Decoding cold tolerance in chilli: An integrated assessment of morphological, physiological, biochemical, and molecular responses

This study evaluated multifaceted cold tolerance mechanism in twelve hot pepper genotypes by assessing morphological, physiological, biochemical, and molecular responses associated with cold stress resilience. Considerable genotypic variation was observed across all evaluated parameters. Among the yield traits, fruit weight ranged from 0.80 g to 6.87 g with highest value recorded in EC382017, while EC771555 produced the maximum number of fruits per plant (121.67). The genotype IC643853 exhibited the highest seed count per fruit (50.56). Physiological evaluation revealed that EC771555 had the greatest membrane stability (86.10%), whereas stomatal conductance was highest in IC643853, IC119465, and Kashi Anmol. EC737650 recorded the highest intercellular CO₂ concentration (414.7 μmoles/mole) and photosynthetic rate (7.77 μmoles CO₂ m²/s). Biochemical analysis showed maximum, superoxide dismutase activity in EC771555 (562.50 U g −1 FW), indicating enhanced antioxidant defence under cold stress. Gene expression analysis further demonstrated significant upregulation of cold-responsive genes, with CaEREBP-C2 exhibiting the highest expression (19.14-fold) in EC771555. Principal component analysis (PCA) revealed that fruit weight, phenolic content, and glutathione peroxidase activity together explained41.9% of the total variability. Overall, the identified cold-tolerant genotypes EC771555, EC382017, EC769427, and EC737650 represent valuable genetic resources for breeding programs aimed at developing hot pepper cultivars with enhanced cold stress tolerance and improved adaptation to low-temperature environments.