Dear Dr. Cao,

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 Oct 10 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.

• 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,

Mojtaba Kordrostami, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

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

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. Please note that PLOS One has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse.

3. We note that your Data Availability Statement is currently as follows: All relevant data are within the manuscript and its Supporting Information files.

Please confirm at this time whether or not your submission contains all raw data required to replicate the results of your study. Authors must share the “minimal data set” for their submission. PLOS defines the minimal data set to consist of the data required to replicate all study findings reported in the article, as well as related metadata and methods (https://journals.plos.org/plosone/s/data-availability#loc-minimal-data-set-definition).

For example, authors should submit the following data:

- The values behind the means, standard deviations and other measures reported;

- The values used to build graphs;

- The points extracted from images for analysis.

Authors do not need to submit their entire data set if only a portion of the data was used in the reported study.

If your submission does not contain these data, please either upload them as Supporting Information files or deposit them to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see https://journals.plos.org/plosone/s/recommended-repositories.

If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. If data are owned by a third party, please indicate how others may request data access.

4. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process.

5. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well.

6. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise.

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

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

Reviewer #1: Partly

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: N/A

**********

3. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

Reviewer #1: Mu et al. submitted the manuscript dealing with hormonal dynamics and transcriptomic regulatory mechanisms during seed dormancy release in herbaceous perennial plant Aconitum kusnezoffii.

Here are my comments:

1. For an unknown reason, the manuscript is written in the MDPI (Agronomy) template. The pages and lines are not numbered, so I refer to the chapter/paragraph titles in my review.

2. Abstract - a) in the study, determination of GA3, ABA, IAA and cytokinin representative zeatin riboside (ZR) was performed. This compound occurs in plant tissue in two isomeric forms, i.e., trans- (tZR) and cis-ZR (cZR), which differ in their biological activity. It is not specified which isomer of ZR the authors determined. Was it tZR or cZR?

b) The cytokinins (CKs) generally promote dormancy release. However, the free bases (tZ, cZ, ...) have greater activity in this direction than corresponding ribosides (tZR, cZR). They are more of a transport form that retains some biological activity, but are not the main actor, although they are able to reversibly release the free base under certain conditions by cleavage of ribose. Thus, it would therefore be more relevant in this case to determine the level of free CK bases rather than CK ribosides.

3. GA3 is of fungal origin (Fusarium fujikuroi) and occurs only to a limited extent in higher plants (http://www.phytohormones.info/ga3refsL.htm). According to this literature source and other sources, GA3 has not been identified in Aconitum kusnezoffii yet. According to the level presented in Figure 2 it could be a contamination from external source. Among 136 known gibberellins (GAs), there are six of them biologically active (GA1, GA3, GA4, GA5, GA6 and GA7). The most common are GA1 and GA4 in higher plants. I would recommend to determine the level of other biologically active GA than GA3.

4. Brassinolide, a representative of bioactive brassinosteroids (BRs), was also performed. Why is not mentioned in an abstract? Further, common abbreviation for this plant hormone is BL, not BR.

5. A) The paragraph “Hormone Quantification lacks the information about sample preparation. How were the hormones extracted from the seeds? How was the crude extract further treated until the sample was pipetted into the ELISA plate?

B) In the paragraph the authors write that the absorbance was measured. with what instrument? Each of the instruments used should be specified by model name, manufacturer and country of origin. The same applies to chemicals, the list of which should be given in a separate paragraph "Chemicals and Reagents".

C) Since we do not know the validation parameters of the ELISA kits used, I recommend quantifying plant hormones for a scientific article using some other validated and published method, e.g., LC-MS.

6. Figure 1 is missing a caption.

7. Results - a) The paragraph “Dynamic changes of six endogenous hormones during dormancy release…” - Why is there no description of developmental stages in the Material and methods section? Furthermore, why are the developmental stages numbered I, II and IV and not I, II and III?

b) When expressing the amount of a hormone, it is not necessary to write a dot between the unit (ng/g) and the FW.

Although the manuscript contains partially relevant experimental data, I cannot recommend it for publication in its current form for the reasons mentioned above.

Reviewer #2: The present study has outstanding strengths. The integration of physiology, hormonal profiling, and transcriptomics is among the strengths of the paper. The data validation is also good, and the paper is well-structured and scientifically sound. However, a few points and suggestions are made below that I hope will improve the quality of the paper:

More details should be given on the number of biological replicates and the choice of ELISA should be justified.

The discussion of ecological and agronomic implications should be expanded.

The discussion could better address practical agricultural implications.

The figures are informative and could be simplified for clarity.

**********

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: Danuse Tarkowska

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.

Attachments

Attachment

Submitted filename: PONE-D-25-34985_rev.pdf

Dear Dr. Cao,

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 29 2026 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.

• A 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 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,

Mojtaba Kordrostami, Ph.D.

Academic Editor

PLOS One

Journal Requirements:

If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise.

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

Reviewer #1: (No Response)

Reviewer #2: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions??>

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

Reviewer #1: The most of comments are successfully reflected. However, there are still some issues to be clarified/ solved.

1. In the Data availability section (lines 584-586), the authors state that the manuscript data has been uploaded to a public database. However, no link to this database or DOI of the data is provided.

2. In the study, brassinolide (BL) was quantified, among other plant hormones, as a biologically active representative of the brassinosteroid group (BRs). When revising the manuscript, the authors replaced all original BR abbreviations with BL in most places in the text. However, the abbreviation in the caption of Figure 2 (line 191) still needs to be corrected. This caption also needs to indicate that the ZR values correspond to the sum of the trans (t) and cis (c) isomers of this plant hormone. The cross-reactivity against cZR and tZR of the antibody used for the quantification of both isomers using the ELISA kit should be stated at an appropriate place in the text (e.g., line 88) so that the reader can get an idea of the approximate ratio of cZR and tZR in the quantified sum presented in the manuscript.

3. The authors were recommended to add a paragraph to the Material and Methods section, which would describe the detailed procedure for sample preparation before its analysis by ELISA. The authors have not yet fulfilled this. It is necessary to state the composition of the extraction reagent, the method of homogenization including a description of the conditions (temperature, duration of homogenization, type of device, grinding frequency, etc.), centrifugation conditions, the method of purification using PVPP or other materials. The authors only added abbreviations of chemicals used in sample preparation to the manuscript (lines 115-117). These abbreviations must be explained to the readers, i.e. the full name accompanied by a hyphen in parentheses should be given if this abbreviation is used further in the text.

Reviewer #2: Considering the responses provided to the first and second reviewers at the end of the text (more detailed explanations, acceptance of limitations, etc.), it can be said that the responses were well prepared. The authors responded to each comment professionally and systematically. Finally, according to this version, the responses were satisfactory and the necessary changes were made, and the article is ready for publication.

**********

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 ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures

You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation.

NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications.

Hormonal Dynamics and Transcriptomic Regulatory Mechanisms During Seed Dormancy Release in Aconitum kusnezoffii

PONE-D-25-34985R2

Dear Dr. Cao,

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. For questions related to billing, please contact billing support .

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,

Mojtaba Kordrostami, Ph.D.

Academic Editor

PLOS One

Additional Editor Comments (optional):

Reviewers' comments: