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

Lead Research Organisation: Imperial College London
Department Name: Earth Science and Engineering


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


10 25 50
Description In the work package of the research grant we were involved in, we addressed the question why some rice genotypes can take up the micronutrient Zinc better than the others.
To that end, we studied the isotope fractionation of Zn during uptake and we constrained the isotopic fractionation occurring during the complexation of Zn with ligands (photo-siderophores) using laboratory experiments and theoretical calculations.
Our work confirmed previous work that (i) isotopically heavy Zn is taken up and (ii) that direction and extent agree determined from lab experiments and theoretical calculations agree with that observed in field.
This suggests that the involvement of the phytosiderophore mugeneic acid is a key component in this process.
Another important contribution was that we developed an analytical technique that enables the determination of labile Zn in paddy soils. that in turn enables us now to study the dynamics of the Zn uptake in paddy soils. This was not achieved to date
Exploitation Route This work will now help plant breeders at IRRI to decide on which genotypes to concentrate and which genotypic trait to promote.
To date, it was not clear what controls the uptake.
We are closely working with the International Rice Research Institute.
The next step will be to study the photosiderophore dynamics during the plant cycle and investigate how much is excreted and when.
We also will use the spiking techniques to study now the uptake mechanisms as we have developed the analytical method.
Finally, we are now using the isotope ratios to study the movement of Zn within the plant. We have published a first paper (Arnold et al., CR Geosciences, 2015)
Sectors Agriculture, Food and Drink,Environment

URL http://www.imperial.ac.uk/people/d.weiss
Description Our work shows strong evidence for what controls the uptake mechanism of Zn in rice. It is the excretion of organic molecules that bind to Zn and remove it from soil solution to be taken up by the plant. These findings are now taken further by plant breeders at IRRI. The analytical method developed to study the Zn dynamics in soils (see Izquierdo et al., Eur J Soil Sci, 2014) has been adapted by other researchers. For example, the group of Frossard at the ETH Zurich is studying the uptake of Zn in organic fertilizers using the isotope dilution method.
First Year Of Impact 2010
Sector Agriculture, Food and Drink
Impact Types Societal,Economic

Description IsoPlant
Amount £189,000 (GBP)
Organisation European Research Council (ERC) 
Sector Public
Country European Union (EU)
Start 07/2012 
End 01/2015
Description IsoTrace
Amount £169,000 (GBP)
Organisation European Research Council (ERC) 
Sector Public
Country European Union (EU)
Start 10/2013 
End 09/2015
Description PhD scholarship from Islamic Development Bank
Amount £70,000 (GBP)
Organisation Islamic Development Bank (IDB) 
Sector Private
Country Saudi Arabia, Kingdom of
Start 03/2017 
End 02/2021
Title Stable Isotope Fractionation 
Description stable isotopes indicate biochemical mechanism of uptake 
Type Of Material Model of mechanisms or symptoms - non-mammalian in vivo 
Provided To Others? No  
Impact the techniques enables in vivo assessment of biogeochemical processes 
Title Stable isotope spiking 
Description stable isotope spiking combined with high precision isotope measurements explain mechanisms of Parkinson 
Type Of Material Model of mechanisms or symptoms - human 
Provided To Others? No  
Impact show that high precision isotope measurements identify metabloisi of metals in humans and plants and environment 
Description Chemistry Department - Ramon Vilar 
Organisation Imperial College London
Department Department of Chemistry
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution analytical expertise problem definition supervison of students
Collaborator Contribution synthetic work
Impact papers funding joint supervision
Start Year 2008
Description Cranfield University 
Organisation Cranfield University
Department Cranfield Soil and Agrifood Institute
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Measurements of isotope ratios Analytical consulting
Collaborator Contribution Lab experiments re Zn dissolution
Impact multi disciplinary
Description International Rice Research Institute 
Organisation International Rice Research Institute
Country Philippines, Republic of the 
Sector Charity/Non Profit 
PI Contribution Isotope ratio determinations
Collaborator Contribution Field study
Impact na
Description JIRCAS 
Organisation Japan International Research Center for Agricultural Sciences (JIRCAS)
Country Japan 
Sector Public 
PI Contribution isotope measurements
Collaborator Contribution expertise in genotyping seeds deliverable
Impact identification of Zn uptake mechanisms
Title Stable isotope technique to measure exchangeable Zn in paddy soils 
Description improved way to determine available Zn for uptake in submerged soils 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2016 
Impact method to determine exchangeable Zn in submerged soils 
Description Goldschmidt Conference (Czech Republic) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact We gave a talk at the Goldschmidt Conference, Prague, Czech Republic
Year(s) Of Engagement Activity 2016
Description Goldschmidt Conference Prague 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference presentation (Goldschmidt) in Prague by Tamara Markovic
Year(s) Of Engagement Activity 2015
Description Teaching on NERC Soil Course in 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I was teaching a lecture course on soil chemistry to PhD students with a NERC Soil Course
Year(s) Of Engagement Activity 2014
Description Workshop on Rice Efficiency 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact workshop with approx 60 people
Year(s) Of Engagement Activity 2012