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Drought is a natural disaster that negatively impacts agricultural crops. Understanding the mechanisms of water deficit response is key to improving drought-tolerant crops. This study focused on comprehending the drought-tolerant mechanisms of a mutant chili, CaWDT-2, by investigating its physiological phenotypes and gene expression under PEG-induced drought condition compared to Tavee 60 as the original cultivar. Chili physiological status was monitored by shoot height, root length, leaf number, leaf area, shoot mass and root mass at 10 d after drought initiation. Relative water content (RWC), malondialdehyde (MDA), proline, soluble sugar and sucrose were measured during drought and after recovery. Transcriptome analysis using sequencing of RNA (RNA-seq) was employed to examine gene expression profiling under drought for 24 h. Results revealed diverse changes in physiological mechanism in response to drought between CaWDT-2 and Tavee 60 cultivars. Comparative transcriptomic analysis is helpful in understanding the differences in drought tolerance mechanisms between 2 crop varieties. Major differences that emerged from the physiological and transcriptomic analyses included drought-stressed injury level, proline accumulation, root cell wall adaptation, ABA biosynthesis, stress detoxification, heat shock proteins and transcription factors. Our data will contribute to further research in developing droughttolerant crops. An improved understanding of drought tolerance mechanisms will enhance agricultural resilience and mitigate the impact of drought on crop yield. [ABSTRACT FROM AUTHOR]