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

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.

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.

In addition to the academic beneficiaries listed above, the project will benefit rice breeders and agronomists concerned with genetic improvement for Zn deficient soils and biofortification of rice varieties, and related management practices, and, in the medium- and longer-term, rice producers and consumers, particularly those in areas with Zn deficient soils.

By the end of the project we will have identified genetic markers for relevant traits for use in marker-assisted breeding, we will have begun introgression of the markers into major Bangladeshi and Philippine rice varieties, and we will have developed agronomic management recommendations for optimizing the function of these new varieties. We will facilitate the adoption of the new varieties and management strategies by farmers in Asia through existing technology-transfer programmes with which IRRI and the project team are involved.

A key issue in the adoption of new varieties with traits that do not have any obvious effects of yields - such as high grain Zn - is how to convince farmers to give up their tried and tested varieties in favour of new ones. The recent success of the Sub1 gene for submergence tolerance in rice has shown that adoption is fast if key traits are added to already-established varieties. In this project, by finding loci for better Zn uptake and loading into grains, we will allow modifications of existing varieties to be made, and will therefore facilitate smoother adoption. Hence we will strongly compliment IRRI's existing, less-targeted biofortification work.

These relevant technology-transfer programmes at IRRI are HarvestPlus, concerned with micronutrient malnutrition and biofortification; the Cereal Systems Initiative for South Asia (CSISA), for accelerated development and deployment of new varieties, management technologies and policies for cereal systems in South Asia; and Stress-tolerant Rice for Africa and South Asia (STRASA) concerned with varieties and technologies for rainfed rice systems. Each of these has components for germplasm testing with farmers, followed by seed multiplication, distribution, and impact evaluation. These programmes are designed for accelerated product development and deployment; the current project will assure that new genetic material and breeding tools will enter the product development pipeline.

CSISA is also promoting a decision-support tool for nutrient management called Nutrient Manager, which allows farmers to receive field- and season-specific fertilizer recommendations after answering an interactive series of 10-15 questions about their specific environment. This is available on the internet and, in the Philippines and coming soon to Bangladesh, through a mobile phone application via SMS messaging. A team at IRRI is in the process of including genotype information and irrigation and crop establishment recommendations in this decision tool. The findings of the proposed project, as generalised through the modeling in WP3, will allow fine-tuning of nutrient management advice for Zn-deficient areas.

The project's findings will be will transferred to breeders and agronomists at IRRI and its partners through direct interactions with members of the project team. The main route for dissemination to other scientists will be through publications in high impact journals and presentations at international conferences. All members of the project team have strong track records in publishing in top-ranked journals in their areas and in broad-reach journals. We will make all datasets and models produced in the project available to other researchers, following publication of papers, via websites at the project team's host organizations.

IRRI has strong links with rice policy makers in Asia and globally. We will exploit these direct contacts. We will produce regular reports for websites and newsletters of our respective organizations, to communicate with policy makers and the general public.