Salt tolerance evaluation of seven evergreen Ilex germplasms and transcriptomic insights into photosynthetic inhibition in a sensitive species

Global soil salinization calls for the exploration of salt‑tolerant plant resources for ecological restoration. Ilex species possess both ornamental value and moderate salt tolerance, yet systematic evaluations remain scarce. To address this gap, seven evergreen Ilex germplasms were treated with graded NaCl concentrations, and their physiological performance was assessed through photosynthetic parameters, malondialdehyde (MDA), osmoregulatory substances, and chloroplast pigments. Combined with salt injury index (SI), random forest modeling, membership function analysis and transcriptomic sequencing, we comprehensively evaluated salt tolerance and screened core evaluation indicators. It was observed that net photosynthetic rate (Pn), stomatal conductance (Gs), and transpiration rate (Tr) initially increased and then decreased with rising salt concentration. MDA accumulated progressively, while chlorophyll content declined steadily. Osmoregulatory substances exhibited a similar unimodal pattern. Correlation analysis further revealed that SI was positively associated with MDA and proline, but negatively associated with Pn, Tr, and Gs. In addition, random forest analysis indicated that Pn was the primary contributor to salt injury variation (59.3%), followed by Tr (13.6%) and Gs (9.4%), demonstrating photosynthetic capacity as the core indicator for salt tolerance evaluation. Transcriptomic analysis of the most sensitive species, Ilex dabieshanensis K. Yao & M. B. Deng, showed that transcriptional regulation gradually shifts from light harvesting to carbon assimilation under salt stress. The pathway “Carbon fixation in photosynthetic organisms” was specifically enriched only under prolonged stress, and Calvin cycle genes exhibited differentiated expression rather than global suppression. Together, these findings present a multi-physiological evaluation framework for salt tolerance in Ilex , highlight photosynthetic parameters as promising rapid‐assessment indicators, and offer molecular‐level clues regarding photosynthetic inhibition in salt‐sensitive germplasm, which may contribute to the breeding and selection of salt‐tolerant Ilex germplasms for saline‐alkali land greening.