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Research article
Chunji Liu
CSIRO Queensland Bioscience Precinct Agriculture and Food Unit
Corresponding Author
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Background: Fusarium crown rot is a chronic disease in cereal production worldwide. The impact of this disease is highly environmentally dependant and significant yield losses occur mainly in drought-affected crops.
Results: In the study reported here, we evaluated possible relationships between genes conferring FCR resistance and drought tolerance using two approaches. The first approach studied FCR induced DEGs (differentially expressed genes) targeting two barley and one wheat loci against a panel of selected genes with known functions in drought tolerance. Of the 149 selected genes, 61% were responsive to FCR infection across the three loci. The second approach was an comparison of the global DEGs induced by FCR infection with the global transcriptomic responses under drought in wheat. This analysis found that approximately 48.0% percent of the DEGs detected one week following drought treatment and 74.4% of the DEGs detected three weeks following drought treatment were also differentially expressed between the susceptible and resistant isolines under FCR infection at one or more timepoints. As for the results from the first approach, the vast majority of common DEGs were downregulated under drought and expressed more highly in the resistant isoline than the sensitive isoline under FCR infection.
Conclusions: Results from this study suggest that the resistant isoline in wheat was experiencing less drought stress, which could contribute to the stronger defence response than the sensitive isoline. However, most of the genes induced by drought stress in barley were more highly expressed in the susceptible isolines than the resistant isolines under infection, indicating that genes conferring drought tolerance and FCR resistance may interact differently between these two crop species. Nevertheless, the strong relationship between FCR resistance and drought responsiveness provide further evidence indicating the possibility to enhance FCR resistance by manipulating genes conferring drought tolerance.
Keywords
Fusarium, wheat, barley, crown rot, drought tolerance, transcriptome, RNA-seq
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This is a list of supplementary files associated with this preprint. Click to download.
- Finalsuppfigures.pptx
Supplementary Figure 1. Venn diagrams displaying the overlaps between up-regulated and down-regulated DEGs identified in the comparison between resistant versus susceptible isolines targeting the 3BL locus with DEGs responsive to drought in wheat. Panel A displays the overlap between up-regulated SI vs RI DEGs (3dpi and 5dpi) and Panel B displays down-regulated SI vs RI DEGs versus DEGs downregulated under drought (T4 and T6). Panel C displays the overlap between up-regulated SI vs RI DEGs (3dpi and 5dpi) and Panel D displays down-regulated SI vs RI DEGs versus DEGs up-regulated under drought (T4 and T6). Supplementary Figure 2. Scatterplots showing the correlation between DEG expression values for SI vs RI up-regulated genes versus genes down-regulated under drought. Panels A and C compare 3dpi SI vs RI up-regulated genes with drought T4 and drought T6 down-regulated genes respectively. Panels B and D compare 5dpi SI vs RI up-regulated genes with drought T4 and drought T6 down-regulated genes, respectively. r values show the correlation co-efficient (Pearson) between DEG expression values. Axes display the log2 differential expression fold-changes for SI vs RI (x-axis) versus log2 differential expression fold-changes under drought (y-axis). Blue lines represent the line of best fit and shading shows the pointwise 95% confidence interval of the regression.
- Finalsuppfigures.pptx
Supplementary Figure 1. Venn diagrams displaying the overlaps between up-regulated and down-regulated DEGs identified in the comparison between resistant versus susceptible isolines targeting the 3BL locus with DEGs responsive to drought in wheat. Panel A displays the overlap between up-regulated SI vs RI DEGs (3dpi and 5dpi) and Panel B displays down-regulated SI vs RI DEGs versus DEGs downregulated under drought (T4 and T6). Panel C displays the overlap between up-regulated SI vs RI DEGs (3dpi and 5dpi) and Panel D displays down-regulated SI vs RI DEGs versus DEGs up-regulated under drought (T4 and T6). Supplementary Figure 2. Scatterplots showing the correlation between DEG expression values for SI vs RI up-regulated genes versus genes down-regulated under drought. Panels A and C compare 3dpi SI vs RI up-regulated genes with drought T4 and drought T6 down-regulated genes respectively. Panels B and D compare 5dpi SI vs RI up-regulated genes with drought T4 and drought T6 down-regulated genes, respectively. r values show the correlation co-efficient (Pearson) between DEG expression values. Axes display the log2 differential expression fold-changes for SI vs RI (x-axis) versus log2 differential expression fold-changes under drought (y-axis). Blue lines represent the line of best fit and shading shows the pointwise 95% confidence interval of the regression.
- SuppFile1GOenrichmentsfor3loci.xlsx
Gene Ontology enrichment analysis outputs for DEGs from various NIL/treatment comparisons.
- SuppFile1GOenrichmentsfor3loci.xlsx
Gene Ontology enrichment analysis outputs for DEGs from various NIL/treatment comparisons.
- SuppFile2149selecteddroughtgenes.xlsx
Details of the 149 drought tolerance associated genes curated from the literature for the targeted comparison of shared drought and crown rot transcriptional responses.
- SuppFile2149selecteddroughtgenes.xlsx
Details of the 149 drought tolerance associated genes curated from the literature for the targeted comparison of shared drought and crown rot transcriptional responses.
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A new preprint design is coming!
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See the published version of this preprint at BMC Plant Biology.
This is a preprint, 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
Chunji Liu
CSIRO Queensland Bioscience Precinct Agriculture and Food Unit
Corresponding Author
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
View the published article at BMC Plant Biology.
Version 1
Posted 19 Nov, 2020
No community comments so far
Review #3 received
Received 06 Dec, 2020
Editorial decision: Major revision
On 06 Dec, 2020
Review #17 received
Received 06 Dec, 2020
Review #6 received
Received 06 Dec, 2020
Review #5 received
Received 05 Dec, 2020
Review #1 received
Received 02 Dec, 2020
Review #10 received
Received 01 Dec, 2020
Reviewer #20 agreed
On 23 Nov, 2020
Reviewer #19 agreed
On 23 Nov, 2020
Reviewer #16 agreed
On 22 Nov, 2020
Reviewer #17 agreed
On 22 Nov, 2020
Reviewer #18 agreed
On 22 Nov, 2020
Reviewer #15 agreed
On 22 Nov, 2020
Reviewer #14 agreed
On 20 Nov, 2020
Reviewer #13 agreed
On 20 Nov, 2020
Reviewer #2 agreed
On 19 Nov, 2020
Reviewer #3 agreed
On 19 Nov, 2020
Reviewer #4 agreed
On 19 Nov, 2020
Reviewer #5 agreed
On 19 Nov, 2020
Reviewer #6 agreed
On 19 Nov, 2020
Reviewer #7 agreed
On 19 Nov, 2020
Reviewer #8 agreed
On 19 Nov, 2020
Reviewer #9 agreed
On 19 Nov, 2020
Reviewer #10 agreed
On 19 Nov, 2020
Reviewer #11 agreed
On 19 Nov, 2020
Reviewer #12 agreed
On 19 Nov, 2020
Editor assigned
On 19 Nov, 2020
Reviewers invited
Invitations sent on 19 Nov, 2020
Reviewer #1 agreed
On 19 Nov, 2020
Review #2 received
Received 19 Nov, 2020
Review #4 received
Received 19 Nov, 2020
Submission checks complete
On 16 Nov, 2020
Editor invited
On 15 Nov, 2020
First submitted
On 29 Oct, 2020
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 article at BMC Plant Biology.
Background: Fusarium crown rot is a chronic disease in cereal production worldwide. The impact of this disease is highly environmentally dependant and significant yield losses occur mainly in drought-affected crops.
Results: In the study reported here, we evaluated possible relationships between genes conferring FCR resistance and drought tolerance using two approaches. The first approach studied FCR induced DEGs (differentially expressed genes) targeting two barley and one wheat loci against a panel of selected genes with known functions in drought tolerance. Of the 149 selected genes, 61% were responsive to FCR infection across the three loci. The second approach was an comparison of the global DEGs induced by FCR infection with the global transcriptomic responses under drought in wheat. This analysis found that approximately 48.0% percent of the DEGs detected one week following drought treatment and 74.4% of the DEGs detected three weeks following drought treatment were also differentially expressed between the susceptible and resistant isolines under FCR infection at one or more timepoints. As for the results from the first approach, the vast majority of common DEGs were downregulated under drought and expressed more highly in the resistant isoline than the sensitive isoline under FCR infection.
Conclusions: Results from this study suggest that the resistant isoline in wheat was experiencing less drought stress, which could contribute to the stronger defence response than the sensitive isoline. However, most of the genes induced by drought stress in barley were more highly expressed in the susceptible isolines than the resistant isolines under infection, indicating that genes conferring drought tolerance and FCR resistance may interact differently between these two crop species. Nevertheless, the strong relationship between FCR resistance and drought responsiveness provide further evidence indicating the possibility to enhance FCR resistance by manipulating genes conferring drought tolerance.
Figure 1
Figure 1
Figure 2
Figure 2
Figure 3
Figure 3
Figure 4
Figure 4
Figure 5
Figure 5
This is a list of supplementary files associated with this preprint. Click to download.
- Finalsuppfigures.pptx
Supplementary Figure 1. Venn diagrams displaying the overlaps between up-regulated and down-regulated DEGs identified in the comparison between resistant versus susceptible isolines targeting the 3BL locus with DEGs responsive to drought in wheat. Panel A displays the overlap between up-regulated SI vs RI DEGs (3dpi and 5dpi) and Panel B displays down-regulated SI vs RI DEGs versus DEGs downregulated under drought (T4 and T6). Panel C displays the overlap between up-regulated SI vs RI DEGs (3dpi and 5dpi) and Panel D displays down-regulated SI vs RI DEGs versus DEGs up-regulated under drought (T4 and T6). Supplementary Figure 2. Scatterplots showing the correlation between DEG expression values for SI vs RI up-regulated genes versus genes down-regulated under drought. Panels A and C compare 3dpi SI vs RI up-regulated genes with drought T4 and drought T6 down-regulated genes respectively. Panels B and D compare 5dpi SI vs RI up-regulated genes with drought T4 and drought T6 down-regulated genes, respectively. r values show the correlation co-efficient (Pearson) between DEG expression values. Axes display the log2 differential expression fold-changes for SI vs RI (x-axis) versus log2 differential expression fold-changes under drought (y-axis). Blue lines represent the line of best fit and shading shows the pointwise 95% confidence interval of the regression.
- Finalsuppfigures.pptx
Supplementary Figure 1. Venn diagrams displaying the overlaps between up-regulated and down-regulated DEGs identified in the comparison between resistant versus susceptible isolines targeting the 3BL locus with DEGs responsive to drought in wheat. Panel A displays the overlap between up-regulated SI vs RI DEGs (3dpi and 5dpi) and Panel B displays down-regulated SI vs RI DEGs versus DEGs downregulated under drought (T4 and T6). Panel C displays the overlap between up-regulated SI vs RI DEGs (3dpi and 5dpi) and Panel D displays down-regulated SI vs RI DEGs versus DEGs up-regulated under drought (T4 and T6). Supplementary Figure 2. Scatterplots showing the correlation between DEG expression values for SI vs RI up-regulated genes versus genes down-regulated under drought. Panels A and C compare 3dpi SI vs RI up-regulated genes with drought T4 and drought T6 down-regulated genes respectively. Panels B and D compare 5dpi SI vs RI up-regulated genes with drought T4 and drought T6 down-regulated genes, respectively. r values show the correlation co-efficient (Pearson) between DEG expression values. Axes display the log2 differential expression fold-changes for SI vs RI (x-axis) versus log2 differential expression fold-changes under drought (y-axis). Blue lines represent the line of best fit and shading shows the pointwise 95% confidence interval of the regression.
- SuppFile1GOenrichmentsfor3loci.xlsx
Gene Ontology enrichment analysis outputs for DEGs from various NIL/treatment comparisons.
- SuppFile1GOenrichmentsfor3loci.xlsx
Gene Ontology enrichment analysis outputs for DEGs from various NIL/treatment comparisons.
- SuppFile2149selecteddroughtgenes.xlsx
Details of the 149 drought tolerance associated genes curated from the literature for the targeted comparison of shared drought and crown rot transcriptional responses.
- SuppFile2149selecteddroughtgenes.xlsx
Details of the 149 drought tolerance associated genes curated from the literature for the targeted comparison of shared drought and crown rot transcriptional responses.
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