Genome-Wide Identification, Characterization, and Expression Profiles of the CCO Gene Family in Raphanus sativus L. Response to Fusarium oxysporum Resistance

Carotenoid cleavage oxygenases (CCOs) constitute a pivotal enzyme family that catalyze the oxidative cleavage of carotenoids to produce apocarotenoids, which are important signaling molecules involved in plant development, stress adaptation, and immunity responses. Notably, several CCOs, particularly NCED members, contribute to pathogen resistance by mediating abscisic acid (ABA) biosynthesis and apocarotenoid-derived defense signaling. While this gene family has been characterized in diverse plant species, its composition and functions in radish (Raphanus sativus L.) remain poorly understood. This study presents the comprehensive, genome-wide identification of the CCO gene family in radish, revealing 19 putative RsCCO members. A combination of phylogenetic, gene structure, chromosomal localization, and synteny analyses revealed conserved evolutionary patterns and species-specific diversification of the RsCCO family within the Brassicaceae. Promoter analysis identified an abundance of cis-acting regulatory elements related to phytohormone signaling, light perception, and stress responses, suggesting complex transcriptional regulation. Crucially, transcriptomic profiling following infection with Fusarium oxysporum revealed that two genes, RsNCED6 and RsNCED9b, were significantly upregulated in a resistant radish inbred line (‘T5’) compared to a susceptible line (‘T24’), identifying them as key candidate genes involved in ABA-mediated defense responses. This work provides a foundational characterization of the radish CCO gene family, offering novel insights into its role in carotenoid metabolism and pathogen defense.