Breakthrough in Nutrient Use Efficiency for Rice by Genetic Improvement and Fertility Sensing Techniques in Africa



Rice yields in Africa are remarkably low. The purpose of this research project is to develop techniques for evaluating nutrient deficiencies observed in weathered African soils and to dramatically improve rice yields in regions where fertilizer application is limited by combining local fertilizer application in response to local nutrient deficiency with the genetic engineering of cultivars that are able to efficiently use available nutrients. We will also leverage this project to train future researchers and field staff and establish local analysis stations with the aim of building an international joint research structure capable of performing a leadership role in developing crop cultivation techniques for efficient resource use that can be applied not only to low-input, low-fertility environments but also to address fertilizer depletion, which is a matter of increasing concern worldwide.


Output 1. Development of a simple method for evaluating field nutrient characteristics and distribution

We will analyze the relationship between visible soil characteristics and spectral reflectance from satellite images to develop a model for estimating soil organic carbon (SOC), which is closely related to soil nitrogen supply, and create a map of SOC distribution in the two provinces that comprise the project’s field sites. We will then develop a soil analysis method suitable for evaluating phosphorus (P), sulfur (S), and silicon (Si) deficiency. By correlating the results of soil analysis with the topographical attributes and spectral reflectance in multiple locations, we will identify field conditions and locations likely to be deficient in these nutrients. We will also develop a nutrient deficiency evaluation method involving rice growth diagnosis and portable analytical instruments that farmers can use in the field as indicators to locally manage cultivar selection or fertilizer regime on a per field basis.

Output 2. Development of breeding materials with superior nutrient uptake and use traits

In addition to the known Pup1 locus (including the PSTOL1 gene) that contributes to P uptake, we will identify new quantitative trait loci (QTLs), together with their molecular markers, that contribute to P, S, and Si uptake and use efficiency. We will use these molecular markers to create and field-test QTL-rich lines and to identify and register at least two cultivars suited to low-input, low-fertility soil conditions. We will also identify three or more genes associated to nutrient deficiency tolerance and their functions through gene expression analysis of candidate genes identified by QTL fine-mapping, gene function analysis using transformants, and physiological analysis.

Output 3. Development of local fertilizer management techniques for high nutrient uptake by combining fertilizer application with breeding materials

We will develop techniques based on field nutrient characteristics for improving rice yield and fertilizer application efficiency by over 50% compared to customary practice by using phosphate ore and guano deposits concentrated on Madagascar’s western coast, ammonium sulfate produced as a byproduct of nickel mining in Madagascar funded by Japan, and paddy straw, rice husks and other organic matter produced by rice farmers as local sources of P, S, and Si, respectively, in combination with the high nutrient use efficiency cultivars identified in Output 2.

Output 4. Elucidation of factors affecting the dissemination of rice cultivation technology and impact evaluation

We will survey the current status of the target area and conduct field tests in farmer fields to elucidate factors related to the selection of cultivation techniques and quantitatively evaluate the impact of the developed techniques on farmer income and nutritional improvement. Based on these analyses, we will draw up recommendations for promoting the adoption of these techniques.

Implementation Structure

FY VARY is an international joint research project led jointly by the Japan International Research Center for Agricultural Sciences (JIRCAS) and the Malagasy Ministry for Agriculture, Livestock and Fishing (MINAE). Other participating organizations are Kyoto University, the University of Tokyo, and Yamanashi Eiwa College on the Japan side, and the National Center for Applied Research and Rural Development (FOFIFA), the Radioisotopes Laboratory of the University of Antananarivo (LRI), and the National Nutrition Office (ONN) on the Malagasy side. Researchers from these organizations are leveraging their respective specializations to conduct joint research on Outputs 1–4 and develop rice cultivation techniques designed for high nutrient use efficiency that are suited to low-input, low-fertility environments.