Rice germplasm for high grain Zn content and tolerance of Zn deficient soils

Lead Research Organisation: University of Southampton
Department Name: Faculty of Engineering & the Environment

Abstract

Zinc (Zn) is an essential nutrient in micro-quantities for all living organisms. Deficiencies limit crop production in many parts of the world, and Zn is often deficient in the diet of humans subsisting on staple-food crops, causing severe health problems. An important strategy for dealing with this is to breed crops that are efficient in taking up Zn and concentrating it in edible plant parts. Rice is one of the main crops being targeted because of its global importance and the prevalence of Zn deficiency in populations subsisting on rice.

However rice is unusual in its Zn relations compared with other cereals in two respects. First, it is mainly grown in submerged soils, and because of the peculiar biogeochemistry of submerged soils, Zn deficiency in the crop is widespread, affecting up to 50% of rice soils globally. Second, as a result of inherent physiological differences, little Zn is remobilized from existing plant reserves to grains during the grain filling growth stages, as in other cereals, so that Zn uptake appears to be one of the main bottlenecks limiting rice grain Zn contents. Research has shown that grain Zn concentrations in rice - already low compared with other cereals or pulses - are further reduced in Zn deficient soils, and large fertilizer additions are needed to overcome this. Dietary and crop Zn deficiency are inevitably linked in areas with low Zn soils, as in most parts of Asia where rice is the staple. Enhancing the Zn uptake capacity of rice varieties will therefore be crucial to increasing grain contents. It will also be important to understand long-term sustainability of growing high grain Zn rice under inherently Zn-limited conditions, and what can be done to avoid problems in the future.

Current research at the International Rice Research Institute (IRRI) is using classical plant breeding combined with molecular biological markers for useful plant traits to develop rice varieties with high grain Zn contents and improved yields on Zn-deficient soils. Research is also underway to enhance grain Zn through agronomic means, including fertilizer and water management. However progress in these activities, and in understanding long-term sustainability issues, is constrained by our poor understanding of the mechanisms underlying genotype differences, and of the dynamics of plant-available Zn in the soil within the growing season and longer term.

In recent research by members of the project team, we have shown that three key mechanisms enhance growth of rice seedlings in Zn deficient soil: (a) secretion from roots of Zn-chelating compounds called phytosiderophores and subsequent uptake of chelated Zn in the rhizosphere, (b) maintenance of new root growth, and (c) prevention of root damage by oxygen radicals linked to high bicarbonate concentrations. Studies with a limited set of genotypes suggest that Zn loaded into grains mostly comes from Zn uptake during the reproductive stages rather than by re-translocation from vegetative tissue. The mechanisms listed above in relation to seedling growth may also assure adequate Zn uptake during the reproductive phase. However, this has not been systematically investigated so far, nor have any genes related to reproductive-stage Zn uptake been tagged.

The proposed research addresses these knowledge gaps with an interdisciplinary approach linking fundamental research on soil biogeochemistry, molecular physiology and genetics with applied work on agronomy and plant breeding, with a conceptual framework provided by mathematical modelling. Our goal is to develop genotypes and management practices for growing high Zn rice in Zn deficient soils, suitable for resource-poor farmers. This will encompass agronomic interventions based on understanding of limiting factors for Zn uptake and translocation, and breeding approaches based on understanding of genetic factors controlling key tolerance mechanisms.

Technical Summary

The project is in four work packages corresponding to the above four specific objectives. In WP1 we will use field, controlled environment and laboratory experiments to assess whether the mechanisms we have identified for seedling-stage tolerance of Zn deficiency universally separate tolerant from sensitive genotypes under seedling-stage Zn deficiency in different soils, and whether they continue to enhance uptake and grain filling during reproductive stages. The field experiments will be at four sites in the Philippines and four in Bangladesh, covering the range of soil types in which Zn deficiency occurs. We will use a common set of 12 contrasting genotypes. Methods will include a novel stable-isotope technique for studying uptake processes. In WP2 we will seek to identify loci and genes enhancing Zn uptake during vegetative and reproductive growth stages, leading to high grain Zn concentrations. Two methods will be used: (a) conventional QTL mapping based on a bi-parental cross, and (b) genome wide association mapping (GWAM) based on a panel of 178 genebank accessions. We will use the results for fine mapping and candidate gene identification. In WP3, we will develop and experimentally test mathematical models of Zn uptake processes in rice paddies, allowing for the biogeochemistry of Zn in submerged soils over the growing season and longer term, and the mechanisms of root-soil interactions. We will use the models and parameter values from the field and other experiments to assess strategies for increasing uptake in different environments and to predict the long-term sustainability of growing high Zn rices in Zn-deficient environments. In WP4 we develop rice breeding and management options and feed them into existing technology-transfer programmes at IRRI. This will include introgression of markers identified in WP2 into major Bangladeshi and Philippine rice varieties.

Planned Impact

See main proposal.

Publications

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Cooper LJ (2017) Fluid flow in porous media using image-based modelling to parametrize Richards' equation. in Proceedings. Mathematical, physical, and engineering sciences

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Daly K (2017) Modelling water dynamics in the rhizosphere in Rhizosphere

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Daly KR (2016) Image-based modelling of nutrient movement in and around the rhizosphere. in Journal of experimental botany

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Kirk GJD (2019) Soil carbon dioxide venting through rice roots. in Plant, cell & environment

 
Description Soil CO2 and plant nutrient uptake are correlated and how this could be use for better plant breeding and soil management in submerged soils.
Exploitation Route Engagement with crop breeders and policy makers.
Sectors Agriculture, Food and Drink

 
Description By engagement with Bayer and Syngenta we have contributed to transferring the state of the art modelling technology from academia to industry.
First Year Of Impact 2016
Sector Agriculture, Food and Drink
Impact Types Societal,Economic

 
Description The Parliamentary and Scientific Committee Discussion meeting on "Are we looking after our soils?" organised by Stephen Metcalfe MP
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
Impact This meeting on Nov 3rd 2015 was to discuss the importance of soils on the UK plc. One of the recommendations was to look into introducing "caring for soils" into farmer tenancy agreements as part of the revised bill dealing with short term tenants. Ie similar to housing tenants who are required to take care of the house they are renting and hand it back in a good conditions, it was suggested that the farmers should also take care of the soil and hand it back in equally good or improved conditions at the end of their term.
 
Description ERC Consolidator Grant
Amount € 1,996,246 (EUR)
Funding ID 646809 
Organisation European Research Council (ERC) 
Sector Public
Country Belgium
Start 09/2015 
End 08/2020
 
Title Data for paper titled "Image based modeling of nutrient movement in and around the rhizosphere eprints: http://eprints.soton.ac.uk/384747/ data doi:10.5258/SOTON/384747 data eprints: http://eprints.soton.ac.uk/384502" 
Description Image based modeling of nutrient movement in and around the rhizosphere eprints: http://eprints.soton.ac.uk/384747/ data doi:10.5258/SOTON/384747 data eprints: http://eprints.soton.ac.uk/384502 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Image based modeling of nutrient movement in and around the rhizosphere eprints: http://eprints.soton.ac.uk/384747/ data doi:10.5258/SOTON/384747 data eprints: http://eprints.soton.ac.uk/384502 
URL http://eprints.soton.ac.uk/384502
 
Description An invited talk at Bayer CropScience's Workshop titled "Soil and Root Health" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Feb 2016: Bayer CropScience's - Soil and Root Health Symposium. This event will take place on February 16-17, 2016 at the headquarter campus of Bayer CropScience at Monheim, Germany.
Year(s) Of Engagement Activity 2016
 
Description Conference talk at Rhizosphere 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Talk titled "Fusing synchrotron imaging, spectroscopy and computational modelling for enhanced understanding of nutrient dynamics" by S.D. Keyes, K. R. Daly and T. Roose at Rhizosphere 2015 conference in Maastricht sparked questions and discussion.

after the talk several international people approached us for potential future collaborations and lab visits.
Year(s) Of Engagement Activity 2015
 
Description Conference: Rhizo4, Maastricht 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A large conference held every 4 years concerning all aspects of plant and soil modelling given to a wide audience. Great networking opportunity and experience of lots of other academic work in a similar field. Poster entitled "Using a whole plant crop model to assess phosphate fertiliser use in barley".
Year(s) Of Engagement Activity 2015
URL http://www.rhizo4.org
 
Description Feb 14-17 2018 Phenome 2018 Tuscon Arizona US. Keynote speaker for the theme "Algorithms and Data Management for Phenotype Quantification and Analysis". 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Feb 14-17 2018 Phenome 2018 Tuscon Arizona US. Keynote speaker for the theme "Algorithms and Data Management for Phenotype Quantification and Analysis".
Year(s) Of Engagement Activity 2018
 
Description July 2018 Plenary speaker at Society of Mathematical Biology conference in Sydney. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact July 2018 Plenary speaker at Society of Mathematical Biology conference in Sydney.
Year(s) Of Engagement Activity 2018
 
Description K.R. Daly, S.D. Keyes and T. Roose, Image based modelling of plant scale soil properties, BSSS/SSP conference 7th-8th September 2016 (poster) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster at the British Soil Science Society Conference:
K.R. Daly, S.D. Keyes and T. Roose, Image based modelling of plant scale soil properties, BSSS/SSP
conference 7th-8th September 2016 (poster)
Year(s) Of Engagement Activity 2016
 
Description Keynote Talk at British Society of Soil Science Annual Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This was a talk to 100-200 delegates of the annual national conference of the British Society of Soil Science

Abstract:

The mechanical impedance of soils inhibits the growth of plant roots, often being the most significant physical limitation to root system development. We require approaches to observe and quantify the link between root growth traits, soil properties, and the way roots ingress the soil.

In this study, we first developed an experimental assay and methodology for rapid, four-dimensional, in vivo X-ray Computed Tomography (XCT) of single maize roots growing unconstrained in a field-derived soil. Then, a Digital Volume Correlation (DVC) approach was used to analyse the soil fabric, permitting quantification of local deformations in three dimensions. This revealed the full-field soil displacement behaviour around a growing root tip for the first time. The quantification approach was separately validated for the soil using a compression rig to induce soil displacements of known magnitude and direction. Significance thresholds of displacement and strain measurement were also robustly calculated. When applied to quantify deformations over 20 h of growth of a maize cultivar, the results reveal the heterogeneity of the soil displacements in both space and time. An oscillatory pattern of displacement magnitude and direction was revealed, which may relate to biophysical oscillations of the plant root. Because it was possible to quantify root growth velocity alongside the soil deformations, these data could be fused for the first time, allowing the relative directions of soil displacement and root growth to be compared in vivo.

This fusion of methods paves the way for comparative studies of root ingress to soils at a range of scales, using a panel of contrasting soil properties and plant genotypes. Such studies will aid our understanding of beneficial root traits for maintaining root architecture development under challenging soil conditions (i.e. local compaction and drought).
Year(s) Of Engagement Activity 2016
URL http://www.soils.org.uk/event/920
 
Description Keynote talk at Keystone 2016 "Microphytobiomes". Title of the talk "Multiscale Modelling of Plant-Soil Interaction" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Nov 2016: Keystone Symposia on Molecular and Cellular Science. Invited to give a Keynote address by Drs. Jan E. Leach, Kellye A. Eversole, Jonathan A. Eisen, Gwyn Beattie and Marcos A. Machado, we are Keystone Symposia on Phytobiomes: From Microbes to Plant Ecosystems, held in Santa Fe.
Year(s) Of Engagement Activity 2016
URL https://www.keystonesymposia.org/17S2
 
Description Keynote talk at Kirkham Conference 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact April 2016: Kirkham conference invited speaker; talk titled "Multiscale mathematical modelling of plant-soil interaction"
Year(s) Of Engagement Activity 2016
URL https://www.soils.org/membership/divisions/soil-physics-and-hydrology/kirkham-conferences
 
Description Minisymposia at BAMC titled "Multi scale analysis of porous media" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Porous materials are a fundamental building block of many terrestrialmaterials, eco-systems, biological tissues, and manmade engineering materials. There are numerous examples of porous materials for which enhanced modelling and optimisation techniques will offer significant gains in efficiency and productivity. In agriculture, 30% of UK wheat currently needs to be grown on drought-prone land, where yields are limited by the scarcity of water in the soil. In the construction industry, the reuse of pulverised fuel ash as a low porosity material for flood embankments is limited by the potential leaching of heavy metals into the surrounding environment. To overcome these, and many other problems there is a clear need to go beyond idealised models and develop a more detailed understanding of flow and transport phenomena in such systems.
The mathematics of multiscale modelling in porous media is a rapidly growing field with wide ranging applications and collaborative opportunities. In this mini symposium we will discuss the mathematics of porous media. We will focus on pore scale and continuous descriptions of transport, fluid dynamics and structural mechanics. In addition talks will focus on how asymptotic techniques can be used to exploit the large variations in scales within these materials to link properties on the pore scale to macro-scale observations.
Whilst the main focus of the session is on the mathematical developments occurring in different areas of porous media, we will also focus on application and how mathematical techniques can be integrated with Computed Tomography and continuum scale measurements to inform industry practise, answer fundamental questions, and optimise porous materials across a range of different applications
Speakers
The session will include talks from five speakers working in different areas of porous media at different scales.
Dr Keith Daly - University of Southampton
Combining homogenisation theory and image based modelling to predict the poro-elastic properties of multi-constituent soils
Dr Laura Cooper - University of Warwick
Macroscopic effects of microscale interfaces
Dr Rebecca Shipley - University College London
Porous medium models to predict spatial heterogeneity in anti-cancer therapy efficacy
Mr Simon Duncan - University of Southampton
Solute movement and uptake in dynamic poroelastic materials
Dr Matteo Icardi - University of Nottingham
Upscaling reactive and electrochemical transport in porous media
Year(s) Of Engagement Activity 2018
 
Description On the Need to Establish an International Soil Modelling Consortium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Type Of Presentation keynote/invited speaker
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference presentation preparation for Complex Soil Systems Conference in Berkeley Sept 3-5 2014.
Full list of authors of this presentation is:
Vereecken H., Vanderborght J., Schnepf A., Brüggemann N., Amelung W., Herbst M., Javaux M., Van der Zee S.E.A.T.M., Or D., Šimunek J., van Genuchten M. Th., Vrugt J.A., Hopmans J.W., Young M.H., Baveye P., Pachepsky Y., Vanclooster M., Hallett P.D., Tiktak A., Jacques D., Vogel T., Jarvis N., Finke P., Jiménez J.J., Garnier P., Li C., Ogee J, Mollier A., Lafolie F., Cousin I., Pot V., Maron P.A., Roose T., Wall D.H., Schwen, A., Doussan C., Vogel H.J., Govers G., Durner W., Priesack E., Roth K., Horn R., Kollet S., Rinaldo A., Whitmore A., Goulding K., Parton, W.J.

Establishment of the world wide soil modelling consortium.
Year(s) Of Engagement Activity 2014
 
Description On the need to establish an international soil modelling consortium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Type Of Presentation keynote/invited speaker
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was a presentation at the Soil Science Society of America Meeting in Longreach CA Nov 2-5 2014
Full author list of the presentation is:
Vereecken H., Vanderborght J., Schnepf A., Brüggemann N., Amelung W., Herbst M., Javaux M., Van der Zee S.E.A.T.M., Or D., Šimunek J., van Genuchten M. Th., Vrugt J.A., Hopmans J.W., Young M.H., Baveye P., Pachepsky Y., Vanclooster M., Hallett P.D., Tiktak A., Jacques D., Vogel T., Jarvis N., Finke P., Jiménez J.J., Garnier P., Li C., Ogee J, Mollier A., Lafolie F., Cousin I., Pot V., Maron P.A., Roose T., Wall D.H., Schwen, A., Doussan C., Vogel H.J., Govers G., Durner W., Priesack E., Roth K., Horn R., Kollet S., Rinaldo A., Whitmore A., Goulding K., Parton, W.J.

Formation of the international soil modelling consortium
Year(s) Of Engagement Activity 2014
 
Description Talk at AGU Fall meeting 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Type Of Presentation keynote/invited speaker
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk titled "Current advancements and challenges in soil-root interactions modelling" by A. Schnepf, K. Huber, B. Abesha, F. Meaner, D. Leitner, T. Roose, M. Javaux, J. Vanderbroght, H. Vereecken was given at AGU Fall meeting 15-19 Dec 2014 in San Francisco.

Collaborations discussed
Year(s) Of Engagement Activity 2014
 
Description Talk titled "High resolution synchrotron imaging of rhizosphere structure " at the EGU 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact High resolution synchrotron imaging of rhizosphere structure ; European Geophysical Union 2018 meeting

Nicolai Koebernick1, Keith R. Daly1, Samuel D. Keyes1, Timothy S. George2, Lawrie K. Brown2, Annette Raffan3, Laura J. Cooper1, Muhammad Naveed3, Anthony G. Bengough2,4, Ian Sinclair1, Paul D. Hallett3 and Tiina Roose1,$
1 Bioengineering Sciences Research Group, Engineering Sciences Academic Unit, Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, United Kingdom
2 Ecological Sciences Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
3 Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen AB24 3UU , United Kingdom
4 School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
$ corresponding author
Email corresponding author: t.roose@soton.ac.uk
Keywords: non-invasive imaging, rhizosphere, root hairs, soil structure, root exudates

Plant roots induce hydromechanical stresses and release organic compounds into soil, which are major drivers of soil structure formation. Whilst it is well known that roots impact the structure and physico-chemical properties of the rhizosphere, the underlying processes and their impact on resource flows to plants require greater investigation. We are exploring how different root traits physically manipulate soils, drawing on near isogenic barley lines that differ in root hairs, architecture and exudation, as well as new imaging approaches to quantify rhizosphere impacts.
A barley wildtype and its mutant with greatly reduced root hair growth were grown in specially designed assays that enabled high-resolution synchrotron imaging of rhizosphere structure with resolutions sufficient to detect root hairs. A sandy loam textured soil (Dystric Cambisol, sieved to < 1 mm) was used as a growth medium. The results showed that root hairs may play an important role in rhizosphere structure formation by alleviating the compression that is induced by growing roots. Root induced compression was evidenced by decreased air-filled pore space between 0.1 and 0.8 mm from the root surface. However, at the root-soil interface, the pore space increased for the root hair bearing barley genotype, but not for the barley mutants with no root hairs.
In a similar experiment, conducted with a remoulded soil (Dystric Cambisol, sieved to <250 um), both genotypes showed increased porosity at the root soil interface with no significant differences between the genotypes. Pore size distribution was narrower at the root-soil interface and became wider with distance from the root due to the decreased volume of large pores near the root surface.
Increased porosity near the root is discussed as an effect of the geometry of soil particles at the root surface. A model is proposed that describes the variation in porosity around roots, taking into account both root induced compression and the simplified geometry of solid mineral particles at the root surface.
Year(s) Of Engagement Activity 2018
 
Description Talk titled "Imaging and modelling of rhizosphere processes" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Geophysical Research Abstracts
Vol. 20, EGU2018-18157, 2018
EGU General Assembly 2018
© Author(s) 2018. CC Attribution 4.0 license.
Imaging and modelling of rhizosphere processes
Arjen van Veelen, Nico Koebernick, Dan McKay Fletcher, Callum Scotson, Keith Daly, Robbie Mayone, Simon Duncan, and Tiina Roose
University of Southampton, Faculty of Engineering and the Environment, United Kingdom (a.van-veelen@soton.ac.uk)
Most human food relies on the production of crops. Crops get their nutrients and water from the soil. In addition, soil has many other important functions, including the buffering of hydrological systems to prevent flooding and the provision of a carbon sink, lowering atmospheric carbon. Although bulk soil chemical processes are relatively well understood, there is a critical lack of studies characterising the dynamics of physico-chemical properties in the rhi- zosphere, such as nutrient cycles and release of plant exudates. These changes to the soil can drastically change the soil's hydraulic, nutrient and carbon functionality. This emphasises the importance to visualise physico-chemical information, in order to understand key processes of plant-soil interactions. In our interdisciplinary project, Data Intensive Modelling of the Rhizosphere Processes (DIMR), we aim to characterise and visualise these dynamics. The aim of the programme is to visualise pore geometry in soils using X-ray Computed Tomography (CT), com- bined with Nuclear Magnetic Resonance Imaging (NMRI) to visualize plant exudates and water distribution. In addition, we use synchrotron X-ray Fluorescence (XRF) and X-ray Absorption Spectroscopy (XAS) to understand both soil chemistry and speciation at the root-soil interface, all leading to a better understanding of rhizosphere processes. These methods can be combined with predictive models of soil-root processes to understand rhizosphere functionality. We will discuss how chemical data obtained from both NMR and XRF and XAS spectroscopy can enable a step change in multiscale modelling of rhizosphere processes.
Year(s) Of Engagement Activity 2018