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Elements in grain crops such as iron, zinc and selenium are essential in the human diet, whereas elements such as arsenic are potentially toxic to humans. This study aims to identify quantitative trait loci (QTLs) for trace elements in rice grain. A field experiment was conducted in an arsenic enriched field site in Qiyang, China using the Bala × Azucena mapping population grown under standard field conditions. Grains were subjected to elemental analysis by inductively coupled plasma mass spectroscopy. QTLs were detected for the elemental composition within the rice grains, including for iron and selenium, which have previously been detected in this population grown at another location, indicating the stability of these QTLs. A correlation was observed between flowering time and a number of the element concentrations in grains, which was also revealed as co-localisation between flowering time QTLs and grain element QTLs. Unravelling the environmental conditions that influence the grain ionome appears to be complex, but from the results in this study one of the major factors which controls the accumulation of elements within the grain is flowering time.