Flooded cultivation improves grain yield and appearance quality while reducing nutritional quality in Shanlan upland rice (Oryza sativa L.).

Shanlan upland rice (Oryza sativa L.) is a traditional landrace native to Hainan Province, recognized for its exceptional nutritional quality. However, its broader adoption remains constrained by low yield potential under traditional rainfed cultivation. Although flooded cultivation can enhance rice yield, its effects on grain quality, particularly nutritional quality, remain unclear. Here, we evaluated the feasibility of flooded cultivation by assessing grain yield, appearance and milling qualities, and metabolites associated with nutritional quality in 26 Shanlan upland rice varieties grown under rainfed and flooded conditions. Flooded cultivation significantly increased grain yield and improved both appearance and milling qualities. However, flooded cultivation reduced the accumulation of several health-promoting metabolites, including vitamins, anthocyanins, and phenylpropanoids, indicating a diminished nutritional quality. These results provide metabolite-level evidence for a trade-off between productivity and nutritional value under contrasting water management strategies. Optimized water management and appropriate varietal selection are therefore essential to optimize grain yield, while maintaining nutritional quality in Shanlan upland rice.