Integrated Transcriptomic and Metabolomic Profiling Identifies Candidate Genes and Pathways Associated With Pedicel Abscission Susceptibility in .

Pedicel abscission susceptibility in affects fruit retention and harvesting efficiency, making it a key agronomic trait in pepper breeding. In this study, two germplasm lines (LC-8 and LC-17) exhibiting distinct abscission characteristics were analyzed to explore the molecular basis underlying this trait. Although phenotypic differences have been documented, the molecular mechanisms regulating abscission susceptibility remain largely unclear. We performed a comprehensive analysis integrating morphological observations with transcriptomic and metabolomic profiling. Anatomical analysis revealed differential lignification patterns in the abscission zone (AZ), suggesting structural specialization. Transcriptome profiling identified 4635-7519 differentially expressed genes (DEGs), with KEGG enrichment highlighting phenylpropanoid biosynthesis and plant hormone signal transduction as core regulatory pathways. Metabolomic profiling detected 966 metabolites, including significantly altered flavonoids (e.g., apigenin O-hexosyl-O-pentoside, naringenin O-malonylhexoside) and phytohormones (e.g., abscisic acid, GA). Integrated multi-omics analysis revealed that key genes and metabolites involved in lignin biosynthesis and hormone signaling displayed distinct expression and accumulation patterns between the two lines. These findings suggest that these metabolic pathways play central roles in modulating pedicel abscission susceptibility. This study lays a theoretical foundation for regulating abscission and supports the breeding of pepper cultivars optimized for mechanical harvesting.