Chlorophyll fluorescence kinetics and transcriptomic analysis provide a new insight into Populus euphratica response to natural high temperature and drought

As global warming intensifies, increasingly frequent and intense heatwaves are affecting plant growth and development. Despite long-term adaptation to aridity, desert plants often operate near physiological limits, making them especially vulnerable to extreme heat. However, most heat-tolerance studies rely on controlled experiments that cannot replicate the compound conditions of natural heatwaves (e.g., high radiation and low humidity), limiting the scope of ecological inference. To close this knowledge gap, we combined chlorophyll fluorescence (ChlF) kinetics and transcriptome sequencing to investigate how Populus euphratica responds to heatwaves under different water conditions (W1: riparian habitat, W2: desert habitat). Overall, heatwave exposure impaired the photosynthetic system of P. euphratica . Under both water conditions, several key chlorophyll fluorescence parameters decreased following heatwave exposure; however, only the W1 condition exhibited statistically significant changes ( P < 0.05). Transcriptome analysis revealed that P. euphratica in W2 activated a more intricate transcriptional program, characterized by a larger set of DEGs and a greater diversity of transcription factor families (18) compared with W1 (9). Under the W1 condition, heatwaves primarily triggered a conserved response focused on maintaining protein homeostasis, whereas under W2 specifically activated the regulatory modules associated with cell wall remodeling. Weighted Gene Co-expression Network Analysis (WGCNA) identified six gene modules strongly correlated with photosynthetic physiology, which were functionally enriched for photosynthesis and membrane-associated pathways. By integrating field-based ChlF kinetics with transcriptomics, this study links rapid photosynthetic dynamics to transcriptional regulatory mechanisms, providing important mechanistic insights for predicting desert plant vulnerability under increasingly intensified climate extremes. • Heatwaves generally inhibited the photosynthesis in P. euphratica . • Significant changes in fluorescence parameters occurred only under W1 condition. • W2 showed more complex transcriptional regulation with more DEGs and TF families. • Heatwaves activated “protein homeostasis” in W1 and “cell wall remodeling” in W2. • WGCNA identified 6 gene modules linked to photosynthesis under heat stress.