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Research article
Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis
Shubho Chaudhuri
Bose Institute
Corresponding Author
ORCiD: https://orcid.org/0000-0003-2247-0030
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
Background: Cellular reprogramming in response to environmental stress involves alteration of gene expression, changes in the protein and metabolite profile for ensuring better stress management in plants. Similar to other plant species originating in tropical and sub-tropical areas, indica rice is highly sensitive to low temperature that adversely affects its growth and grain productivity. Substantial work has been done to understand cold induced changes in gene expression in rice plants. However, adequate information is not available for early gene expression, especially in indica variety. Therefore, a transcriptome profile was generated for cold shock treated seedlings of IR64 variety to identify early responsive genes.
Results: The functional annotation of early DEGs shows enrichment of genes involved in altered membrane rigidity and electrolytic leakage, the onset of calcium signaling, ROS generation and activation of stress responsive transcription factors in IR64. Gene regulatory network suggests that cold shock induced Ca2+ signaling activates DREB/CBF pathway and other groups of transcription factors such as MYB, NAC and ZFP; for activating various cold-responsive genes. The analysis also indicates that cold induced signaling proteins like RLKs, RLCKs, CDPKs and MAPKK and ROS signaling proteins. Further, several late-embryogenesis-abundant (LEA), dehydrins and low temperature-induced-genes were upregulated under early cold shock condition, indicating the onset of water-deficit conditions. Expression profiling in different high yielding cultivars shows high expression of cold-responsive genes in Heera and CB1 indica varieties. These varieties show low levels of cold induced ROS production, electrolytic leakage and high germination rate post-cold stress, compared to IR36 and IR64. Collectively, these results suggest that these varieties may have improved adaptability to cold stress.
Conclusions: The results of this study provide insights about early responsive events in Oryza sativa L.ssp. indica cv IR64 in response to cold stress. Our data shows the onset of cold response is associated with upregulation of stress responsive TFs, hydrophilic proteins and signaling molecules, whereas, the genes coding for cellular biosynthetic enzymes, cell cycle control and growth-related TFs are downregulated. This study reports that the generation of ROS is integral to the early response to trigger the ROS mediated signaling events during later stages.
Keywords
IR64, Cold shock, Transcriptome, Differentially Expressed Genes (DEGs), Transcription factors (TFs), Calcium signaling, Kinases, Redox signaling, DRE motif
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CURRENT STATUS: Published
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Posted 18 Jun, 2020
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Editorial decision: Minor revision
On 08 Jun, 2020
Review #3 received
Received 07 Jun, 2020
Review #1 received
Received 04 Jun, 2020
Review #2 received
Received 30 May, 2020
Reviewer #3 agreed
On 10 May, 2020
Reviewer #2 agreed
On 09 May, 2020
Reviewers invited
Invitations sent on 06 May, 2020
Reviewer #1 agreed
On 06 May, 2020
Editor assigned
On 20 Mar, 2020
Submission checks complete
On 19 Mar, 2020
Editor invited
On 19 Mar, 2020
No comments provided
Editorial decision: Major revision
On 13 Jan, 2020
Review #3 received
Received 24 Dec, 2019
Review #1 received
Received 23 Dec, 2019
Review #2 received
Received 18 Dec, 2019
Reviewer #3 agreed
On 05 Dec, 2019
Reviewer #2 agreed
On 05 Dec, 2019
Reviewers invited
Invitations sent on 04 Dec, 2019
Reviewer #1 agreed
On 04 Dec, 2019
Editor assigned
On 02 Dec, 2019
Submission checks complete
On 01 Dec, 2019
Editor invited
On 01 Dec, 2019
First submitted
On 29 Nov, 2019
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis
Shubho Chaudhuri
Bose Institute
Corresponding Author
ORCiD: https://orcid.org/0000-0003-2247-0030
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 3
Posted 18 Jun, 2020
No comments provided
Editorial decision: Minor revision
On 08 Jun, 2020
Review #3 received
Received 07 Jun, 2020
Review #1 received
Received 04 Jun, 2020
Review #2 received
Received 30 May, 2020
Reviewer #3 agreed
On 10 May, 2020
Reviewer #2 agreed
On 09 May, 2020
Reviewers invited
Invitations sent on 06 May, 2020
Reviewer #1 agreed
On 06 May, 2020
Editor assigned
On 20 Mar, 2020
Submission checks complete
On 19 Mar, 2020
Editor invited
On 19 Mar, 2020
No comments provided
Editorial decision: Major revision
On 13 Jan, 2020
Review #3 received
Received 24 Dec, 2019
Review #1 received
Received 23 Dec, 2019
Review #2 received
Received 18 Dec, 2019
Reviewer #3 agreed
On 05 Dec, 2019
Reviewer #2 agreed
On 05 Dec, 2019
Reviewers invited
Invitations sent on 04 Dec, 2019
Reviewer #1 agreed
On 04 Dec, 2019
Editor assigned
On 02 Dec, 2019
Submission checks complete
On 01 Dec, 2019
Editor invited
On 01 Dec, 2019
First submitted
On 29 Nov, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
Background: Cellular reprogramming in response to environmental stress involves alteration of gene expression, changes in the protein and metabolite profile for ensuring better stress management in plants. Similar to other plant species originating in tropical and sub-tropical areas, indica rice is highly sensitive to low temperature that adversely affects its growth and grain productivity. Substantial work has been done to understand cold induced changes in gene expression in rice plants. However, adequate information is not available for early gene expression, especially in indica variety. Therefore, a transcriptome profile was generated for cold shock treated seedlings of IR64 variety to identify early responsive genes.
Results: The functional annotation of early DEGs shows enrichment of genes involved in altered membrane rigidity and electrolytic leakage, the onset of calcium signaling, ROS generation and activation of stress responsive transcription factors in IR64. Gene regulatory network suggests that cold shock induced Ca2+ signaling activates DREB/CBF pathway and other groups of transcription factors such as MYB, NAC and ZFP; for activating various cold-responsive genes. The analysis also indicates that cold induced signaling proteins like RLKs, RLCKs, CDPKs and MAPKK and ROS signaling proteins. Further, several late-embryogenesis-abundant (LEA), dehydrins and low temperature-induced-genes were upregulated under early cold shock condition, indicating the onset of water-deficit conditions. Expression profiling in different high yielding cultivars shows high expression of cold-responsive genes in Heera and CB1 indica varieties. These varieties show low levels of cold induced ROS production, electrolytic leakage and high germination rate post-cold stress, compared to IR36 and IR64. Collectively, these results suggest that these varieties may have improved adaptability to cold stress.
Conclusions: The results of this study provide insights about early responsive events in Oryza sativa L.ssp. indica cv IR64 in response to cold stress. Our data shows the onset of cold response is associated with upregulation of stress responsive TFs, hydrophilic proteins and signaling molecules, whereas, the genes coding for cellular biosynthetic enzymes, cell cycle control and growth-related TFs are downregulated. This study reports that the generation of ROS is integral to the early response to trigger the ROS mediated signaling events during later stages.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6