Enhancement of chilling stress tolerance in ornamental chilli by exogenous application of salicylic acid and ascorbic acid revealed through transcriptomic profiling

Ornamental Chillies are valued for their potential to be marketed as potted plants, given their diversity in color and fruit shape. Despite their market value, Chillies are highly susceptible to chilling stress. Salicylic acid (SA) and ascorbic acid (AA) enhance plant cold tolerance by modulating antioxidant defense systems and stress-responsive signaling pathways. However, insufficient information exists on the overall gene expression induced by the combined foliar application of SA and AA under chilling stress in Chillies. In this study, RNA sequencing was utilized to elucidate the molecular mechanisms of combined SA+AA under chilling stress. A comprehensive transcriptomic analysis following exogenous treatment highlighted the impact of 2 mM SA and 2 mM AA on genes contributing to fundamental Chilling stress adaptation. The combined foliar application of SA+AA significantly reduced ROS accumulation by 48% in V1 and 54% in V2 compared with the control. Similarly, MDA content decreased to 3% in V1 relative to 9% and 8% in the control and V2, respectively, indicating reduced oxidative damage and enhanced cellular stability under chilling stress. There were 48346 gene transcripts, and within the sets, 210 genes were differently expressed (DEGs) following V1 treatment and 3933 genes following V2 treatment by SA and AA compared with the control. The cultivar WIZ-21 contains 123 Upstream and 77 downstream DEGs, and cultivar Golden Heart has 44 Upstream and 3979 downstream DEGs. Transcriptome analysis identified 48,346 expressed transcripts, of which a subset met predefined statistical thresholds and were classified as differentially expressed genes (DEGs). Six representative DEGs were selected for RT-qPCR validation of the RNA-seq results in both cultivars. The combined foliar treatment of SA and AA also stimulated the hormonal signaling in cytoplasm, and response to stress-related genes, such as COBRA, MYB14, MYC, GRP, ANK, and ERF proteins. The present investigation, therefore, pinpointed key genes that exhibited altered expression patterns in treated Chillies exposed to chilling stress, which were associated with hormone signaling and metabolism, redox, cellulose synthase-like proteins, and stress defense.