that the crop scientist Jonathan Lynch has called for a 'Second Green Revolution' focussing on root architecture, and that this should be made 'a priority for plant biology in the 21st century'. This research proposal aims to first identify the genes that regulate root architecture in the simple plant Arabidopsis thaliana, then use this information to manipulate equivalent genes in cereals, with the ultimate goal of altering their root architecture and improving nutrient use efficiency. The ambitious programme of research relies on a new X-ray based technique (called Micro-CT) that can image the 3D arrangement of living roots in soil. We will use the Micro-CT technique to identify Arabidopsis mutants (which lack a specific gene) with an altered arrangement of roots. This will enable us to pinpoint exactly which genes regulate root architecture. Identifying equivalent genes in cereal crops is relatively straight forward since barley and rice are distantly related to Arabidopsis. We will then use advanced genetic techniques to inactivate these barley and rice genes and then examine their consequences on root architecture and nutrient use efficiency. Promising rice and barley lines will be made available to professional breeders at IRRI and SCRI with the ultimate aim to introgress their modified root traits into elite crop varieties.

Technical Summary

Crops with improved nutrient use efficiency are urgently required. Root architecture critically influences nutrient and water uptake efficiency. Despite the importance of root traits such as angle, depth and density, the genes that regulate these processes in crops remain to be identified. A key impediment to studying root architecture in plants grown in soil has been the inability to non-invasively image live roots. Recent advances in digital imaging using microscale X-ray Computed Tomography (Micro-CT) now permit their visualisation. The BBSRC Professorial Fellowship aims to exploit the recent advances in micro-CT imaging, together with integrative systems biology and plant genomic resources at Nottingham; with the ultimate aim to engineer the root architecture of crops in a predictive manner. Micro-CT imaging will be used to characterise the root architectures of new and existing Arabidopsis mutants and accessions. The genes identified will be integrated into models developed within the Centre for Plant Integrative Biology (CPIB) then be used to predictively guide the engineering of equivalent morphological changes in crop species. Our efforts will be focused in rice and barley, taking advantage of the genomic/genetic resources available for these systems in our collaborators laboratories as well as physiological expertise in rice and barley at Nottingham. Promising rice and barley lines will be made available to breeders at IRRI and SCRI with the ultimate aim of introgressing their modified root traits into elite crop varieties. The fellowship will also facilitate the integration of root-related research communities at Nottingham, by bringing crop researchers and soil scientists together with mathematicians, engineers, computer scientists and Arabidopsis systems biologists at CPIB to create a unique multi-disciplinary research environment to study and model rhizosphere processes in Arabidopsis and crop plants.

Publications

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Ahmadi N (2014) The roots of future rice harvests. in Rice (New York, N.Y.)

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Atkinson JA (2015) Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat. in Journal of experimental botany

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Atkinson JA (2017) An Updated Protocol for High Throughput Plant Tissue Sectioning. in Frontiers in plant science

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Band L (2012) Growth-induced hormone dilution can explain the dynamics of plant root cell elongation in Proceedings of the National Academy of Sciences

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Band LR (2013) Mapping the site of action of the Green Revolution hormone gibberellin. in Proceedings of the National Academy of Sciences of the United States of America

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Baskin TI (2010) Shootward and rootward: peak terminology for plant polarity. in Trends in plant science

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Benfey PN (2010) Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research. in The Plant journal : for cell and molecular biology

 
Description The project initially pioneered the use of an X-ray based imaging technique called CT to image roots in soil. By analyzing the CT images using specially developed software we were able to reconstruct images of roots as they grew through the soil.

Using this new imaging approach, we were able to discover entirely new ways that roots interact with their local environment and adapt their growth and branching patterns.

We were also able to uncover the genetic mechanisms controlling a number of these root responses and then manipulate these traits in crops in an attempt to improve ways that these plants obtain water and nutrients.
Exploitation Route The molecular and cellular mechanisms discovered during the award have been widely adopted and integrated into the fields understanding of how lateral roots initiate pattern and emerge. The review and research papers generated have been widely and highly cited and have had a major impact on the scientific thinking within the field.
Sectors Agriculture, Food and Drink,Chemicals,Digital/Communication/Information Technologies (including Software),Education,Environment,Leisure Activities, including Sports, Recreation and Tourism,Government, Democracy and Justice,Culture, Heritage, Museums and Collections,Pharmaceuticals and Medical Biotechnology

URL https://www.cpib.ac.uk/research/projects/root-systems-architecture/
 
Description A key challenge to studying roots of crops has been the inability to image roots in soil. The project pioneered the use of an X-ray imaging technique called microCT through the development of innovative software to reconstruct images of roots in small volumes of soil. This interdisciplinary approach have recently been 'up-scaled' (through an ERC Advanced Investigator Award) to enable scans of much larger soil columns through the creation of a multimillion pounds root imaging laboratory termed the Hounsfield Facility. Using this new imaging approach, we have been able to characterize • Entirely new (and also previously described) root adaptive responses in soil for the very first time such as hydropatterning and hydrotropism, respectively. • The effect of manipulating key genes controlling root processes, such as branching, angle and adaptive responses, in both model and crop plants.
First Year Of Impact 2010
Sector Agriculture, Food and Drink,Communities and Social Services/Policy,Digital/Communication/Information Technologies (including Software),Education,Environment,Government, Democracy and Justice,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Cultural,Societal,Economic,Policy & public services