Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress
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 sig...
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| Published in | Frontiers in plant science Vol. 14; p. 1269995 |
|---|---|
| Main Authors | , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
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Frontiers Media S.A
25.10.2023
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| 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 Os
CCO
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. |
|---|---|
| AbstractList | 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.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. 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 Os CCO 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. 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. 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 ( ) 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 and their potential role in abiotic stress, their utilization in stress-resistant genetic breeding remains limited. The current research identified 16 genes within the group. These Os genes can be bifurcated into three categories based on their conserved sequences: (9-Cis-epoxycarotenoid dioxygenases), (Carotenoid cleavage dioxygenases) and (Carotenoid cleavage dioxygenases-like). Conserved motifs were found in the gene sequence via MEME analysis and multiple sequence alignment. Stress-related cis-elements were detected in the promoter regions of 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 . Only and significantly up-regulated during salt stress, as per RNA seq analyses. and levels were also higher in the group during the inflorescence growth stage. This provides insight into the function of rice in abiotic stress response and identifies possible genes that could be beneficial for stress-resistant breeding. |
| Author | Sami, Adnan Haider, Muhammad Zeshan Shafiq, Muhammad Ali, Daoud Alarifi, Saud Ali, Sajid Muhammad, Sher Manzoor, Irfan Anwar, Waheed Ali, Qurban Shahid, Muhammad Adnan |
| AuthorAffiliation | 4 Department of Agronomy, Faculty of Agricultural Sciences, University of the Punjab , Lahore , Pakistan 1 Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab , Lahore , 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 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 5 Department of Bioinformatics and Biotechnology, Government College University Faisalabad , Faisalabad , Pakistan |
| AuthorAffiliation_xml | – name: 1 Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab , Lahore , Pakistan – name: 7 Department of Zoology, College of Science, King Saud University , Riyadh , Saudi Arabia – name: 5 Department of Bioinformatics and Biotechnology, Government College University Faisalabad , Faisalabad , Pakistan – name: 6 Horticultural Sciences Department, University of Florida/Institute of Food and Agricultural Sciences (IFAS), North Florida Research and Education Center , Quincy, FL , United States – name: 2 Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab , Lahore , Pakistan – name: 3 Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab , Lahore , Pakistan – name: 4 Department of Agronomy, Faculty of Agricultural Sciences, University of the Punjab , Lahore , Pakistan |
| Author_xml | – sequence: 1 givenname: Muhammad Zeshan surname: Haider fullname: Haider, Muhammad Zeshan – sequence: 2 givenname: Adnan surname: Sami fullname: Sami, Adnan – sequence: 3 givenname: Muhammad surname: Shafiq fullname: Shafiq, Muhammad – sequence: 4 givenname: Waheed surname: Anwar fullname: Anwar, Waheed – sequence: 5 givenname: Sajid surname: Ali fullname: Ali, Sajid – sequence: 6 givenname: Qurban surname: Ali fullname: Ali, Qurban – sequence: 7 givenname: Sher surname: Muhammad fullname: Muhammad, Sher – sequence: 8 givenname: Irfan surname: Manzoor fullname: Manzoor, Irfan – sequence: 9 givenname: Muhammad Adnan surname: Shahid fullname: Shahid, Muhammad Adnan – sequence: 10 givenname: Daoud surname: Ali fullname: Ali, Daoud – sequence: 11 givenname: Saud surname: Alarifi fullname: Alarifi, Saud |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/37954992$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | Copyright © 2023 Haider, Sami, Shafiq, Anwar, Ali, Ali, Muhammad, Manzoor, Shahid, Ali and Alarifi. Copyright © 2023 Haider, Sami, Shafiq, Anwar, Ali, Ali, Muhammad, Manzoor, Shahid, Ali and Alarifi 2023 Haider, Sami, Shafiq, Anwar, Ali, Ali, Muhammad, Manzoor, Shahid, Ali and Alarifi |
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| Keywords | Oryza sativa carotenoid cleavage oxygenases 9-cisepoxycarotenoid dioxygenases transcriptome O. sativa abscisic acid apocarotenoids RNA seq analysis |
| Language | English |
| License | Copyright © 2023 Haider, Sami, Shafiq, Anwar, Ali, Ali, Muhammad, Manzoor, Shahid, Ali and Alarifi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Edited by: Syed Adeel Zafar, University of California, Riverside, United States Reviewed by: Irfan Ali Sabir, Shanghai Jiao Tong University, China; Xiaoyu Wang, University of Maryland, College Park, United States |
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| Title | Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress |
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