Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress

Abstract

Rice constitutes a foundational cereal and plays a vital role in the culinary sector. However, the detriments of abiotic stress on rice quality and productivity are noteworthy. Carotenoid cleavage oxygenases (<i>CCO</i>) hold vital importance as they enable the particular breakdown of carotenoids and significantly contribute towards the growth and response to abiotic stress in rice. Due to the insufficient information regarding rice <i>CCOs</i> and their potential role in abiotic stress, their utilization in stress-resistant genetic breeding remains limited. The current research identified 16 <i>CCO</i> genes within the <i>Oryza sativa japonica</i> group. These Os<i>CCO</i> genes can be bifurcated into three categories based on their conserved sequences: <i>NCEDs</i> (9-Cis-epoxycarotenoid dioxygenases), <i>CCDs</i> (Carotenoid cleavage dioxygenases) and <i>CCD-like</i> (Carotenoid cleavage dioxygenases-like). Conserved motifs were found in the <i>OsCCO</i> gene sequence via MEME analysis and multiple sequence alignment. Stress-related cis-elements were detected in the promoter regions of <i>OsCCOs</i> genes, indicating their involvement in stress response. Additionally, the promoters of these genes had various components related to plant light, development, and hormone responsiveness, suggesting they may be responsive to plant hormones and involved in developmental processes. MicroRNAs play a pivotal role in the regulation of these 16 genes, underscoring their significance in rice gene regulation. Transcriptome data analysis suggests a tissue-specific expression pattern for rice <i>CCOs</i>. Only <i>OsNCED6</i> and <i>OsNCED10</i> significantly up-regulated during salt stress, as per RNA seq analyses. <i>CCD7</i> and <i>CCD8</i> levels were also higher in the <i>CCD</i> group during the inflorescence growth stage. This provides insight into the function of rice <i>CCOs</i> in abiotic stress response and identifies possible genes that could be beneficial for stress-resistant breeding.