Transcriptional analysis of wheat seedlings inoculated with Fusarium culmorum under continual exposure to disease defence inductors

Zuzana Antalová; Dominik Bleša; Petr Martinek; Pavel Matušinsky

doi:10.1371/journal.pone.0224413

Peer Review History

Original SubmissionOctober 10, 2019
4 Nov 2019 Decision Letter - Binod Bihari Sahu, Editor PONE-D-19-28330 Transcriptional analysis of wheat seedlings inoculated with Fusarium culmorum under continual exposure to disease defence inductors PLOS ONE Dear Dr. Matusinsky, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. We would appreciate receiving your revised manuscript by Dec 19 2019 11:59PM. When you are ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. 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Competing interests can arise in relationship to an organization or another person. Please follow this link to our website for more details on competing interests: http://journals.plos.org/plosone/s/competing-interests Additional Editor Comments (if provided): Please comply the concerns raised by the reviewer before it is ready for publication. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: No ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: This is an interesting paper that shows the effect on Fusarium inoculation in susceptible and resistant wheat of several different treatments in an attempt to identify potential treatments that can inhibit Fusarium inoculation and DON production during wheat production. I di have several concerns about the manuscript that are discussed below. There is little to no indication why the authors choose the specific treatments of prochloraz, sodium bicarbonate, ergosterol, aescin and potassium iodide for this research. The authors need to provide an explanation of why these specific treatments were chosen. The heat map of expression levels in Figure 3 is frankly quite confusing. How are shades of light to dark chosen; Is there an expression range for each shade of grey to black? How do you distinguish between up and down regulation relative to the treatment? Both the figure explanation and perhaps the figure itself needs some modification to make the heat map data/results clearer to the reader. I think the realtime QPCR and ELIZA results should be included as supplementary data. In the results and discussion sections, it is clear that the 10,000 ppm iodide treatment had a deleterious effect on germination and seedling growth. The literature cited (31-33) document this growth inhibition. Consequently, it is not clear why the 10,000 ppm concentration was chosen. Is this the only concentration that inhibits Fusarium growth? I am not sure of the value of having potassium-iodine included as a treatment in this paper unless it is actively thought of as a potential treatment to wheat to inhibit Fusarium growth and DON production during wheat production. The authors, in the conclusion, state that sodium bicarbonate is a possible treatment of wheat to reduce infection and growth of Fusarium. I agree with this conclusion. However, I see that prochloraz shows results very similar to sodium bicarbonate yet it is not identified as a possible treatment. I do not understand why both of these treatments are not indicated as such in the conclusion unless prochloraz has a deleterious effect on plant growth. If this is the case there is no data presented that suggests that. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files to be viewed.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0224413.r001
Revision 1
29 Nov 2019 Author Response Dear Editor and Reviewers Thank you for your comments and for reviewing our article. Please find below our reaction to all recommendations. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at http://www.journals.plos.org/plosone/s/file?id =wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf We checked PlosOne style requirements according to style formats. We made these changes: We formatted title and subtitle. We removed ZIP and Postal Codes and street addresses from affiliations. We included departments (Department of plant breeding and genetics and Department of plant pathology) in affiliation of Agrotest. We improved email address format of corresponding author. We set the double-spacing format in whole manuscript. We used Level 1 and 2 heading for sections and subsections. We changed citation of references to square brackets. We removed funding from Acknowledgments. We included “doi” codes to the list of references. 2. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. We included data in Supporting Information files (S1 Supporting Information and S1 Figure) where necessary we removed the mentioned phrases. 3. Thank you for stating the following in the Competing Interests section: 'The authors have declared that no competing interests exist.' We note that one or more of the authors are employed by a commercial company: Agrotest Fyto, Ltd. We stated in the Competing Interest section that: “The authors have declared that no competing interests exist. There are no patents, products in development or marked product to declare. This does not alter our adherence to all the PlosOne policies on sharing data and materials.” 4. Please provide an amended Funding Statement declaring this commercial affiliation, as well as a statement regarding the Role of Funders in your study. If the funding organization did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript and only provided financial support in the form of authors' salaries and/or research materials, please review your statements relating to the author contributions, and ensure you have specifically and accurately indicated the role(s) that these authors had in your study. You can update author roles in the Author Contributions section of the online submission form. Our commercial affiliation did not play a role in our study. We included the following statement within our amended Funding Statement. “This work and ZA, DB, PeM and PaM have been supported by the Ministry of Agriculture of the Czech Republic (project no. MZE RO1118). PaM have been supported by the Ministry of Agriculture of the Czech Republic (project no. QK1910197) and Internal Grant of Palacky University (project no. IGA_PrF_2019_004). PeM have been supported by the Ministry of Agriculture of the Czech Republic (project no. QK1910343). The funder Agrotest Fyto, Ltd provided support in the form of salaries for all authors, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.” 5. Please also provide an updated Competing Interests Statement declaring this commercial affiliation along with any other relevant declarations relating to employment, consultancy, patents, products in development, or marketed products, etc. Within your Competing Interests Statement, please confirm that this commercial affiliation does not alter your adherence to all PLOS ONE policies on sharing data and materials by including the following statement: "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” (as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests) . If this adherence statement is not accurate and there are restrictions on sharing of data and/or materials, please state these. Please note that we cannot proceed with consideration of your article until this information has been declared. Please include both an updated Funding Statement and Competing Interests Statement in your cover letter. We will change the online submission form on your behalf. We stated in the Competing Interest section that: “The authors have declared that no competing interests exist. There are no patents, products in development or marked product to declare. This does not alter our adherence to all the PlosOne policies on sharing data and materials.” 6. While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org. Please note that Supporting Information files do not need this step. We checked all figures by PACE and converted them to right format. Response to Reviewers 1. Reviewer #1: This is an interesting paper that shows the effect on Fusarium inoculation in susceptible and resistant wheat of several different treatments in an attempt to identify potential treatments that can inhibit Fusarium inoculation and DON production during wheat production. I did have several concerns about the manuscript that are discussed below. We thank reviewers for helpful comments, critical reading and the interest in improving the manuscript quality. We have processed the comments on our best. We hope that our amendments to the manuscript are suitable. All changes have been tracked using the revision mode in Word. 2. There is little to no indication why the authors choose the specific treatments of prochloraz, sodium bicarbonate, ergosterol, aescin and potassium iodide for this research. The authors need to provide an explanation of why these specific treatments were chosen. We agree that this point was not clear enough. We have added appropriate explanation to the manuscript in Introduction part and also in Supplementary Information (S1 Figure): “Prochloraz, potassium iodide and sodium bicarbonate were chosen for their antifungal effects in preliminary in vitro experiments (S1 Figure) and aescin and ergosterol because of their expected effect on plant triggered immunity.” 3. The heat map of expression levels in Figure 3 is frankly quite confusing. How are shades of light to dark chosen; Is there an expression range for each shade of grey to black? How do you distinguish between up and down regulation relative to the treatment? Both the figure explanation and perhaps the figure itself needs some modification to make the heat map data/results clearer to the reader. We accepted the reviewer opinion and for a better clarity, the heat map (Figure 3) has been rearranged to the table (Table 2). Depending on these changes, we renumbered the other following figures. 4. I think the realtime QPCR and ELIZA results should be included as supplementary data. We accepted the reviewer opinion and we moved qPCR and ELISA to the Supplementary Information section (Supplementary Information 1). 5. In the results and discussion sections, it is clear that the 10,000 ppm iodide treatment had a deleterious effect on germination and seedling growth. The literature cited (31-33) document this growth inhibition. Consequently, it is not clear why the 10,000 ppm concentration was chosen. Is this the only concentration that inhibits Fusarium growth? I am not sure of the value of having potassium-iodine included as a treatment in this paper unless it is actively thought of as a potential treatment to wheat to inhibit Fusarium growth and DON production during wheat production. We thank the reviewer for comment regarding iodide treatment. We added explanation to the manuscript and appropriate results of in vitro preliminary test to the Supplementary Information (S1 Figure). „Used concentration inhibited F. culmorum growth in preliminary in vitro test (S1 Figure). The observed toxicity of potassium iodide for wheat seedlings is thus understandable and such a high concentration suppress natural plant immunity, thus allowing us to see the effect of immunity on the intensity of the pathogen development (Fig 1).“ 6. The authors, in the conclusion, state that sodium bicarbonate is a possible treatment of wheat to reduce infection and growth of Fusarium. I agree with this conclusion. However, I see that prochloraz shows results very similar to sodium bicarbonate yet it is not identified as a possible treatment. I do not understand why both of these treatments are not indicated as such in the conclusion unless prochloraz has a deleterious effect on plant growth. If this is the case there is no data presented that suggests that. Indeed, the prochloraz is not in conclusions so it was corrected in the manuscript and we changed the first sentence in Conclusion to this form: “We conclude that prochloraz and sodium bicarbonate has the greatest potential for suppression of fungal development without having a negative effect on plant growth.” Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0224413.r002
21 Jan 2020 Decision Letter - Binod Bihari Sahu, Editor Transcriptional analysis of wheat seedlings inoculated with Fusarium culmorum under continual exposure to disease defence inductors PONE-D-19-28330R1 Dear Dr. Matusinsky, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. With kind regards, Binod Bihari Sahu, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0224413.r003
Formally Accepted
24 Jan 2020 Acceptance Letter - Binod Bihari Sahu, Editor PONE-D-19-28330R1 Transcriptional analysis of wheat seedlings inoculated with Fusarium culmorum under continual exposure to disease defence inductors Dear Dr. Matušinsky: I am pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Binod Bihari Sahu Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0224413.r004

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