PONE-D-24-17942Quantitative trait loci for grain mineral element accumulation in Vietnamese rice landracesPLOS ONE

Dear Dr. Grondin,

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.

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ACADEMIC EDITOR:  I recommend that the authors address the reviewers' comments and revise the manuscript accordingly.==============================

Please submit your revised manuscript by Nov 11 2024 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.

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Karthikeyan Adhimoolam

Academic Editor

PLOS ONE

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5. Thank you for stating the following financial disclosure: Hien Linh Tran is supported by the France Excellence Scholarship Program from the French Embassy in Vietnam. This work was supported by the “QUARION” EPPN European Plant Phenotyping Network (EPPN) 2020 project, the “RICE-VN” TRENPLIN-ASEAN prize awarded by the French Academy of Science and the French Ministry of Higher Education and Research (2023-2026). 

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6. Thank you for stating the following in the Acknowledgments Section of your manuscript: Hien Linh Tran is supported by the France Excellence Scholarship Program from the French Embassy in Vietnam. This work was supported by the “QUARION” EPPN European Plant Phenotyping Network (EPPN) 2020 project, the “RICE-VN” TRENPLIN-ASEAN prize awarded by the French Academy of Science and the French Ministry of Higher Education and Research (2023-2026). The authors would like to thank Nguyen Van Toan, Vu Thi Huong and Vu Manh An for their valuable support in field care and rice grain sample harvesting.

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Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: Hien Linh Tran is supported by the France Excellence Scholarship Program from the French Embassy in Vietnam. This work was supported by the “QUARION” EPPN European Plant Phenotyping Network (EPPN) 2020 project, the “RICE-VN” TRENPLIN-ASEAN prize awarded by the French Academy of Science and the French Ministry of Higher Education and Research (2023-2026). 

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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

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: 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: No

Reviewer #2: Yes

Reviewer #3: 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: No

Reviewer #2: Yes

Reviewer #3: 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: Quantitative trait loci for grain mineral element accumulation in Vietnamese rice landraces.

# Title: Rewriting suggested.

Abstract: OK

Keywords: OK

A dedicated Abbreviation section suggested (including transporters, QTLs etc.).

Authors are advised to add a note on deprivation of elements among the population (age and sex wise etc.).

Role of As and Cd in minimizing elemental content in raw and cooked rice.

Clearly mention the gap area and aim and scope of the study (bullet).

Line 133: 50 cm spacing or 5.0 cm spacing?

SRM recovery should be presented in tabular format in supplementary file.

Line:168: mean of how many replications?

In the discussion section, authors are required to interpret the varieties having greater elemental profile linked with QTL in terms of RDA or RDI for greater acceptability.

Moreover, how climatic fluctuations can influence the elemental profile will be highly appreciated.

Reviewer #2: The manuscript entitled “Quantitative trait loci for grain mineral element accumulation in Vietnamese rice landraces” focuses on identifying the QTL regions and candidate genes for different mineral elements in rice landraces. The manuscript is clear, concise, and informative. The methods are appropriate and the results are presented in a logical and transparent manner. The discussion is balanced and comprehensive. I have only a few minor comments and suggestions for improvement:

Introduction: The Introduction has been well drafted, with extensive collection of points related to the study, highlighting the rationale behind it. However, the chronology of these sentences may have to be organised for clarity. The following corrections may be carried out for improvement of the manuscript,

Comment 1: Line 42–62, 1st paragraph contains the brief introduction about biofortification and its improvement, while 2nd paragraph (line 64-81) contains other elements and its correlation with harmful heavy metals, followed by its improvement. This could be modified as stating brief introduction of different elements in 1st paragraph and improvement strategies in 2nd paragraph.

Comment 2: Line 83, introductory sentences need to be added to this paragraph. Instead of starting with different GWAS studies, mention about other mapping strategies and how advantageous GWAS is over them with respect to grain ions trait.

Comment 3: Line 108, the concluding statement, which defines the objective of the study needs clarity. Just mention the objective and delete the findings, which may be discussed in results section.

Materials and methods: The methodology has been presented well in different subsections viz., Plant materials and genotypic data, Field experiment, Grain ion phenotyping, Statistical analysis, Genome-wide association studies and Linkage disequilibrium (LD) heatmap and identification of candidate genes. However, the following corrections may be carried out in the manuscript for its improvement,

Comment 4: Were the ions estimated in soil where the crop has been raised? And mention crop production methods, whether any nutrients were supplemented?

Comment 5: Line 168, “Means, standard deviations, and coefficients of variation” may be modified as “Mean, standard deviation, and coefficients of variation”

Comment 6: Line 175, mention the model which has been used for calculation of BLUEs for your incomplete block design.

Results: The results has been presented well in different subsections viz., Variation in grain ion content in Vietnamese rice landraces, Identification of QTL related to grain ion content in Vietnamese rice landraces and Potential candidate genes related to grain ion content in Vietnamese rice landraces. However, the following corrections may be carried out in the manuscript for its improvement,

Comment 7: Line 220, “analyses were performed” may be modified as “analyses was performed”

Comment 8: Line 227, it is “(R < -0.34)” or “(R = -0.34)”? check all instances.

Comment 8: Line 228, it is “co-variations” or “correlations”?

Comment 9: Table 2 may be modified for clarity. It should be organised based on the traits (ions). Additionally, points in the results section should reflect in the table (model in which it was associated, bonferroni threshold, etc.).

Comment 10: Line 247-258, these results may also be added for investigation of candidate genes in Table 3. The relevance for these genes with associated traits should be established, or else delete it.

Comment 11: Line 266, is it 3.6% or 3.6ppm? check all instances

Comment 12: Line 261-287, the paragraphs looks more like a discussion. Modify it. The results section for these should only contain the findings of this study.

Discussion: The discussion has been presented well and schematically organised. However, the following corrections may be carried out in the manuscript for its improvement,

Comment 13: Line 311, modify “with K, Mg, P showing smallest variation and Fe, Zn” as “with K, Mg and P showing smallest variation, while, Fe, Zn”

Abstract: The abstract is well drafted and sequentially written which reflects the contents of the manuscript. However, the corrections if made in the above sections need to be addressed in abstract also.

General comments:

1. Check whether the reference format is according to the journal style

2. Grammatical and typographic errors may be checked and corrected

Reviewer #3: Overall the findings of the study is compelling. Although there are few typographical error in some statements that could also be addressed, the efforts made by the authors are appreciable. Moreover, the findings of this study is almost agreed to support the previous works, QTL mapping studies for instance.

However, I have listed few corrections for the authors to look over it.

•Correct the typographical and grammatical errors in the following line numbers, 98,112,119,155 169 etc…

•Did authors measured phytic acid levels? If so it would be good to included phytic acid contents in WR and BR grains

•Check for the references as per the journal format!

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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: Dr. Debojyoti Moulick

Reviewer #2: Yes: Manoharan Akilan

Reviewer #3: Yes: Vellaichamy Gandhimeyyan Renganathan

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PONE-D-24-17942R1Quantitative trait loci for grain mineral element accumulation in Vietnamese rice landracesPLOS ONE

Dear Dr. Grondin,

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 04 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,

Karthikeyan Adhimoolam

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.

Additional Editor Comments:

Minor revision

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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

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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

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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: No

Reviewer #2: Yes

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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 #1: It seems the authors have answered the queries raised by the reviewers in a more or less satisfactory manner and improvement in quality of MS in R1 version can be seen.However, the final call will be from editor's desk.

Reviewer #2: Reviewer’s comments for the author’s response

I have carefully reviewed the revised manuscript and the author’s responses to my comments. I am pleased to report that the authors have adequately addressed my suggestions and made the necessary revisions to improve the clarity and quality of the manuscript. I would suggest one more change to be made to improve the quality of the manuscript.

Comment 1: Table 2, differentiate the SNPs that are associated in multiple GWAS models (14 SNPs) and which are exclusively associated in BLINK model (13 SNPs) using footnotes.

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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: Yes: Dr. Debojyoti Moulick

Reviewer #2: Yes: Manoharan Akilan

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[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.

Quantitative trait loci for grain mineral element accumulation in Vietnamese rice landraces

PONE-D-24-17942R2

Dear Dr. Grondin,

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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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,

Karthikeyan Adhimoolam

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 #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 #2: Yes

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

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 #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 #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 #2: Reviewer’s comments for the author’s response

I have carefully reviewed the revised manuscript “Quantitative trait loci for grain mineral element accumulation in Vietnamese rice landraces” and the author’s responses to my comments. I am pleased to report that the authors have adequately addressed all of my suggestions and made the necessary revisions to improve the clarity and quality of the manuscript. The authors have demonstrated a thorough consideration of the feedback, and the manuscript now meets the standards required for publication. I find no further revisions necessary and would recommend accepting the manuscript for publication.

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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 #2: Yes: Manoharan Akilan

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