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Climate change has resulted in a continuous increase in the frequency and intensity of chilling events in cold regions. In Northeast China, chilling at the booting and flowering stages negatively affects japonica rice grain yield. In this field experiment study, we conducted a 2‐year temperature‐controlled experiment to investigate the effects of chilling temperature and duration applied at the booting and flowering stages on japonica rice. The results showed that chilling at the two study stages delayed the rice phenology and decreased the grain yield. In particular, japonica rice was more sensitive to chilling at the booting stage than at the flowering stage. The rice grain yield was reduced by more as the chilling temperature decreased and the chilling duration increased. As for the yield components, the spikelet fertility and grain number per spike were more sensitive to chilling at the booting stage than at the flowering stage. Variations in the grain yield per plant were primarily contributed by the differences in spikelet fertility and grain number per spike, especially the spikelet fertility. In addition, cooling degree days showed statistically significant negative correlations with grain yield per plant, grain number per spike and spikelet fertility. For every 10°C·day increase in CDD at the booting (flowering) stage, the grain yield per plant, spikelet fertility and grain number per spike decreased by 7.1%, 6.2% and 3.4% (3.9%, 5.0% and 1.2%) respectively. As the spikelet fertility and grain number per spike decreased, the sink capacity decreased as well with the increasing of allocated assimilation to the stem and leaf while decreasing the assimilation allocated to the panicle. Increasing cooling degree days at the booting and flowering stages increased the allocations of assimilation to the stem and leaf. As a result, less assimilation was allocated to the panicle. This study suggests that breeding cultivars to improve the spikelet fertility and grain number per spike could help to minimize the potential rice grain yield loss due to the increase in chilling events occurring at the booting and flowering stages.

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