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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.

Selenium (Se) is an essential element for human health. However, our knowledge of the prevalence of Se deficiency is less than for other micronutrients of public health concern such as iodine, iron and zinc, especially in sub-Saharan Africa (SSA). Studies of food systems in SSA, in particular in Malawi, have revealed that human Se deficiency risks are widespread and influenced strongly by geography. Direct evidence of Se deficiency risks includes nationally representative data of Se concentrations in blood plasma and urine as population biomarkers of Se status. Long-range geospatial variation in Se deficiency risks has been linked to soil characteristics and their effects on the Se concentration of food crops. Selenium deficiency risks are also linked to socio-economic status including access to animal source foods. This review highlights the need for geospatially-resolved data on the movement of Se and other micronutrients in food systems which span agriculture–nutrition–health disciplinary domains (defined as a GeoNutrition approach). Given that similar drivers of deficiency risks for Se, and other micronutrients, are likely to occur in other countries in SSA and elsewhere, micronutrient surveillance programmes should be designed accordingly.