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

Muhammad Zeshan Haider; Adnan Sami; Muhammad Shafiq; Waheed Anwar; Sajid Ali; Qurban Ali; Sher Muhammad; Irfan Manzoor; Muhammad Adnan Shahid; Daoud Ali; Saud Alarifi

doi:10.3389/fpls.2023.1269995

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

Front Plant Sci. 2023 Oct 25:14:1269995. doi: 10.3389/fpls.2023.1269995. eCollection 2023.

Authors

Affiliations

¹ Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
² Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
³ Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
⁴ Department of Agronomy, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
⁵ Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan.
⁶ Horticultural Sciences Department, University of Florida/Institute of Food and Agricultural Sciences (IFAS), North Florida Research and Education Center, Quincy, FL, United States.
⁷ Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia.

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 (CCO) 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 CCOs and their potential role in abiotic stress, their utilization in stress-resistant genetic breeding remains limited. The current research identified 16 CCO genes within the Oryza sativa japonica group. These OsCCO genes can be bifurcated into three categories based on their conserved sequences: NCEDs (9-Cis-epoxycarotenoid dioxygenases), CCDs (Carotenoid cleavage dioxygenases) and CCD-like (Carotenoid cleavage dioxygenases-like). Conserved motifs were found in the OsCCO gene sequence via MEME analysis and multiple sequence alignment. Stress-related cis-elements were detected in the promoter regions of OsCCOs 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 CCOs. Only OsNCED6 and OsNCED10 significantly up-regulated during salt stress, as per RNA seq analyses. CCD7 and CCD8 levels were also higher in the CCD group during the inflorescence growth stage. This provides insight into the function of rice CCOs in abiotic stress response and identifies possible genes that could be beneficial for stress-resistant breeding.

Keywords: 9-cisepoxycarotenoid dioxygenases; O. sativa; Oryza sativa; RNA seq analysis; abscisic acid; apocarotenoids; carotenoid cleavage oxygenases; transcriptome.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work was funded by Researchers Supporting Project number (RSP-2023R27), King Saud University Riyadh, Saudi Arabia.