Physiological and Transcriptomic Analyses Reveal Divergent Responses of Vegetative Growth and Inflorescence Development to Temperature in Chrysanthemum × morifolium

Temperature strongly affects chrysanthemum flowering, but its stage-specific effects on vegetative and reproductive development remain unclear. Here, the obligate short-day chrysanthemum cultivar Chrysanthemum × morifolium ‘Zijiao’ was grown under three different day/night temperature regimes. We anatomically identified eight stages of floral induction and differentiation by observing the shoot apical meristem. The 25/16 °C treatment promoted coordinated inflorescence development, with floral bud differentiation completed within 42 days, the greatest number of florets, and the largest floral buds among the treatments. In contrast, the 30/18 °C regime enhanced plant height and internode elongation but delayed late floral bud differentiation. Photosynthetic pigment levels were generally maintained under the two warmer treatments relative to 20/13 °C, whereas carbohydrates, soluble proteins, superoxide dismutase, and peroxidase showed temperature- and stage-dependent changes. Leaf transcriptome profiling after 10 days revealed the differential regulation of hormone signaling, primary metabolism, antioxidant responses, and peroxisome-related pathways. The developmental expression of heat shock transcription factors A (CmHSFA4), CmWRKY40, CmMYB, and CmGATA8 further indicated stage-specific transcriptional responses. T2 and T3 showed significant positive relationships with CmMYB and CmWRKY40 expression, respectively. Thus, under the conditions tested, intermediate temperature favored reproductive development, whereas warmer conditions sustained vegetative growth and acclimation but compromised late floral organogenesis. These findings provide a physiological and transcriptional basis for cultivar-specific temperature management in chrysanthemum production.