Molecular mechanisms and genomic strategies for enhancing stress resilience in pepper crop

Pepper ( Capsicum annuum L.) is an important crop, but its yield remains highly sensitive to abiotic and biotic stresses, including drought, diseases, and extreme temperatures. To ensure sustainable production, there is a pressing need to integrate advanced genetic and molecular approaches into pepper improvement programs. New genomic breakthroughs from CRISPR-Cas9 editing to multi-omics integration are opening the door to developing stress-resistant varieties. The objective of this review is to synthesize these recent advancements and outline a roadmap for enhancing stress resilience in pepper. We examine how key genes (e.g., CaSBP13, CaDR1 ), identified through RNA-seq and GWAS, regulate stress responses and how their manipulation can improve tolerance. Beyond cataloging genetic variation, we highlight transformative applications such as single-cell transcriptomics for cell-type-specific insights, pangenomes to access unexplored diversity, and machine learning for predicting elite alleles. Despite significant progress, challenges remain, including limited genetic resources and incomplete functional annotation of candidate genes. To address these gaps, we propose future strategies focused on the interdisciplinary integration of omics technologies, functional genomics, and advanced breeding platforms. In conclusion, this review provides a comprehensive overview of technological advances and a clear path toward securing pepper productivity under increasingly variable environmental conditions.