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.
Organisations
Publications
Zhang W
(2013)
Cytokinin induces cell division in the quiescent center of the Arabidopsis root apical meristem.
in Current biology : CB
Zappala S
(2013)
Quantifying the effect of soil moisture content on segmenting root system architecture in X-ray computed tomography images
in Plant and Soil
Zappala S
(2013)
Effects of X-Ray Dose On Rhizosphere Studies Using X-Ray Computed Tomography.
in PloS one
Yang J
(2017)
Dynamic Regulation of Auxin Response during Rice Development Revealed by Newly Established Hormone Biosensor Markers.
in Frontiers in plant science
Wilson M
(2013)
SnapShot: Root development.
in Cell
Wells DM
(2012)
Recovering the dynamics of root growth and development using novel image acquisition and analysis methods.
in Philosophical transactions of the Royal Society of London. Series B, Biological sciences
Wells DM
(2010)
Feeling UPBEAT about growth: linking ROS gradients and cell proliferation.
in Developmental cell
Voß U
(2015)
The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana.
in Nature communications
Von Wirén N
(2016)
Crosstalk between Gibberellin Signaling and Iron Uptake in Plants: An Achilles' Heel for Modern Cereal Varieties?
in Developmental cell
Von Wangenheim D
(2020)
Early developmental plasticity of lateral roots in response to asymmetric water availability.
in Nature plants
Ugartechea-Chirino Y
(2009)
The AUX1 LAX family of auxin influx carriers is required for the establishment of embryonic root cell organization in Arabidopsis thaliana
in Annals of Botany
Twycross J
(2010)
Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study.
in BMC systems biology
Swarup R
(2016)
One Gene, Many Proteins: Mapping Cell-Specific Alternative Splicing in Plants.
in Developmental cell
Scofield S
(2018)
Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network.
in Development (Cambridge, England)
Schoenaers S
(2018)
The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth.
in Current biology : CB
Scherzer S
(2017)
Insect haptoelectrical stimulation of Venus flytrap triggers exocytosis in gland cells.
in Proceedings of the National Academy of Sciences of the United States of America
Sager R
(2020)
Auxin-dependent control of a plasmodesmal regulator creates a negative feedback loop modulating lateral root emergence.
in Nature communications
Roy S
(2017)
MtLAX2, a Functional Homologue of the Arabidopsis Auxin Influx Transporter AUX1, Is Required for Nodule Organogenesis.
in Plant physiology
Rossall S
(2016)
A 'growing' role for phosphites in promoting plant growth and development
in Acta Horticulturae
Reinhardt H
(2016)
Tonoplast Aquaporins Facilitate Lateral Root Emergence.
in Plant physiology
Péret B
(2012)
AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during Arabidopsis development.
in The Plant cell
Péret B
(2013)
Sequential induction of auxin efflux and influx carriers regulates lateral root emergence.
in Molecular systems biology
Pound M
(2013)
RootNav: Navigating Images of Complex Root Architectures
in Plant Physiology
Postma JA
(2017)
OpenSimRoot: widening the scope and application of root architectural models.
in The New phytologist
Porco S
(2016)
Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3.
in Development (Cambridge, England)
Porco S
(2016)
Dioxygenase-encoding AtDAO1 gene controls IAA oxidation and homeostasis in Arabidopsis.
in Proceedings of the National Academy of Sciences of the United States of America
Perrine-Walker F
(2010)
Auxin carriers localization drives auxin accumulation in plant cells infected by Frankia in Casuarina glauca actinorhizal nodules.
in Plant physiology
Passot S
(2016)
Characterization of Pearl Millet Root Architecture and Anatomy Reveals Three Types of Lateral Roots.
in Frontiers in plant science
Pandey BK
(2021)
Plant roots sense soil compaction through restricted ethylene diffusion.
in Science (New York, N.Y.)
Orosa-Puente B
(2018)
Root branching toward water involves posttranslational modification of transcription factor ARF7.
in Science (New York, N.Y.)
Orman-Ligeza B
(2013)
Post-embryonic root organogenesis in cereals: branching out from model plants.
in Trends in plant science
Orman-Ligeza B
(2016)
RBOH-mediated ROS production facilitates lateral root emergence in Arabidopsis.
in Development (Cambridge, England)
Muraro D
(2011)
Root development: cytokinin transport matters, too!
in Current biology : CB
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
Muraro D
(2013)
Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana.
in IEEE/ACM transactions on computational biology and bioinformatics
Morris EC
(2017)
Shaping 3D Root System Architecture.
in Current biology : CB
Mooney S
(2011)
Developing X-ray Computed Tomography to non-invasively image 3-D root systems architecture in soil
in Plant and Soil
Middleton AM
(2010)
Mathematical modelling of the Aux/IAA negative feedback loop.
in Bulletin of mathematical biology
Middleton AM
(2012)
Mathematical modeling elucidates the role of transcriptional feedback in gibberellin signaling.
in Proceedings of the National Academy of Sciences of the United States of America
Mellor N
(2016)
Dynamic regulation of auxin oxidase and conjugating enzymes AtDAO1 and GH3 modulates auxin homeostasis.
in Proceedings of the National Academy of Sciences of the United States of America
Marín-De La Rosa N
(2015)
Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins.
in PLoS genetics
Mairhofer S
(2013)
Recovering complete plant root system architectures from soil via X-ray µ-Computed Tomography.
in Plant methods
Mairhofer S
(2012)
RooTrak: automated recovery of three-dimensional plant root architecture in soil from x-ray microcomputed tomography images using visual tracking.
in Plant physiology
Mairhofer S
(2017)
X-Ray Computed Tomography of Crop Plant Root Systems Grown in Soil.
in Current protocols in plant biology
Mairhofer S
(2015)
Extracting multiple interacting root systems using X-ray microcomputed tomography
in The Plant Journal
Mairhofer S
(2015)
On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images.
in Functional plant biology : FPB
Lucas M
(2011)
Plant systems biology: network matters.
in Plant, cell & environment
Lucas M
(2011)
Short-Root regulates primary, lateral, and adventitious root development in Arabidopsis.
in Plant physiology
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 |