This study investigated the impact of three different fertilization modes (traditional [FP1], one-time application of organic and inorganic fertilizer [FP2], and one-time application of inorganic fertilizer [OPT]) on the quality of japonica rice (O. sativassp.japonica) during storage under a rice–crab co-culture system. A field study was conducted, with rice samples collected every two months over a one-year storage period for quality analysis. The results showed that protein accumulated with increasing the amount of nitrogen fertilization, whereas amylose content and eating quality showed the opposite trend, further causing changes in rice quality during storage. After 12 months of storage, the FP2 group had the highest breakdown value (1972.50); its chalkiness degree (6.15), setback value (−788.5), and malondialdehyde content (2.03 μmol/g) were the lowest. These results indicated that FP2 treatment improved the appearance quality and starch pasting properties of rice. Additionally, the head milled rice rate improved in all fertilization treatment groups, while the eating quality scores in the FP1 and OPT groups, as well as the pH of rice soup in all fertilization treatment groups, decreased. Overall, the initial harvest of rice treated with FP2 boasted high quality and maintained superior appearance, eating, and nutritional qualities throughout storage. These findings show that FP2 may be an ideal fertilization mode under an ecological rice–crab co-culture system.
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