Non-destructive visualisation and in situ quantification of micronutrient mobilisation in germinating rice grains using synchrotron-based X-ray fluorescence microscopy

Maintaining micronutrient availability in germinating rice tissues is crucial for seedling vigour and agronomic performance. However, current methods for visualising micronutrient dynamics often require destructive sample preparation. Here we report that synchrotron-based X-ray fluorescence microscopy (XFM) could enable non-destructive, in situ visualisation and quantification of zinc (Zn) mobilisation in intact, germinating rice grains. Using XFM on whole grains of salt-tolerant Pokkali and salt-sensitive Nipponbare varieties, we generated high-resolution elemental maps revealing the spatiotemporal distribution of Zn and other micronutrients. Direct quantification by seed volume using element association window proved inaccurate due to tissue heterogeneity. However, normalisation by areal density showed Zn accumulation was highest in the embryo, followed by the aleurone layer and shoots. Zn was initially localised in the aleurone layer and embryo, with subsequent mobilisation to developing shoots and roots during germination. Calcium was predominantly detected in the hull, while potassium was enriched in growing roots and shoots. This non-destructive XFM method provides unprecedented insights into real-time micronutrient fluxes during rice germination, offering a powerful tool for studying nutrient dynamics in diverse contexts such as biofortification, stress responses, and varietal differences. Our findings contribute to understanding the mechanisms underlying micronutrient allocation during early seedling development, with potential applications in improving rice nutritional quality and seedling establishment. • Non-destructive XFM reveals micronutrient dynamics of intact rice paddy. • High-resolution zinc mapping shows redistribution patterns during germination. • Areal density normalisation enables quantification of micronutrients in situ. • Salt tolerance in rice linked to distinct micronutrient mobilisation patterns.