PONE-D-20-37524

Meta-analysis of QTLs associated with popping traits in maize (Zea mays L.)

PLOS ONE

Dear Dr. Rakshit,

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 Mar 11 2021 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.

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We look forward to receiving your revised manuscript.

Kind regards,

Ajay Kumar

Academic Editor

PLOS ONE

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"The work was carried out under the financial assistance from the Indian Council of

346 Agricultural Research, New Delhi (India). Inputs of Dr. Shelly Parveen, Indian Agricultural Research Institute,

347 New Delhi (India) for discussion on biochemical interpretation. The first author thanks Punjab Agricultural

348 University for the logistic support during course of investigation."

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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

**********

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

**********

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: 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: Minor comments:

1- Abbreviations should be explained in their very first appearance in the text, please explain these abbreviations: QTL (line 9), CGAR (line 28), psi (line 39), PEV (line 54), DAP ( line 320), and describe what is B73 (line 329).

2- Line 180, there should be space in “tenmetaQTL”

3- Line 206- 271: As describing the “The features of the four major metaQTLs identified in the study” no need of describing the features of the metaQTLs that already mentioned in the Table 3. Most of the features already mentioned in Table 3.

4- You could add a supplementary table describing the features of the individual QTL from different studies that used in this article.

Reviewer #2: Summary:

With the goal to compile QTLs for popping-related traits, the authors collected 99 QTLs from eight studies. They came up with 10 meta-QTLs on chromosomes 1 and 6. They related these metaQTLs to 229 candidate genes that expressed in pericarp, endosperm, or both. Finally, this study revealed consensus metaQTLs for popping traits, which the authors recommended for markers-assisted breeding. This study has the merit of identifying consensus genomic regions that could be important for popping quality traits. However, I will pinpoint some of the missing things in the paper and my comments/suggestions as follows:

1. Only papers published between 2006 and 2012 are included for the metaQTL analysis. It is not clear why you did not included papers after 2012. At lease, I find one paper in 2021 "Thakur, S., Kumar, R., Vikal, Y. et al. Molecular mapping of popping volume QTL in popcorn (Zea maize L.). J. Plant Biochem. Biotechnol. (2021). " ext-link-type="uri" xlink:type="simple">https://doi.org/10.1007/s13562-020-00636-y". I think it needs some justification for not including papers published after 2012.

2. There is inconsistency in citing references in text. You used both "number" and "author-date" styles. Your citations in the text need to be consistent as recommended by the journal.

3. The Figures are poor in quality and I think they need to be improved in the final submission.

4. I think it is good to avoid using "etc" in listing things (example on line 19: "MetaQTL1_1 at bin location 1.01 coincided with the reported QTLs related to various agronomic traits like stalk diameter, tassel length etc."). If the list is not big enough, I think it is better to mention all of them. This works for the other "etc" mentioned in the text.

5. Abbreviations must be defined first before they can be used the next time it comes in the text. (examples: "PEV" on line 54 and "PVE" on line 81).

6. The discussion part: The first part (paragraphs 1 and 2) is discussed in comparison with past research or generally describing concept or facts referring to literature. I think this is good. The second part (paragraph 3) seems a repetition of the results part. I suggest you look into the discussion part and try to improve it.

7. Line 204-206: You declared 4 metaQTLs important because they were represented by 5-8 QTLs. Is this enough to classify some as important and the others as not important. I have not seen any other criteria for your decision to classify as important and not important. I think this needs some explanation. I think some other criteria should be added in addition to the number of QTLs. This simple classification may sideline some of the metaQTLs which can be important in breeding.

8. Overall, I suggest a through review of the manuscript according to the guideline of the journal.

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Reviewer #1: No

Reviewer #2: No

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PONE-D-20-37524R1

Meta-analysis of QTLs associated with popping traits in maize (Zea mays L.)

PLOS ONE

Dear Dr. Rakshit,

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 Jun 12 2021 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. 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-emailutm_source=authorlettersutm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Ajay Kumar

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.

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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: 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 #1: (No Response)

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: (No Response)

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: Line 117:” Lod value” Lod should be capitalized.

Line 128, table 2: Row 2 and 3, in Reference column, there is no need to add semicolon after references. row 5 in reference column ” ) [7, 24]”, there is a redundant parenthesis. Also, at the footnote of table 2 describe what is RIL, BC and F mapping population.

Line 185: write the reference of the “q teller”.

Line 124, and 210 : Fig 2 and 3: All the caption of figures should be Bold.

Line 78, 128 and 215: Table, 1,2, 3 captions font are not consistent with the figures caption font , they are smaller.

Line 312: There is a redundant parenthesis at the end of sentences .”Features of the individual QTL related to popping traits in maize reported in different studies)”

General comment: Fig 2 and Fig 3 do not have good quality and resolution.

Reviewer #2: All comments except one addressed satisfactorily. I still prefer some recent studies to be included. But the authors preferred to keep 8 studies for their Meta-QTL analysis. That could be fine and recent QTL studies could be addressed in a different study. I prefer listing all the items without using “etc”. If the lists are too long, it is possible to use the word “including” followed by listing of the first few items. That is just personal preference. Overall, I can say the review comments addressed.

Some other changes that I want to suggest are as follows:

It seems rephrasing sentences necessary in several places in the manuscript:

Example1--- Line 16-17: The clustered QTLs were from ≥2 different experiments and out of the 19 genes specifically involved in carbohydrate metabolism, eleven were in these regions thus considered as most important.

Could be re-written as: The clustered QTLs were from two or more experiments. Of the 19 genes specifically involved in carbohydrate metabolism, 11 of them were in these regions, implying the importance of these clustered QTLs.

Example2--- Line 18-19: A total of 229 genes were shortlisted in these regions on the basis of their expression in endosperm and pericarp tissues using qteller option in maizeGDB, out of which 19 were specifically involved in carbohydrate metabolism.

Could be re-written as: Based on the expression pattern in endosperm and pericarp tissues, a total of 229 genes were selected. Nineteen of these genes involves in carbohydrate metabolism.

In general, it may be good to go through the manuscript and make changes as required.

**********

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.]

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.

PONE-D-20-37524R2

Meta-analysis of QTLs associated with popping traits in maize (Zea mays L.)

PLOS ONE

Dear Dr. Rakshit,

Thank you for submitting your manuscript to PLOS ONE. There are few minor revisions still required. 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 Aug 13 2021 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. 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-emailutm_source=authorlettersutm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Ajay Kumar

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

**********

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: 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: 1- The Fig 2 and 3 still do not have good quality and resolution. In Fig 3, name of the markers should be clear.

2- Make sure that Table 3 is in good shape:

a) It has one redundant row at the bottom, that should be deleted,

b) Choose brief header, and make the font of the headers and the content of the Table smaller (for example 7)

until they can be fit in on or two lines,

c) All digits in Table 3 with decimal should be rounded to 1 or 2 decimal places, be consistent all over the digits.

d) Explain what chr, CI, R2, AIC, kb, and cM are at the footnote of Table.

Reviewer #2: The authors addressed all the comments satisfactorily. I believe the manuscript is acceptable for publication.

**********

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.]

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.

Meta-analysis of QTLs associated with popping traits in maize (Zea mays L.)

PONE-D-20-37524R3

Dear Dr. Rakshit,

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,

Ajay Kumar

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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