Long-term salinity reveals genotype-specific transcriptional reprogramming in eggplant

Abstract Salinity severely limits eggplant productivity, yet the transcriptional bases of tolerance to prolonged salt exposure remain incompletely understood. Here, we analyzed long-term salinity responses in two contrasting eggplant ( Solanum melongena L.) genotypes from the G2P-SOL core collection, focusing on genotype-dependent transcriptional regulation under chronic stress. Plants were exposed to 200 mM NaCl for 23 days at the reproductive stage, and transcriptome profiling was performed at the end of the stress period. Physiological assessment and high-throughput phenotyping confirmed a strong divergence in water status and plant architecture between genotypes under salinity, providing a reference framework for transcriptomic interpretation. RNA-seq analysis revealed marked genotype-specific differences in transcriptional responses. While both genotypes activated a conserved salt-stress program involving redox homeostasis, proteostasis and growth repression, the tolerant genotype displayed a substantially broader and more coordinated transcriptional reprogramming. This response involved large-scale modulation of pathways related to translation and RNA metabolism, hormone signaling crosstalk, membrane transport, cell wall remodeling and oxidative stress management, together with the selective repression of growth- and signaling-related functions. In contrast, the sensitive genotype showed a more limited response dominated by defense- and damage-associated transcripts. Overall, these results indicate that long-term salt tolerance in eggplant is associated with genotype-specific transcriptional reprogramming superimposed on a shared basal stress response. This work highlights regulatory pathways and candidate genes potentially relevant for breeding strategies targeting salt resilience.