Transcriptomic Analysis of Leaf Tissues in Capsicum an-nuum L. Subjected to Drought Stress

Abstract

Drought stress presents a significant risk to the viability of Capsicum annuum L., compelling the plant to execute a very intricate molecular response. This study seeks to delineate the transcriptome profile of chilli pepper leaves subjected to severe water scarcity in order to uncover critical genetic factors that facilitate adaptation. Gene expression profiles were comparatively assessed between control and treatment groups using an RNA-Seq method and differential analysis with DESeq2 software. Quantitative data analysis demonstrated a significant increase in transcriptional regulation of the plastid translational apparatus. The loci encoding chloroplast ribosomal RNA components, specifically C329_r008 (log2 FC 9.38), demonstrated the most significant up-regulation. This condition signifies the hyperactivation of de novo chloroplast repair mechanisms to mitigate photosystem breakdown resulting from the accumulation of Reactive Oxygen Species (ROS). Moreover, an unexpected defensive aspect was identified through the heightened responsia significante secondary genetic elements. Non-coding RNAs (e.g., LOC107852800) and several pseudogenes had a pronounced response, hypothesised to act as molecular sponges that mitigate post-transcriptional suppression. This genomic mapping effectively identified clusters of orphan genes whose roles remain uncharacterized, yet are highly relevant (P-adj < 0.05) for cellular defence. This reorganisation of molecular architecture demonstrates that chilli pepper adaptation is not solely governed by traditional protein-coding genes. The discovery of these non-coding regulatory elements and dark loci profoundly alters the paradigm of genetic selection and reactive oxygen species biomarker resources for developing future breeding programmes for chilli pepper cultivars that are resistant to climate anomalies.