PONE-D-19-19629

Genetic Characterization for Lesion mimic and other Traits in Relation to Spot blotch Resistance in Spring Wheat

PLOS ONE

Dear Dr. Mishra,

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.

==============================

ACADEMIC EDITOR:

You will see that both the reviewers made critical recommendations, but an important consideration is whether the study describes a technically sound research and made significant advances in the relevant area. However, as reviewers pointed out, I think that this manuscript needs additional works. Therefore, I encourage the authors to perform the revision as per the reviewer’s suggestions and if these were meticulously performed, then I am sure that the MS could be reconsidered on a later date

==============================

We would appreciate receiving your revised manuscript by Sep 24 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.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Manoj Prasad, PhD

Academic Editor

PLOS ONE

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When submitting your revision, we need you to address these additional requirements.

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1. In your Methods or in a Supporting Information file, please include a full list of all the wheat accessions included in your study.

2. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information.

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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: Partly

Reviewer #2: Partly

**********

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

Reviewer #1: Yes

Reviewer #2: No

**********

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: 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: No

Reviewer #2: No

**********

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: Spot blotch is an important wheat disease in tropical and sub-tropical regions, especially India, China, Mexicao, etc. Identifying genetic loci responsible for Spot blotch resistance are important for wheat breeding and also for following genomic analysis. The manuscript performed genome wide association analysis of spot blotch (AUDPC) and lesion mimic (Lm) as well as leaf tip necrosis (Ltn), glaucousness index (GI) and latent period (LP) using a 289 GWAS panel and SNP assay. Positive association between AUDPC of spot blotch and Lm was found and negative correlation between Lm and GI, Ltn and LP were observed. SNP loci associated with Lm, AUDPC of spot blotch, were also identified. These information are valuable for wheat breeding and further fine gene mapping and cloning.

However, this manucript didn't conduct further analysis of their findings using currently available wheat genomic sequences resources which makes the current manusciprt less informative for the community. The authors should perform further analysis of the identified SNP loci, for example Lm on 6A (90-91 cM), AUDPC on 5A and 5B, etc.) in putative gene annotation and breeder friendly markers (like KASP) markers development and validation.

In addition, the authors found the AUDPC of spot blotch associated SNPs on 5A and 5B are deirved from the same sets of probes. This should be explained further to clearify if these two locus on 5A and 5B are orthologous? or just missclassification of SNP signals of the same probe.

Reviewer #2: The manuscript presents results aiming at analysing relationships between several wheat traits (lesion mimic symptoms, leaf tip necrosis symptom, glaucousness index, latent period, and resistance to spot blotch), and identifying markers associated to those traits. Several issues prevent publication at this stage, they are indicated below.

* Materials and methods need to be described with more details. For example, the rationale of the choice of varieties used needs to be described.

* Because the description of disease assessment is not sufficiently described, one cannot assess if the analyses conducted from these assessments are correct. More specifically, the "2-digit" scale needs to be explicitly described. It may be that this scale mixes two very different assessments, and that the analysis conducted is not correct. This potential issue needs to be thoroughly addressed.

* The Introduction, Results, and Discussion sections need to be improved, see detailed comments below.

* The text needs to be edited. I provide examples for the beginning of the manuscript, starting at the Introduction, in order to illustrate the editing work required for the whole manuscript: L51 "Lesion mimic are necrotic symptoms…" : should be "Lesion mimic is …"; L52: HR needs to be spelled out the first time it is used; L53-4; there should be comas between te different items; L54: a space is missing before "Lm". Lm needs to be spelled out the first time it is used; L56: "restricts", not "restrict"; L57: "in the case" not "in case"

More detailed comments are given below.

L53-4: are these all examples with biotroph pathogens? This should be stated early.

L59: is it specifically about Lm plants?

L60: what is ltn?

L63: the rust(s) involved need to be indicated here

L65: spell out the latin name in first instance

L65-67: this is too vague and needs more details.

L70: this needs rephrasing

L70-72: this needs rephrasing as the logic is not sound; do QTL refer to QTL for lm or for resistance to spot blotch?

L73: what is LP? If this is latency period, why choose this "trait" and not for example infection efficiency?

Introduction: the introduction needs to be re-worked so that the reader can understand why this study was undertaken. For example, what is known or what can be hypothesized from the literature, about relationships between Lm, Ltn, and resistance to spot blotch. For a example, it is not indicated if spot blotch is considered as a necrotroph or biotroph, and this is needed. Actually, moving the first paragraph of Discussion in the Introduction, and reorganizing this section, could be a way to improve the Introduction.

L80-3: why were these varieties chosen, on what basis?

L101: the title needs to be changed

L102-3: the two first sentences seem contradictory; was Lm assessed once or several times?

L103: what was the sampling design for Lm symptoms assessment? How many flag leaves per elementary plot?

L105-6: what is the unit: % of what?

L106: what was the sampling design?

L108: what is the unit: % of what?

L109: what is GI? This is not mentioned in the introduction. Why is it interesting to measure this trait?

L110: on what basis was this assessment made? Is there a diagram? Or is there an operational description for "most waxiness expression"?

L12: the method used to measure LP is needs to be described, as well as the sampling design.

L116-8: the computation of "percent disease severity" needs to be clearly described here.

Tables 1 and 2: what are the values given in the tables?

L179-80: Figure 2 should be described in more details.

Figure 3: more details are needed as footnotes of the figure; X and y axes need to be described.

Table 3: R2 values seem very small; can this translate into meaningful effects of phenotypes?

L263 This should appear in the Introduction as well

L265-6: this statement needs to be pondered with the other positive effects of Lm versus other wheat diseases

L267: higher LP is not "providing protection", but is a consequence of other mechanisms which increase LP

L268-70: this is an hypothesis, which is not correct for LP: high LP is a consequence of other mechanisms, not a mechanism which will per se reduce the expression of Lm gene

L272: this is an hypothesis; correlation does not indicate any underlying mechanisms, but indicates only association

L284-307: a discussion on low R2 values is needed here.

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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.

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Reviewer #1: Yes: Zhiyong Liu

Reviewer #2: 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.

PONE-D-19-19629R1

Genetic Characterization for Lesion mimic and other Traits in Relation to Spot blotch Resistance in Spring Wheat

PLOS ONE

Dear Dr. Mishra,

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.

==============================

ACADEMIC EDITOR: Recommendations for decision are rather split. However, as one of reviewers (#2) pointed out, I think that this manuscript needs additional works. Therefore, I encourage the authors to perform the revision as per the reviewer’s suggestions and if these were meticulously performed, then I am sure that the MS could be reconsidered on a later date. 

==============================

We would appreciate receiving your revised manuscript by Dec 28 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.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Manoj Prasad, PhD

Academic Editor

PLOS ONE

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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: (No Response)

**********

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: No

**********

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: No

**********

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: The authors revised the manuscript based on the reviewers' comments and suggestions. The quality of the manuscript was improved and I have no further comments.

Reviewer #2: I have acted as Reviewer #2 in the previous round of assessment of the manuscript. I have now focused on modifications made by the authors on the basis of the comments I have made. There are still a several issues to address, I indicate them below.

1) Rationale of the choice of varieties

Reviewer comment: this comment has not been addressed in the revised manuscript. Again, the comment was about the rationale of the choice of the varieties. This should be described.

2) Comments on further comments:

L60: Ltn was spelled out, but with about 5 edit mistakes: this should be: ". Another trait, leaf tip necrosis (Ltn), "

L63: the comment was addressed, but with mistakes: please edit and use the correct latin name for pathogen causing leaf rust and stripe rust

L65: I was referring to giving the full name instead of B. in B. sorokiniana; please provide the full name

L65-7: I did not see any change in the revised manuscript, in spite of the authors indicating otherwise in there answer to my comment.

L70: the phrase has been changed, but now has additional edit mistakes (spaces missing)

L70-2: although the sentence was rephrased, I still do not see the logics. Please rephrase. Do you mean that QTLs for resistance against head blight and stem rust were identified, and associated to Lm, while QTLs have not been identified in the case of resistance against spot blotch associated to Lm? What is also is not indicated, and what should be clearly stated, is if Lm has been associated to resistance against spot blotch on a phenotypic basis.

Title: "Scoring .." remove "disease" because this is addressed in the next sub-section

Assessments: additional information is needed:

- For Ltn, on what leaves were the assessments made?

- For glaucousness, a description of the 5 classes needs to be included.

- describe how LP was measured, from what observations; what was the frequency of observation? a reference is not sufficient

L267: I insist, this statement is not correct. It should be changed as for example: "The results of this study showed that higher LP is associated to lower levels of spot blotch and Lm." Looking at Table 2, the R2 values between GI and AUDPC and Lm are very small and should not in my view be emphasised in the Discussion.

3) Editing the text

(1) Many occurrences where a space is needed; this needs to be corrected throughout the text. (2) There are still many editorial mistakes which need to be addressed throughout the text.

**********

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

[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.

PONE-D-19-19629R2

Genetic Characterization for Lesion mimic and other Traits in Relation to Spot blotch Resistance in Spring Wheat

PLOS ONE

Dear Dr. Mishra,

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.

==============================

ACADEMIC EDITOR: The revised version is now much improved but still there are several issues as indicated by the reviewer number 2. Therefore, authors are advised to revise their manuscript following reviewer comments.

==============================

We would appreciate receiving your revised manuscript by Mar 07 2020 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.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Manoj Prasad, PhD

Academic Editor

PLOS ONE

[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: (No Response)

**********

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

**********

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: No

**********

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: The authors addressed my concerns and I have no further comment! The manuscript was revised again based on another reviewers comment and the entire manuscript was improved.

Reviewer #2: I have acted as Reviewer #2 in the previous round of assessment of the manuscript. I have now focused on modifications made by the authors on the basis of the comments I have made. There are still a few issues to address, I indicate them below. The main issue I see, for which time will be required, is with respect to editing the English.

1) Rationale of the choice of varieties

This comment is now accounted for but further editing is needed. I suggest to replace the sentence "The population contains elite genetically diverse germplasm and so are stable for the traits under examine on both genotypic and phenotypic level and in general ruled out the chance of any segregation or elimination of charecters at maximum extent."

By the following sentence:

"The population contains elite germplasm displaying considerable genetic and phenotypic variation. Furthermore, the population includes genotypes which are stable for the traits under examination."

2) Further comments:

The whole document should be revised thoroughly for editing, and to remove mistakes (e.g., space missing between two consecutive words). I am indicating additional specific comments are below:

L61: “Another trait, Leaf tip necrosis (Ltn),”: remove the symbols " at the beginning and at the end of this segment

L67: "resistance against spot blotch caused by Bipolaris sorokiniana ": add "the hemibiotroph pathogen" after "caused by"

L68: add "increased" before "latent"

L79-89: there are several problems here. One of them is that Lm is not associated to resistance vs fusarium head blight: the sentence needs to be changed and the reference 27 removed; FHB is caused by Fusarium spp. which are not biotrophic. Also, there are many sentences which repeat what was already written previously, and so which need to be removed. I propose to change this paragraph as follows:

"Associations between Lm, Ltn, GI, and LP, and spot blotch have not been studied."

This sentence is to be followed by the beginning of the next paragraph.

L94: add " Ltn, GI, and LP" after "Lm"

L94: replace "its" by "their"

L123: remove "and disease"

L130-131: delete "was recorded in the field"

L370: "LP also showed negative effect on Lm. Longer LP was not found favorable for the expression of Lm and contributed to enhance resistance against spot blotch": this needs to be changed: LP cannot be the cause for Lm.

Please replace by "LP was negatively associated with Lm. Longer LP contributed to enhance resistance against spot blotch"

L380-2: this needs rephrasing for English and for the meaning.

**********

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: Yes: Zhiyong Liu

Reviewer #2: 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.

PONE-D-19-19629R3

Genetic Characterization for Lesion mimic and other Traits in Relation to Spot blotch Resistance in Spring Wheat

PLOS ONE

Dear Dr. Mishra,

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.

The revised manuscript is now much improved but still there are several problems as pointed out by both the reviewers. Therefore, authors are advised to revise their manuscript following reviewers comments. I would further request the authors to answer the reviewers (particularly reviewer number 4) questions seriously.

We would appreciate receiving your revised manuscript by May 24 2020 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.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Manoj Prasad, PhD

Academic Editor

PLOS ONE

[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 #3: All comments have been addressed

Reviewer #4: (No Response)

**********

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 #3: Yes

Reviewer #4: Yes

**********

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

Reviewer #3: Yes

Reviewer #4: 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 #3: Yes

Reviewer #4: 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 #3: No

Reviewer #4: No

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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 #3: The study defines the genetic characterization of Lm, Ltn, GI, LP, and their association with spot blotch resistance in spring wheat. I could see that the manuscript was previously reviewed by two reviewers who had already commented twice and based on those comments, the manuscript was improved. I have gone through all the versions of the manuscript, reviewers’ comments and the response of authors. The work is scientifically robust and technically sound, as major flaws were addressed during the revisions. However, the authors were repeatedly requested to improve the language, which they were apparently not able to. There are several minor and major issues pertaining to sentence formation, choice of vocabulary, voice agreement and use/misuse of punctuation marks. Plos One does not copyedit accepted manuscripts, and therefore, the language in submitted articles must be clear, correct, and unambiguous. I strongly recommend the authors to take assistance from a professional editing service to resolve the language issues. The certificate stating that the language was professionally edited should also be submitted to the journal for validation.

Reviewer #4: The manuscript is not well written. It needs language and scientific editing. I have highlighted some sentences in abstract that needs attention. Similar problems have been noticed i other portions of the manuscript. I think manuscript has good potential for publication in PLOS ONE but authors shall edit whole manuscript or get the manuscript edited from someone familiar with GWAS.

My feedback for Abstract:

1. The sentence < Lesion mimic (Lm) mutants are hypersensitive responses (HR) phenotype in the absence of the pathogen.> should be rewritten to make meaning clear

2. In sentence < In wheat, such mutants were reported to be resistant against rustsdue to their biotrophic nature.> the authors shall mention clearly which rust because there are three common rust disease in wheat .

3. In sentence < In this study, 289 diverse wheat germplasm were phenotyped for 3 consecutive years (2012 to 2015).> the author shall write 289 genotypes or 289 wheat germplasm lines

4. The sentence < Genotyping was done using Illumina iSelect beadchip assay for wheat having13589 highly polymorphic SNPs used for association mapping.> does not read well

5. The authors wrote < In genome wise association study (GWAS),> but it is < In genome wide association study (GWAS),>

6. < associated to various traits> may be changed with < associated with various traits>

similar problems have been noticed by me in all sections of the manuscript.

General Comments:

1. The manuscript is not well written. It needs both language editing and scientific editing.

2. The results of GWAS are not intelligently presented. There is no mention about contribution of associated markers although same is presented in Table.

3. In structural analysis there is no mention about admixed genotypes although same could be seen in structural plot

4. The quality of figures is poor

5. Manhattan plot are poorly presented. The authors shall highlight the significant SNPs in Manhattan plots

6. The results of ANOVA are not properly discussed

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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 #3: No

Reviewer #4: 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.

PONE-D-19-19629R4

Genetic characterization for lesion mimic and other traits in relation to spot blotch resistance in spring wheat

PLOS ONE

Dear Dr. Mishra,

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.

==============================

ACADEMIC EDITOR:

The reviewers' comments are back on your ms which shows that the work shall be revised and resubmitted. Therefore, authors are advised to modify and submit their work accordingly.

==============================

Please submit your revised manuscript by Aug 23 2020 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Manoj Prasad, PhD

Academic Editor

PLOS ONE

[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 #3: All comments have been addressed

Reviewer #4: All comments have been addressed

**********

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 #3: Yes

Reviewer #4: Yes

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

Reviewer #3: N/A

Reviewer #4: 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 #3: Yes

Reviewer #4: 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 #3: Yes

Reviewer #4: 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 #3: Authors have addressed all the comments raised by the reviewers, and there is no further revisions required.

Reviewer #4: The manuscript has been improved by keeping in view the comments made by reviewers but I think there are still language issues in the manuscript. For instance In material and methods (Plant material section) LN 109-114 the authors are using past tense for <wami obtained="" population="" were=""> as well future tense <to be="" for="" study="" this="" used="">. The authors need to maintain consistency throughout manuscript. In the same section the authors are still using <289 diverse wheat germplasm> despite suggestions were provided in previous revision. In addition I noticed that in table # 3 for LM, Gi etc the different associated markers are on same chromosomes with same position. Can authors have a look on the raw data again because having same position may signal same gene/QTL and not different genes/QTLs on that particular chromosome.</to></wami>

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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 #3: No

Reviewer #4: 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.]

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.

Genetic characterization for lesion mimic and other traits in relation to spot blotch resistance in spring wheat

PONE-D-19-19629R5

Dear Dr. Mishra,

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.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. 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 help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- 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.

Kind regards,

Manoj Prasad, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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 #3: All comments have been addressed

Reviewer #4: All comments have been addressed

**********

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 #3: Yes

Reviewer #4: Yes

**********

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

Reviewer #3: N/A

Reviewer #4: 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 #3: Yes

Reviewer #4: (No Response)

**********

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 #3: Yes

Reviewer #4: 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 #3: Authors have addressed all the comments raised by the reviewers, and there is no further revisions required.

Reviewer #4: (No Response)

**********

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 #3: No

Reviewer #4: No