Dear Dr. Fei,

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: Thank you for submitting your manuscript to PLOS ONE. We were able to secure only one reviewer for your paper, even though we invited many experts on behalf of your paper. After careful editorial consideration, and in view of the comments of the reviewer, we feel that your paper has merit but requires revision. Therefore, we invite you to submit a revised version of the manuscript that addresses comprehensively addresses the points of both the reviewer and the editor.

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Please submit your revised manuscript by Oct 18 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'.
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We look forward to receiving your revised manuscript.

Kind regards,

Andre van Wijnen

Academic Editor

PLOS ONE

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 [This research was funded by the Guangdong Basic and Applied Basic Research Foundation (2022A1515111078) and Guizhou Science and Technology Key Project ([2022] No. 034).].

Please state what role the funders took in the study.  If the funders had no role, please state: ""The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.""

If this statement is not correct you must amend it as needed.

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6.  Thank you for stating the following in the Competing Interests section:

[Guangdong Tinoo’s Food Co., Ltd].  

We note that one or more of the authors are employed by a commercial company: name of commercial company.

1.        Please provide an amended Funding Statement declaring this commercial affiliation, as well as a statement regarding the Role of Funders in your study. If the funding organization did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript and only provided financial support in the form of authors' salaries and/or research materials, please review your statements relating to the author contributions, and ensure you have specifically and accurately indicated the role(s) that these authors had in your study. You can update author roles in the Author Contributions section of the online submission form.

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8. 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. 

Additional Editor Comments:

Editorial Comments:

Please present Figure 1D with the same level of data transparency as Figure 1B. In addition, expand figure 1D by presentation of RNA-seq data for other CREB members (e.g., CREB1/2/3/4) and GIPC members (e.g., GIPC1, GIPC3) to assess whether there is the possibility for gene/mRNA compensation.

Reviewer #1:

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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?

Reviewer #1: Yes

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

Reviewer #1: Yes

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

The PLOS Data policy

Reviewer #1: Yes

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

Reviewer #1: Yes

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Reviewer #1: This manuscript employs a multi-omics approach (transcriptomics and metabolomics) to investigate the molecular basis of variable melanin deposition in the breast muscle of 35-day-old Muchuan Black-Bone chickens. The study identifies novel candidate genes (CREB5, GIPC2) and metabolites beyond the well-characterized melanogenic pathway, providing new insights into a commercially important trait. However, the manuscript requires significant revisions to:

Abstract Discrepancy: A critical inconsistency exists where the abstract highlights "Glucose-6-phosphate" as a key metabolite, but this compound is absent from the main results and discussion, which focus on entirely different metabolites (e.g., CDP-ethanolamine, UDP-glucuronic acid). This must be corrected for accuracy.

Superficial Interpretation of Pathways: The authors list enriched pathways (e.g., Arginine-Proline metabolism, Histidine metabolism) but do not adequately discuss their plausible biological connection to melanogenesis. The manuscript would be significantly strengthened by deeper mechanistic hypothesizing.

Insufficient Methodological Detail: Key details are missing from the methods section, preventing full reproducibility. Most critically, the qPCR primer sequences and reference genes are omitted. The metabolomics extraction solvent and chromatography conditions are also not specified.

Underdeveloped Integration: While both omics datasets are presented, their true integration is limited to showing correlations between modules (WGCNA) and joint variation (O2PLS). The most valuable step—directly correlating key DEGs with key metabolites to generate testable hypotheses—is missing.

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what does this mean? ). If published, this will include your full peer review and any attached files.

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Reviewer #1: No

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Attachments

Attachment

Submitted filename: PONE-D-25-36595.pdf

Dear Dr. Fei,

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 Dec 24 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 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,

Andre van Wijnen

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.

Additional Editor Comments:

Editorial Comments: This paper is acceptable for publication pending final revisions that address minor comments.

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

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #1: All comments have been addressed

**********

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

Reviewer #1: Yes

**********

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

Reviewer #1: Yes

**********

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

The PLOS Data policy

Reviewer #1: Yes

**********

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

Reviewer #1: Yes

**********

Reviewer #1: The manuscript presents a well-designed multi-omics study that "Integrated Transcriptome and Metabolome Analysis of Melanin-related genes and Metabolites in Muchuan Black Bones Chickens". The identification of novel candidate genes, and metabolites is a valuable contribution to the field. The revisions made in response to the previous editorial and reviewer comments have significantly improved the manuscript's clarity and depth.

However, several issues, primarily concerning language, clarity, and data interpretation, still need to be addressed before the manuscript is suitable for publication.

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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:  Owais Iqbal

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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.]

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.

Integrated Transcriptome and Metabolome Analysis of Melanin-related genes and Metabolites in Muchuan Black Bones Chickens

PONE-D-25-36595R2

Dear Dr. Fei,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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

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Kind regards,

Andre van Wijnen

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #1: All comments have been addressed

**********

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

Reviewer #1: Yes

**********

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

Reviewer #1: Yes

**********

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

The PLOS Data policy

Reviewer #1: Yes

**********

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

Reviewer #1: Yes

**********

Reviewer #1: There are some spelling, space and formatting issues in the manuscript. Please check and revised carefully

**********

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:  Owais Iqbal

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