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

backgroundCarotenoid 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

resultsIn 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.

conclusionsThese 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.