Unravelling the expression patterns of the CCO gene family in Barley (Hordeum vulgare) under various stress conditions.

BACKGROUND: Carotenoid cleavage oxygenases (CCOs) are non-heme iron-dependent enzymes that catalyze the oxidative cleavage of carotenoids and play important roles in the biosynthesis of apocarotenoids involved in plant growth, development, and stress responses. However, a comprehensive genome-wide characterization of the CCO gene family in barley (Hordeum vulgare L.) has not been reported. METHODS AND RESULTS: In this study, a genome-wide analysis was performed to identify and characterize CCO genes in barley using comparative genomics and bioinformatics approaches. A total of 11 HvCCO genes were identified and classified into three subfamilies: carotenoid cleavage dioxygenases (CCDs), carotenoid cleavage dioxygenase-like proteins (CCDLs), and 9-cis-epoxycarotenoid dioxygenases (NCEDs). Gene structure and conserved motif analyses revealed high conservation within subfamilies, while promoter analysis identified 190 cis-regulatory elements associated with light, phytohormone, stress, and developmental regulation. Chromosomal mapping, duplication, and synteny analyses indicated that segmental duplication contributed to HvCCO gene family expansion, while Ka/Ks analysis suggested purifying selection of duplicated gene pairs. Prediction of miRNA targets identified 12 barley miRNAs potentially regulating HvCCO genes. Publicly available RNA-seq datasets revealed tissue-specific expression patterns. Under abiotic and biotic stresses, HvCCD4 and HvCCD6 showed relatively consistent expression, whereas HvNCED1 and HvNCED2 exhibited increased expression under drought conditions in tolerant genotypes. CONCLUSIONS: These findings provide a comprehensive genomic resource for the barley CCO gene family and identify HvCCD4 and HvCCD6 as potential candidate genes for future functional validation and genetic improvement of stress tolerance in barley.