-->PONE-D-24-22600-->-->Investigating Biochemical Variations in Onion Leaves Due to Purple Blotch Disease and its Management through Induced Resistance-->-->PLOS ONE

Dear Dr. Rajput,

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Muhammad Nauman Ahmad, PhD

Academic Editor

PLOS ONE

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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: No

Reviewer #2: Yes

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-->2. Has the statistical analysis been performed appropriately and rigorously? -->

Reviewer #1: Yes

Reviewer #2: Yes

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-->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: Yes

Reviewer #2: Yes

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-->4. Is the manuscript presented in an intelligible fashion and written in standard English?

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Reviewer #1: No

Reviewer #2: Yes

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-->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 study by Asghar et al., is about onion genotypes for resistance against purple blotch and management using different plant activators.

The study is poorly planned, poorly written and the images are not clear to say it is A. porri.

Introduction:

-mention the crop loss in USD not percentages

-use more references to talk about what management options are currently available to manage A.porri and what new the study is addressing.

M&M:

-use disease severity to explain the varietal response.

-Disease control efficacy (%) = 100x[1-B/A]

Results:

Remove table 2, 3. 4

Discussion:

Use references to support/conclude the results you got.

Read more literature to see how results are presented and manuscript is written. The image quality is poor.

This work published in Plos one could be a good starting point (no conflict of interest to reviewer): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8775252/

Reviewer #2: The research article titled “Investigating Biochemical Variations in Onion Leaves Due to Purple Blotch Disease and its Management through Induced Resistance” reports the germplasm of onion against purple blotch disease, biochemical alteration analysis in onion due to pathogen invasion and evaluation of plant activators against purple blotch. This is a well-written article, and I anticipate that the manuscript should be of great interest to the researchers working on plant microbe interactions and pathogenicity. I considered the manuscript suitable for publication, subject to following improvements.

1. The abstract section should be more robust by adding some quantitative data on from the significant results.

2. When a unique noun first appears, and you want to use the abbreviation later on then the full name must be accompanied by the abbreviation. Line 33 or 77: I suggest to add “PB” in the line 33.

3. Line 41: “plant activators” add the names you evaluated.

4. Line 43: Replace “The contemporary study concluded” with “The present study revealed”.

5. Revise the statement in Line 45-46: “While salicylic acid was proved to be highly significant in controlling the purple blotch in onion.”

6. Merge paragraph No 4 from line 77-81 in the 3rd paragraph by adding a statement for coherence.

7. Line 92: remove the word available and add the names.

8. Revise the objective section of your manuscript.

9. Line 97-98: A comprehensive survey was conducted in different onion growing areas of District Faisalabad. Add prominent names of the regions you collected samples.

10. In line 104: the authors used surface sterilization for the samples and then they isolated the pathogens. It is confusing, did you isolated endophytic fungi? As you mentioned that the surface was sterilized. Justify and revise it.

11. Revise the statement Line 117-118: The identification of pathogen was conducted on the basis of morphological and microscopic characters of the isolated pathogen.

12. In results Line 217-219: How you confirmed the fungus at species level? All these phenotypic characters are common in different fungal species.

13. Cite latest references and improve the discussion section.

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Reviewer #1: No

Reviewer #2: Yes:  Sajid Ali

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-->PONE-D-24-22600R1-->-->Investigating Biochemical Variations in Onion Leaves Due to Purple Blotch Disease and its Management through Induced Resistance-->-->PLOS ONE

Dear Dr. Rajput,

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.

Please submit your revised manuscript by Jan 22 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're 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.

Please include the following items when submitting your revised manuscript:-->

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

-->If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols .

We look forward to receiving your revised manuscript.

Kind regards,

Abhay K. Pandey

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

-->Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.-->

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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-->2. 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: No

Reviewer #2: Yes

**********

-->3. Has the statistical analysis been performed appropriately and rigorously? -->

Reviewer #1: Yes

Reviewer #2: No

**********

-->4. 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: Yes

Reviewer #2: Yes

**********

-->5. 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

Reviewer #2: Yes

**********

-->6. 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: Response: In present manuscript we use tha data of disease incidence, not disease severity. It is a reason that we cannot use the disease severity in the manuscript.

When evaluating the varieties for resistance - disease severity has to be taken into account. You have not collected the information. Your evaluation is flawed. A variety is resistant based on disease severity incidence the difference in disease severity. It is a open field experiment. Only disease incidence is not the appropriate measurement to say a variety is resistant.

Nanda et al., 2016 Identification of Novel Source of Resistance and Differential Response of Allium Genotypes to Purple Blotch Pathogen, Alternaria porri (Ellis) Ciferri (no conflict of interest to reviewer)(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5117860/pdf/ppj-32-519.pdf) - used disease incidence and disease severity to identify disease resistant variety. Expt was also conducted in invitro condition to evaluate it.

Specific comments:

Line 73,75, 231, 241, 301, 380, 448, 460 - space between words

Line 135 - specimen

Line 143 - how many days?

L161 - Is the location chosen for the expt is a hotspot for PBD?

L196-Separate

L301- recorded

Table 2&3 , Line 293, 314 - expand SOD - titles should be stand alone

Line 322 - recorded

Table 4, 5 - expand PoD

L334, Table 6&7, Figure 6 - expand CAT

Reviewer #2: The statistical analysis section is not added to the revised manuscript.

It is suggested to add a statistical analysis section in the material and methods.

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-->7. 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

Reviewer #2: Yes:  Sajid Ali

**********

[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.]

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 PLOS at figures@plos.org . Please note that Supporting Information files do not need this step.-->

Investigating Biochemical Variations in Onion Leaves Due to Purple Blotch Disease and its Management through Induced Resistance

PONE-D-24-22600R2

Dear Dr. Rajput,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Abhay K. Pandey

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

authors addressed all reviewer comments

Reviewers' comments: