Micronutrient deficiencies (MNDs) remain widespread among people in sub-Saharan Africa1–5, where access to sufficient food from plant and animal sources that is rich in micronutrients (vitamins and minerals) is limited due to socioeconomic and geographical reasons4–6. Here we report the micronutrient composition (calcium, iron, selenium and zinc) of staple cereal grains for most of the cereal production areas in Ethiopia and Malawi. We show that there is geospatial variation in the composition of micronutrients that is nutritionally important at subnational scales. Soil and environmental covariates of grain micronutrient concentrations included soil pH, soil organic matter, temperature, rainfall and topography, which were specific to micronutrient and crop type. For rural households consuming locally sourced food—including many smallholder farming communities—the location of residence can be the largest influencing factor in determining the dietary intake of micronutrients from cereals. Positive relationships between the concentration of selenium in grain and biomarkers of selenium dietary status occur in both countries. Surveillance of MNDs on the basis of biomarkers of status and dietary intakes from national- and regional-scale food-composition data1–7 could be improved using subnational data on the composition of grain micronutrients. Beyond dietary diversification, interventions to alleviate MNDs, such as food fortification8,9 and biofortification to increase the micronutrient concentrations in crops10,11, should account for geographical effects that can be larger in magnitude than intervention outcomes.

Grain and soil were sampled across a large part of Amhara, Ethiopia in a study motivated by prior evidence of selenium (Se) deficiency in the Region's population. The grain samples (teff, Eragrostis tef , and wheat, Triticum aestivum ) were analysed for concentration of Se and the soils were analysed for various properties, including Se concentration measured in different extractants. Predictive models for concentration of Se in the respective grains were developed, and the predicted values, along with observed concentrations in the two grains were represented by a multivariate linear mixed model in which selected covariates, derived from remote sensor observations and a digital elevation model, were included as fixed effects. In all modelling steps the selection of predictors was done using false discovery rate control, to avoid over-fitting, and using an α-investment procedure to maximize the statistical power to detect significant relationships by ordering the tests in a sequence based on scientific understanding of the underlying processes likely to control Se concentration in grain. Cross-validation indicated that uncertainties in the empirical best linear unbiased predictions of the Se concentration in both grains were well-characterized by the prediction error variances obtained from the model. The predictions were displayed as maps, and their uncertainty was characterized by computing the probability that the true concentration of Se in grain would be such that a standard serving would not provide the recommended daily allowance of Se. The spatial variation of grain Se was substantial, concentrations in wheat and teff differed but showed the same broad spatial pattern. Such information could be used to target effective interventions to address Se deficiency, and the general procedure used for mapping could be applied to other micronutrients and crops in similar settings.