PONE-D-21-08742

Molecular identification of leaf, stem rust resistance in eighteen Egyptian wheat genotypes and the antifungal activity of chitosan-copper nanoparticles by molecular docking analysis

PLOS ONE

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PLOS ONE

Additional Editor Comments (if provided):

The manuscript entitled by Molecular identification of leaf, stem rust resistance in eighteen Egyptian wheat genotypes and the antifungal activity of chitosan-copper nanoparticles by molecular docking analysis by hanaa omar has been critically reviewed by the competent reviewers and based on their comments I will not be positive and authors have to revise the manuscript critically according to the queries. So that all the mistakes will be rectify and have sound message for the audience.

My special comments to authors are:

1. There are lots of mistake so read the manuscript critically and edit it.

2. Improve the Results, Discussion and rewrite the conclusion.

3. The authors have used very small no of phenotype merely 18 and the number is not sufficient for phenotype of rust resistance, Peoples used a panel 200 or 300 phenotype to score the data for at three different places for 3 years. The gene pool is very narrow and results may be biased. Is it possible for authors to increase the number of samples?

In the light of these comments revise the manuscript critically.

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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: Yes

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?

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: No

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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: Comments:

1. Wheat production is negatively affected by the attack of stem and rust diseases in Egypt and worldwide.

Wheat production is negatively affected by the attack of stem and leaf rust diseases in Egypt and worldwide.

2. In this respect, out of 20 scot and SRAP primers eleven and fourteen primers, showed polymorphism in 18 evaluated wheat genotypes, respectively.

3. Query: scot (SCoT), check in all manuscript

4. These markers have been listed in numerous references because they are powerful in determining the genetic diversity of various crops, such as wheat (Abou-Deif, et al., 2013 and El-Moneim, 2019).

Query: only these are markers to show up diversity what about other SSR and ILP markers if any provide references.

5. In this respect, out of 20 scot and SRAP primers eleven and fourteen primers, showed polymorphism in 18 evaluated wheat genotypes, respectively. SCoT and SRAP ones generated 140 and 121 polymorphic bands with 97 and 99% polymorphism, respectively

Query: rate of polymorphism is very high, is any positive or negative control were taken ?

6. Diverse wheat genotypes belong to same background or different?

Discussion section

7. Write concluding lines that showed the implementation of chitosan nanoparticles methods mostly suitable for which type of rust infection whether for leaf or stem.

8. Docking discussion is missing put concluding lines about what are the future aspect and what you conclude from this data

9. Heat map quality is poor improve it, check all image quality

10. What is the actual product size of eleven ScoT primers

11. What is the future aspect of overall study?

12. Insert line number in all manuscript

Reviewer #2: The manuscript is a useful work and may be considered after the following comments are addressed.

Title needs to be changed.

Abstract:

Uniform primer name SCoT not Scot.

It is unclear in abstract if the chitosan nanoparticles play important role in stem or leaf rust or both?

You mentioned SRAP and SCoT markers are useful for microbial diversity and cultivar? Why they are suitable in case of wheat? Why not other markers such as SSR or SNP?

Why diversity analysis was performed in wheat genotypes? What was its relation with rust?

How the authors avoided the rust pathogen DNA during molecular fingerprinting? These markers will amplify every DNA.

Give a brief description about each marker type used and their advantages.

CuChNp mention full form at its first occurrence in text.

Why SWISS model was preferred for modelling MAPK?

What are ideal criteria for a homology model to be stable and good for analysis?

Elaborate methods for structure modelling, validation (parameters), ligand-protein interaction and docking. Make it more clear.

Table 4 and 5 Where are high infection genotypes as mentioned in foot notes?

Using what data and how heat map was generated. Mention in the methods.

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Reviewer #1: Yes: Pankaj Kumar

Reviewer #2: No

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Genetic Diversity, Antifungal Evaluation and Molecular Docking Studies of Cu-chitosan nanoparticles as Prospective Stem rust Inhibitor Candidates among some Egyptian wheat genotypes

PONE-D-21-08742R1

Dear Dr. Omar,

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.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Himanshu Sharma

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Based on the recommendations of the reviewers manuscript is accepted for publication, there are always possibilities for improvement So authors can improve the manuscript at the time of proofread.

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: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

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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: Authors fulfill all comments now, i think its more stream line and ready for publishing.

Reviewer #2: The questions raised were appropriately answered. The revised manuscript may be considered for publishing.

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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: No