Genomic dissection of methane emission traits in cattle: A meta-GWAS and heritability analysis across populations

Sare Golpasand; Navid Ghavi Hossein-Zadeh; Shahrokh Ghovvati

doi:10.1371/journal.pone.0344752

Peer Review History

Original SubmissionOctober 28, 2025
5 Feb 2026 Decision Letter - Hayrunnisa Nadaroglu, Editor Genomic dissection of methane emission traits in cattle: a meta-GWAS and heritability analysis across populations PLOS One Dear Dr. Ghavi Hossein-Zadeh, 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 22 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.. 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Kind regards, Hayrunnisa Nadaroglu 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. 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. 3. 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Yes Reviewer #2: Yes ******** 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??> Reviewer #1: No Reviewer #2: Yes ****** Reviewer #1: The article contains several grammatical issues (some of which have been highlighted in the text). In addition, self-citations by the authors should be avoided, and alternative references have been suggested. Palangi, V., & Lackner, M. (2022). Management of enteric methane emissions in ruminants using feed additives: A review. Animals, 12(24), 3452. Palangi, V., Taghizadeh, A., Abachi, S., & Lackner, M. (2022). Strategies to mitigate enteric methane emissions in ruminants: A review. Sustainability, 14(20), 13229. Kader Esen, V., Palangi, V., & Esen, S. (2022). Genetic improvement and nutrigenomic management of ruminants to achieve enteric methane mitigation: A review. Methane, 1(4), 342-354. Reviewer #2: Dear authors, I have read the manuscript entitled “Genomic dissection of methane emission traits in cattle: a meta-GWAS and heritability analysis across populations” and consider that it is well written and easy to follow. The methodology used is appropriate for the objectives of the study. I have suggested some minor comments, which can be found in the attached document. ****** what does this mean? ). If published, this will include your full peer review and any attached files.). 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? 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NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. Attachments Attachment Submitted filename: PONE-D-25-57330_reviewer.pdf Attachment Submitted filename: PONE-D-25-57330_R.pdf https://doi.org/10.1371/journal.pone.0344752.r001
Revision 1
6 Feb 2026 Author Response With sincere thanks to the respective reviewers for their constructive comments, we are pointing to the changes we made to the revised manuscript. All changes were highlighted within the revised text. ************************************************ Reviewer #1: 1. Grammar corrections. AU: Thank you for your suggestions. All corrections were made within the revised text as suggested (Lines 21-22, 30-31, 34-35, 39, 43) 2. The self-citations by the authors should be avoided, and alternative references have been suggested. Palangi, V., & Lackner, M. (2022). Management of enteric methane emissions in ruminants using feed additives: A review. Animals, 12(24), 3452. Palangi, V., Taghizadeh, A., Abachi, S., & Lackner, M. (2022). Strategies to mitigate enteric methane emissions in ruminants: A review. Sustainability, 14(20), 13229. Kader Esen, V., Palangi, V., & Esen, S. (2022). Genetic improvement and nutrigenomic management of ruminants to achieve enteric methane mitigation: A review. Methane, 1(4), 342-354. AU: All suggested citations were added to the revised manuscript (Lines 720-725), but it is worth noting that the references of the authors’ works are highly relevant to the topic of this manuscript and were used in several parts of the manuscript. Therefore, we would suggest to keep them in the manuscript. ************************************************************ Reviewer#2: 1. Grammar corrections. AU: Thank you for your suggestions. All corrections were made within the revised text as suggested (Lines 29, 253, 603). 2. Please include a reference for this sentence AU: Reference was added as recommended (Line 43). 3. Please split this into a new paragraph here. AU: Reference was added as recommended (Line 49). 4. REML and Bayesian methods are estimation frameworks, whereas the animal model is a model structure that can be fitted using either approach. Consider rephrasing for clarity. AU: Change made as suggested (Lines 126-128). 5. This seems redundant, as it has already been described in the M&M section. Please consider removing it. AU: It was removed as suggested. 6. Please use a maximum of three decimal places AU: Change made as suggested (Line 242). 7. I suggest ordering the table by chromosome position. AU: Change made as suggested (Table 3). 8. could you explain what Weight means? AU: “Weight indicates the total sample size contributing to the meta-analysis for each SNP, corresponding to the sample-size–weighted Z-score approach implemented in the METAL program”. This information was added to the footnote of Table 3. 9. Could you explain what the different colors in the figure mean? AU: Node color intensity reflects the significance of GO term enrichment (adjusted P-value), with darker colors indicating more significant enrichment (Lines 320-322). 10. Consider not repeating in the text the values that are already clearly shown in the table, to improve readability. Please check it out in this section. AU: Changes made as suggested (Lines 391-402, 422, 430, 436). 11. I suggest to include below the table the descriptions of some of the column names AU: Changes made as suggested (footnotes of Tables 6 and 7). 12. Since heritability is constrained to be non-negative, it is unclear why the confidence intervals in the figure extend below zero. Please provide clarification or justify the estimation approach that leads to this. AU: Some explanations were added to the text for clarification as recommended (Lines 620-625). 13. Please rewrite this sentence and avoid including results (estimated values). Try to focus on discussion and comparison of the results. AU: Changes made as suggested (Lines 610-613). Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0344752.r002
24 Feb 2026 Decision Letter - Hayrunnisa Nadaroglu, Editor Genomic dissection of methane emission traits in cattle: a meta-GWAS and heritability analysis across populations PONE-D-25-57330R1 Dear Dr. Ghavi Hossein-Zadeh, 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 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, Hayrunnisa Nadaroglu Academic Editor PLOS One Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0344752.r003
Formally Accepted
Acceptance Letter - Hayrunnisa Nadaroglu, Editor PONE-D-25-57330R1 PLOS One Dear Dr. Ghavi Hossein-Zadeh, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS One. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Professor Hayrunnisa Nadaroglu Academic Editor PLOS One https://doi.org/10.1371/journal.pone.0344752.r004

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