Abstract

Light quality profoundly influences flowering time in horticultural crops, yet molecular mechanisms remain poorly characterized in emerging species. Comprehensive transcriptomic and metabolomic analyses revealed that blue light significantly delayed pepino ( Solanum muricatum ) flowering while red light accelerated reproductive transitions. Phytohormone profiling identified 20, 28, and 17 differentially expressed hormones at flower bud, bud, and flower stages, respectively, with jasmonic acid components showing near-universal upregulation under blue light. Transcriptome analysis revealed stage-specific responses with minimal overlap—only 3 common DEGs between flower bud and bud stages, 1 between bud and flower stages. Red light triggered broader pathway activation (34 vs. 24 pathways at flower bud stage) and recruited more DEGs in the consistently enriched circadian rhythm pathway. Network analysis revealed maximum regulatory complexity at flower bud stage (two core sub-networks), simplified to single sub-network at flower stage, while bud stage lacked identifiable cores. Blue light activated CRY signaling, inhibiting COP1/SPA and downregulating CO-related genes, whereas red light triggered PHYB activation with coordinated suppression of PIF3, CCA1, LHY, and PRR5. Morphologically, red light enhanced vegetative growth while a suppressed lateral buds, contrasting with blue light's reduction of primary growth but increased lateral bud formation. These findings establish that light quality orchestrates pepino flowering through wavelength-specific circadian-hormone networks, with blue light delaying flowering via CRY-mediated JA upregulation and red light accelerating reproduction through PHY-mediated GA promotion, providing insights for LED-based flowering control in controlled environment agriculture.