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.

The prevalence of micronutrient deficiencies including zinc (Zn) is widespread in Malawi, especially among poor and marginalized rural populations. This is due to low concentrations of Zn in most staple cereal crops and limited consumption of animal source foods. The Zn concentration of cereal grain can be increased through application of Zn‐enriched fertilizers; a process termed agronomic biofortification or agro‐fortification. This trial protocol describes a field experiment which aims to assess the potential of agronomic biofortification to improve the grain Zn concentration of maize, the predominant staple crop of Malawi. The hypotheses of the study are that application of Zn‐enriched fertilizers will create a relatively small increase in the concentration of Zn in maize grains that will be sufficient to benefit dietary supplies of Zn, and that the effectiveness of agronomic biofortification will differ between soil types. The study will be conducted at three sites, Chitedze, Chitala, and Ngabu Agricultural Research Stations, in Lilongwe, Salima, and Chikwawa Districts respectively. These three sites represent locations in the Central and Southern Regions of Malawi. At each site, two different sub‐sites will be used, each corresponding to one of two agriculturally important soil types of Malawi, Lixisols, and Vertisols. Within each sub‐site, three Zn fertilizer rates (1, 30, and 90 kg/ha) will be applied to experimental plots using standard soil application methods, in a randomized complete block design. The number of replicates at plot level has been informed by a power analysis from pilot study data, assuming that a minimum 10% increase in Zn concentration of grain at 90 kg/ha relative to the concentration at 1 kg/ha is of interest. Grain mass (yield), stover mass, and both stover and grain Zn concentrations will be measured at harvest. A second year of cropping will be used to establish whether there are any residual benefits to grain Zn concentration. The potential for Zn agronomic biofortification will be communicated to relevant academic and government stakeholders through a peer review journal article and a briefing paper.

Dietary zinc (Zn) deficiency is widespread globally, and in particular among people in sub-Saharan Africa (SSA). In Malawi, dietary sources of Zn are dominated by maize and spatially dependent variation in grain Zn concentration, which will affect dietary Zn intake, has been reported at distances of up to ~ 100 km. The aim of this study was to identify potential soil properties and environmental covariates which might explain this longer-range spatial variation in maize grain Zn concentration. Data for maize grain Zn concentrations, soil properties, and environmental covariates were obtained from a spatially representative survey in Malawi (n = 1600 locations). Labile and non-labile soil Zn forms were determined using isotopic dilution methods, alongside conventional agronomic soil analyses. Soil properties and environmental covariates as potential predictors of the concentration of Zn in maize grain were tested using a priori expert rankings and false discovery rate (FDR) controls within the linear mixed model (LMM) framework that informed the original survey design. Mean and median grain Zn concentrations were 21.8 and 21.5 mg kg−1, respectively (standard deviation 4.5; range 10.0–48.1). A LMM for grain Zn concentration was constructed for which the independent variables: soil pH(water), isotopically exchangeable Zn (ZnE), and diethylenetriaminepentaacetic acid (DTPA) extractable Zn (ZnDTPA) had predictive value (p < 0.01 in all cases, with FDR controlled at < 0.05). Downscaled mean annual temperature also explained a proportion of the spatial variation in grain Zn concentration. Evidence for spatially dependent variation in maize grain Zn concentrations in Malawi is robust within the LMM framework used in this study, at distances of up to ~ 100 km. Spatial predictions from this LMM provide a basis for further investigation of variations in the contribution of staple foods to Zn nutrition, and where interventions to increase dietary Zn intake (e.g. biofortification) might be most effective. Other soil and landscape factors influencing spatially dependent variation in maize grain Zn concentration, along with factors operating over shorter distances such as choice of crop variety and agronomic practices, require further exploration beyond the scope of the design of this survey.

Zinc (Zn) deficiency remains a public health problem in Malawi, especially among poor and marginalized rural populations, linked with low dietary intake of Zn due to consumption of staple foods that are low in Zn content. The concentration of Zn in staple cereal grain can be increased through application of Zn‐enriched fertilizers, a process called agronomic biofortification or agro‐fortification. Field experiments were conducted at three Agricultural Research Station sites to assess the potential of agronomic biofortification to improve Zn concentration in maize grain in Malawi as described in registered report published previously. The hypotheses of the study were (i) that application of Zn‐enriched fertilizers would increase in the concentration of Zn in maize grain to benefit dietary requirements of Zn and (ii) that Zn concentration in maize grain and the effectiveness of agronomic biofortification would be different between soil types. At each site two different subsites were used, each corresponding to one of two agriculturally important soil types of Malawi, Lixisols and Vertisols. Within each subsite, three Zn fertilizer rates (1, 30, and 90 kg ha −1 ) were applied to experimental plots, using standard soil application methods, in a randomized complete block design. The experiment had 10 replicates at each of the three sites as informed by a power analysis from a pilot study, published in the registered report for this experiment, designed to detect a 10% increase in grain Zn concentration at 90 kg ha −1 , relative to the concentration at 1 kg ha −1 . At harvest, maize grain yield and Zn concentration in grain were measured, and Zn uptake by maize grain and Zn harvest index were calculated. At 30 kg ha −1 , Zn fertilizer increased maize grain yields by 11% compared with nationally recommended application rate of 1 kg ha −1 . Grain Zn concentration increased by 15% and uptake by 23% at the application rate of 30 kg ha −1 relative to the national recommendation rate. The effects of Zn fertilizer application rate on the response variables were not dependent on soil type. The current study demonstrates the importance of increasing the national recommendation rate of Zn fertilizer to improve maize yield and increase the Zn nutritional value of the staple crop.

The dataset comprises primary data for the concentration of 29 mineral micronutrients in cereal grains and up to 84 soil chemistry properties from GeoNutrition project surveys in Ethiopia and Malawi. The work provided insights on geospatial variation in the micronutrient concentration in staple crops, and the potential influencing soil factors. In Ethiopia, sampling was conducted in Amhara, Oromia, and Tigray regions, during the late-2017 and late-2018 harvest seasons. In Malawi, national-scale sampling was conducted during the April–June 2018 harvest season. The concentrations of micronutrients in grain were measured using inductively coupled plasma mass spectrometry (ICP-MS). Soil chemistry properties reported include soil pH; total soil nitrogen; total soil carbon (C); soil organic C; effective cation exchange capacity and exchangeable cations; a three-step sequential extraction scheme for the fractionation of sulfur and selenium; available phosphate; diethylenetriaminepentaacetic acid (DTPA)-extractable trace elements; extractable trace elements using 0.01 M Ca(NO3)2 and 0.01 M CaCl2; and isotopically exchangeable Zn. These data are reported here according to FAIR data principles to enable users to further explore agriculture-nutrition linkages.