Mechanisms and genetics of iron toxicity tolerance in African rice

Rice is a major staple food across sub-Saharan Africa (SSA) and demand for rice is increasing rapidly with changes in consumer preferences and urbanization. However, domestic production currently accounts for only about 60% of consumption; imports to SSA amount to a third of the global rice trade. Accordingly there are various national and international initiatives with ambitious plans for increasing production across SSA. There are ample agro-climatically suitable wetlands in inland valleys and elsewhere to support a large intensification and expansion of rice area. During the rainy season, rice is the only possible crop on low-lying wetlands, so it does not compete with other crops for land or water. However, besides agricultural production, i.e. mainly rice-based systems including fish, vegetable, fruit and livestock production, inland valleys also provide local communities with forest, forage, hunting and fishing resources and they are important for water buffering and as biodiversity hot spots. Development for agricultural production must be done in such a way as to avoid compromising these locally- and regionally-important ecosystem services. This will require improved rice germplasm and nutrient and water management suited to these systems, so as to minimise the land area required. It will also require technologies for assessing which areas across SSA are best suited to intensification and expansion of rice-based farming, without compromising other ecosystem goods and services. It is estimated that with realistic improvements in germplasm and management, less than 10% of the total inland valley area in SSA would be sufficient to meet the total demand for rice in Africa. But various biophysical constraints need to be overcome; one of the most important is the soil health problem iron (Fe) toxicity.

Iron toxicity is a set of severely yield-limiting disorders associated with high concentrations of reduced ferrous iron (Fe(II)) in flooded paddy soils. It is exclusively a problem of paddy rice, linked to the biogeochemistry of flooded, anaerobic soil. It is a particular problem in African rice systems because of the nature of the soils, which are highly weathered, nutrient-depleted and rich in Fe oxides, in contrast to the young alluvial rice soils of the Asian lowlands. It affects a large part of the existing and potential rice area in SSA (estimates vary from 20-60% of the area) and causes large yield losses (up to 90%). There are currently efforts to exploit tolerance of it in the indigenous African rice germplasm in breeding and management programmes at AfricaRice and elsewhere. But this is constrained by the complexity of the disorder and by poor understanding of the underlying mechanisms and genetics of tolerance, which reflects its relative unimportance in Asian rice systems where most rice research has been focused.

We propose to provide the bioscience and tools required to (a) elucidate the mechanisms and genetics of tolerance to Fe toxicity in indigenous African germplasm, in support of rice breeding and management programmes, and (b) assess the potential of improved germplasm and management to raise the productivity of existing and new rice-based farming systems across SSA. We will especially focus on Oryza glaberrima ('African' rice) species, indigenous to W Africa, and sub-species of Oryza sativa ('Asian' rice) indigenous to Madagascar. We will use a combination of soil chemistry, plant physiology and molecular genetics approaches with field work in W Africa and Madagascar, supported by controlled-environment and laboratory work in the UK. We will also map the spatial extent of different types of Fe toxicity in existing and potential rice areas across SSA, and we will develop GIS tools for assessing the potential for improved germplasm and nutrient and water management to raise the productivity of rice-based farming systems in these areas.

We will propose four work packages (WP) corresponding to the above four Objectives.

WP1 We will establish field experiments at sites in W Africa and Madagascar covering the range of Fe toxic conditions and use them for phenotyping of QTL mapping populations and GWAS panels covering the range of promising W African and Malagasy germplasm. We will characterise GxE interactions and identify a set of germplasm with specific adaptions. Key germplasm identified in this WP will be used in WP2 to dissect tolerance mechanisms, and in WP3 for gene mapping and identification of markers.

WP2 We will investigate tolerance mechanisms in key germplasm from WP1 using controlled environment and laboratory experiments with soils brought to Cranfield from the field sites in W Africa and Madagascar, supported by mathematical modelling. We will investigate the following potential tolerance mechanisms: root exclusion of Fe, root-induced changes in the rhizosphere, restricted root:shoot transfer, shoot tolerance, and interactions with other nutrients and stresses.

WP3 Based on results of WP1, genotypes with stable tolerance across years and representing contrasting haplotypes for most influential loci identified in GWAS and standard QTL analyses will be used for studies on possible candidate genes and tolerance mechanisms. These will be tested for gene expression patterns under Fe toxicity. Improved understanding of tolerance mechanisms from WP2 will guide the candidate gene characterization. Marker development for the most influential loci will focus on simple gel-based markers using allele-specific primer design and high-throughput markers such as KASP.

WP4 We will use digital soil mapping and assessment techniques to map the different types of Fe toxicity in existing and potential rice areas across SSA, and use the resulting GIS tool to assess the potential of improved germplasm and management to raise the productivity of rice-based farming systems in these areas.

We aim to support increased African food security through intensification and expansion of rice-based farming systems across SSA, particularly in inland valleys and other areas affected by iron toxicity. We aim to achieve this in the short (project life-time) and medium (within five years) terms through the following beneficiaries:

(1) Plant breeders and agronomists at AfricaRice, National Agricultural Research and Extension Systems (NARES) and elsewhere concerned with developing high-yielding rice varieties and corresponding water and nutrient management technologies for increasing the productivity of rice in existing and new areas across SSA, particularly in inland valleys and other areas with Fe toxicity.

We will transfer the project's findings - including new knowledge and understanding, genetic markers and breeding materials, and models - to plant breeders and agronomists in international and national programmes at AfricaRice, NARES and other partners through direct interactions. Co-I Venuprasad and PP Wissuwa are involved in various national and international programmes relevant to this, as detailed in Pathways to Impact.

(2) Farming systems scientists at AfricaRice, NARES and elsewhere concerned with intensification and expansion of rice rice-based farming systems across SSA whilst minimising detrimental effects on other ecosystem goods and services.

Identifying the most appropriate inland valleys and other areas in SSA for rice intensification and expansion without compromising locally- and regionally-important ecosystem services requires detailed spatial information on land, water and other resources. This will feed into broader land suitability and socio-economic assessments. We will provide GIS tools on soil and water constraints to rice productivity in Fe toxic areas, and the benefits of improved germplasm and management, for incorporation into broader assessment tools being developed by farming systems experts. We propose to link particularly with AfricaRice scientists working on these topics. Their programme combines research on integrated rice-based systems - such as rice and aquaculture, livestock, vegetables and fruit trees - with the development of decision support tools for land suitability and socio-economic assessments, as well as extension to small-holder farmers using ICT tools. We propose to hold a two-day workshop at AfricaRice in Year 3 of the project to disseminate and further develop our GIS tools with relevant stakeholders, particularly farming systems scientists at AfricaRice, NARES and other partners developing decision support tools for land suitability and socio-economic assessments, and representatives of national and regional government organizations, and relevant NGOs.

(3) National and regional land use planners and policy makers concerned with intensification and expansion of rice-based farming systems across SSA whilst minimising detrimental effects on other ecosystem goods and services.

AfricaRice has strong links with rice policy makers in Africa and globally. For example, AfricaRice's Board of Trustees includes ministers of agriculture, university presidents and chief executives of plant science industries. The AfricaRice research programme 'Policy, Innovation Systems and Impact Assessment' works with NARES on this through the 'Rice Policy Taskforce'. AfricaRice also has strong links with smaller government agencies and specific academic institutions within each country. We will exploit these direct contacts.