Dear Dr. Worku,

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.

==============================

Dear Dr., Destaw Worku Worku

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Major Revision.

Comment editor

Additional Editor Comments:

It is necessary to read the reviewers’ comments and make all the required notes carefully.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 1

The study addresses an important topic in animal genetics, focusing on Indian sheep breeds, which are of economic and cultural importance. The identification of candidate genes and QTLs has significant implications for improving breed performance and conservation strategies.

However, the manuscript requires some clarifications and revisions to enhance its scientific rigor and readability.

The manuscript is well-organized overall, but some sections (e.g., methods and results) require more detailed explanations.

Certain paragraphs in the introduction and discussion are redundant and could be condensed.

Specific Comments:

The abstract provides a good summary but lacks specific details about key findings. Including numerical results or specific genes/QTLs would enhance its informativeness.

The introduction is comprehensive but overly descriptive in some parts. Focus more on the knowledge gap and the study's unique contributions.

Include more references to recent studies on selection signals and genomic studies in sheep from diverse geographical contexts.

Describe the data quality control steps in more detail. For example, how were outlier SNPs or missing data handled?

Clarify the composite selection signal (CSS) methodology. Provide justification for using this approach over others (e.g., iHS, XP-EHH).

Were any statistical corrections applied to account for population structure or relatedness among individuals?

The presentation of the results is clear, but:

Include figures or tables summarizing key candidate genes or QTLs identified.

Highlight specific loci and their putative roles in traits relevant to Indian sheep (e.g., drought tolerance, disease resistance).

Consider including a heatmap or Manhattan plot for better visualization of selection signals.

The discussion lacks depth in interpreting biological functions of identified genes. Provide insights into how these genes/QTLs align with known traits in sheep.

Compare findings with results from other studies (e.g., on sheep from different regions or breeds).

Discuss potential limitations of the study, such as sample size or marker density, and how they might affect the robustness of the conclusions.

Figures are clear but lack detailed legends. Add more context to explain what the reader should infer from each figure.

Tables summarizing selection signals should include effect sizes and p-values where relevant.

Reviewer 2

Authors are requested to revise the manuscript as per the comments or suggestions put into the manuscript file uploaded in the system, also expected to address the issues related to Discussion section as under:

1. Link Between Genomic Regions and Local Adaptation: While the discussion mentions the environmental adaptations of the breeds, it could further elaborate on how these adaptations might have influenced the specific genomic regions under selection. For example, more direct comparisons to how the genetic variations might correlate with the climate or geographical features of the areas where these breeds are found could enhance the reader's understanding of the adaptive significance of these genes.

2. Consistency in Gene References: Some genes are mentioned repeatedly (e.g., CNTNAP5), but the context of how they were identified in different breeds could be more explicitly connected to avoid confusion. For instance, you might clarify how CNTNAP5's role in body growth is shared across breeds like CHA and GAR, yet each breed’s unique genomic context could influence the gene's effect.

3. Discussion on Statistical Methodology: The use of the DCMS method is discussed, but more detailed insight into why this method improves the resolution power of the genomic signals could help readers understand the methodological benefits. Briefly touching on the weaknesses of other statistical approaches and how the DCMS method overcomes them would strengthen the argument.

4. Gene Functionality and Mechanisms: While candidate genes are identified, more information on their molecular mechanisms or the processes through which they impact the phenotypic traits (e.g., how MTSS1 influences bacterial resistance) could help provide a clearer understanding of their biological relevance.

5. Comparison with Other Studies: The discussion of prior research, such as the studies from Ahmad et al. (2021) and Zhang et al. (2016), provides useful context. However, it would be helpful to briefly explain how the findings in the current study either align or contrast with these studies, reinforcing the study’s contribution to the field.

Reviewer 3

1. The manuscript, especially the discussion part is exceedingly long with redundancy in a few parts which is repeated in the results and discussion section.

2. Check the spelling “Chantangi” which is wrongly written.

3. Concise the discussion part and avoid redundancy.

==============================

Please submit your revised manuscript by Mar 27 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,

Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

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

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

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

2. In the online submission form, you indicated that The genotypic data and other material related to this study are available with the corresponding author.

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3. Ethics statement does not appear in the manuscript file:

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.

4. Please include a copy of Table 3 which you refer in your text.

Additional Editor Comments:

Dear Dr., Destaw Worku Worku

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Major Revision.

Comment editor

Additional Editor Comments:

It is necessary to read the reviewers’ comments and make all the required notes carefully.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 1

The study addresses an important topic in animal genetics, focusing on Indian sheep breeds, which are of economic and cultural importance. The identification of candidate genes and QTLs has significant implications for improving breed performance and conservation strategies.

However, the manuscript requires some clarifications and revisions to enhance its scientific rigor and readability.

The manuscript is well-organized overall, but some sections (e.g., methods and results) require more detailed explanations.

Certain paragraphs in the introduction and discussion are redundant and could be condensed.

Specific Comments:

The abstract provides a good summary but lacks specific details about key findings. Including numerical results or specific genes/QTLs would enhance its informativeness.

The introduction is comprehensive but overly descriptive in some parts. Focus more on the knowledge gap and the study's unique contributions.

Include more references to recent studies on selection signals and genomic studies in sheep from diverse geographical contexts.

Describe the data quality control steps in more detail. For example, how were outlier SNPs or missing data handled?

Clarify the composite selection signal (CSS) methodology. Provide justification for using this approach over others (e.g., iHS, XP-EHH).

Were any statistical corrections applied to account for population structure or relatedness among individuals?

The presentation of the results is clear, but:

Include figures or tables summarizing key candidate genes or QTLs identified.

Highlight specific loci and their putative roles in traits relevant to Indian sheep (e.g., drought tolerance, disease resistance).

Consider including a heatmap or Manhattan plot for better visualization of selection signals.

The discussion lacks depth in interpreting biological functions of identified genes. Provide insights into how these genes/QTLs align with known traits in sheep.

Compare findings with results from other studies (e.g., on sheep from different regions or breeds).

Discuss potential limitations of the study, such as sample size or marker density, and how they might affect the robustness of the conclusions.

Figures are clear but lack detailed legends. Add more context to explain what the reader should infer from each figure.

Tables summarizing selection signals should include effect sizes and p-values where relevant.

Reviewer 2

Authors are requested to revise the manuscript as per the comments or suggestions put into the manuscript file uploaded in the system, also expected to address the issues related to Discussion section as under:

1. Link Between Genomic Regions and Local Adaptation: While the discussion mentions the environmental adaptations of the breeds, it could further elaborate on how these adaptations might have influenced the specific genomic regions under selection. For example, more direct comparisons to how the genetic variations might correlate with the climate or geographical features of the areas where these breeds are found could enhance the reader's understanding of the adaptive significance of these genes.

2. Consistency in Gene References: Some genes are mentioned repeatedly (e.g., CNTNAP5), but the context of how they were identified in different breeds could be more explicitly connected to avoid confusion. For instance, you might clarify how CNTNAP5's role in body growth is shared across breeds like CHA and GAR, yet each breed’s unique genomic context could influence the gene's effect.

3. Discussion on Statistical Methodology: The use of the DCMS method is discussed, but more detailed insight into why this method improves the resolution power of the genomic signals could help readers understand the methodological benefits. Briefly touching on the weaknesses of other statistical approaches and how the DCMS method overcomes them would strengthen the argument.

4. Gene Functionality and Mechanisms: While candidate genes are identified, more information on their molecular mechanisms or the processes through which they impact the phenotypic traits (e.g., how MTSS1 influences bacterial resistance) could help provide a clearer understanding of their biological relevance.

5. Comparison with Other Studies: The discussion of prior research, such as the studies from Ahmad et al. (2021) and Zhang et al. (2016), provides useful context. However, it would be helpful to briefly explain how the findings in the current study either align or contrast with these studies, reinforcing the study’s contribution to the field.

Reviewer 3

1. The manuscript, especially the discussion part is exceedingly long with redundancy in a few parts which is repeated in the results and discussion section.

2. Check the spelling “Chantangi” which is wrongly written.

3. Concise the discussion part and avoid redundancy.

[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

Reviewer #3: Yes

**********

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

Reviewer #1: I Don't Know

Reviewer #2: Yes

Reviewer #3: Yes

**********

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

Reviewer #3: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

Reviewer #1: The study addresses an important topic in animal genetics, focusing on Indian sheep breeds, which are of economic and cultural importance. The identification of candidate genes and QTLs has significant implications for improving breed performance and conservation strategies.

However, the manuscript requires some clarifications and revisions to enhance its scientific rigor and readability.

The manuscript is well-organized overall, but some sections (e.g., methods and results) require more detailed explanations.

Certain paragraphs in the introduction and discussion are redundant and could be condensed.

Specific Comments:

The abstract provides a good summary but lacks specific details about key findings. Including numerical results or specific genes/QTLs would enhance its informativeness.

The introduction is comprehensive but overly descriptive in some parts. Focus more on the knowledge gap and the study's unique contributions.

Include more references to recent studies on selection signals and genomic studies in sheep from diverse geographical contexts.

Describe the data quality control steps in more detail. For example, how were outlier SNPs or missing data handled?

Clarify the composite selection signal (CSS) methodology. Provide justification for using this approach over others (e.g., iHS, XP-EHH).

Were any statistical corrections applied to account for population structure or relatedness among individuals?

The presentation of the results is clear, but:

Include figures or tables summarizing key candidate genes or QTLs identified.

Highlight specific loci and their putative roles in traits relevant to Indian sheep (e.g., drought tolerance, disease resistance).

Consider including a heatmap or Manhattan plot for better visualization of selection signals.

The discussion lacks depth in interpreting biological functions of identified genes. Provide insights into how these genes/QTLs align with known traits in sheep.

Compare findings with results from other studies (e.g., on sheep from different regions or breeds).

Discuss potential limitations of the study, such as sample size or marker density, and how they might affect the robustness of the conclusions.

Figures are clear but lack detailed legends. Add more context to explain what the reader should infer from each figure.

Tables summarizing selection signals should include effect sizes and p-values where relevant.

Reviewer #2: Authors are requested to revise the manuscript as per the comments or suggestions put into the manuscript file uploaded in the system, also expected to address the issues related to Discussion section as under:

1. Link Between Genomic Regions and Local Adaptation: While the discussion mentions the environmental adaptations of the breeds, it could further elaborate on how these adaptations might have influenced the specific genomic regions under selection. For example, more direct comparisons to how the genetic variations might correlate with the climate or geographical features of the areas where these breeds are found could enhance the reader's understanding of the adaptive significance of these genes.

2. Consistency in Gene References: Some genes are mentioned repeatedly (e.g., CNTNAP5), but the context of how they were identified in different breeds could be more explicitly connected to avoid confusion. For instance, you might clarify how CNTNAP5's role in body growth is shared across breeds like CHA and GAR, yet each breed’s unique genomic context could influence the gene's effect.

3. Discussion on Statistical Methodology: The use of the DCMS method is discussed, but more detailed insight into why this method improves the resolution power of the genomic signals could help readers understand the methodological benefits. Briefly touching on the weaknesses of other statistical approaches and how the DCMS method overcomes them would strengthen the argument.

4. Gene Functionality and Mechanisms: While candidate genes are identified, more information on their molecular mechanisms or the processes through which they impact the phenotypic traits (e.g., how MTSS1 influences bacterial resistance) could help provide a clearer understanding of their biological relevance.

5. Comparison with Other Studies: The discussion of prior research, such as the studies from Ahmad et al. (2021) and Zhang et al. (2016), provides useful context. However, it would be helpful to briefly explain how the findings in the current study either align or contrast with these studies, reinforcing the study’s contribution to the field.

Reviewer #3: 1. The manuscript, especially the discussion part is exceedingly long with redundancy in a few parts which is repeated in the results and discussion section.

2. Check the spelling “Chantangi” which is wrongly written.

3. Concise the discussion part and avoid redundancy.

**********

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: Yes: Dr. Ananta Kumar Das, Ph.D., Associate Professor, Department of Animal Genetics & Breeding, Faculty of Veterinary and Animal Sciences, WB University of Animal and Fishery Sciences, Kolkata-37 (IN)

Reviewer #3: Yes: Partha Pratim Das

**********

[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: Reviewed manuscript-PONE-D-24-51732_reviewer.pdf

Attachment

Submitted filename: Review report.docx

Attachment

Submitted filename: comments.docx

Dear Dr. Destaw Worku Worku,

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.

==============================

Dear Dr., Destaw Worku Worku

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Minor Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 2

Authors are requested to adhere the comments/ suggestion/corrections inscribed in the attached manuscript pdf file for thorough revision satisfying journal's standard presentation style along with reference checking, typographical and grammatical corrections.

Reviewer 3

The authors have addressed the reviewers' comments elaborately. This study highlights important findings on QTL, which encompass significant protein-coding gene traits in Indian indigenous sheep breeds of economic interest. The study presents findings that could have a significant impact on the scientific community in time.

==============================

Please submit your revised manuscript by Jun 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.

• 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,

Lamiaa Mostafa Radwan, Ph.D.

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 (if provided):

Dear Dr., Destaw Worku Worku

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Minor Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 2

Authors are requested to adhere the comments/ suggestion/corrections inscribed in the attached manuscript pdf file for thorough revision satisfying journal's standard presentation style along with reference checking, typographical and grammatical corrections.

Reviewer 3

The authors have addressed the reviewers' comments elaborately. This study highlights important findings on QTL, which encompass significant protein-coding gene traits in Indian indigenous sheep breeds of economic interest. The study presents findings that could have a significant impact on the scientific community in time.

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

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #2: All comments have been addressed

Reviewer #3: All comments have been addressed

**********

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

Reviewer #2: Yes

Reviewer #3: Partly

**********

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

Reviewer #2: Yes

Reviewer #3: Yes

**********

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

The PLOS Data policy

Reviewer #2: Yes

Reviewer #3: Yes

**********

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

Reviewer #2: No

Reviewer #3: Yes

**********

Reviewer #2: Authors are requested to adhere the comments/ suggestion/corrections inscribed in the attached manuscript pdf file for thorough revision satisfying journal's standard presentation style along with reference checking, typographical and grammatical corrections.

Reviewer #3: The authors have addressed the reviewers' comments elaborately. This study highlights important findings on QTL, which encompass significant protein-coding gene traits in Indian indigenous sheep breeds of economic interest. The study presents findings that could have a significant impact on the scientific community in time.

**********

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: Dr. Ananta Kumar Das, Associate Professor, Department of Animal Genetics and Breeding, West Bengal University of Animal and Fishery Sciences, Kolkata (IN)

Reviewer #3: 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

Attachments

Attachment

Submitted filename: Reviewed PONE-D-24-51732_R1_reviewer.pdf

Dear Dr. Worku,

<o:p></o:p>

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.

==============================

Dear Dr., Destaw Worku Worku

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Minor Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 1

This study applied the De-Correlated Composite of Multiple Selection Signals (DCMS) approach to systematically analyze genomic selection signatures in three Indian sheep breeds: Chanthangi, Garole, and Deccani. Candidate genes and QTLs associated with key traits—including growth, reproduction, disease resistance, and environmental adaptation—were successfully identified, offering novel insights into the molecular mechanisms underlying genetic improvement in Indian sheep. However, several questions remain as follows:

1.The manuscript mentions that DCMS combines five statistics including FST, H1, H12, Tajima’s D, and π, but does not elaborate on the rationale for selecting this specific combination of five indicators. Have other statistics (such as iHS and XP-EHH) been evaluated for their complementarity? How are the weights of each statistic determined in the composite calculation?

2.Line81, It is recommended to add literature citations, such as doi: 10.1038/s41467-020-16485-1, doi: 10.24272/j.issn.2095-8137.2022.124.

3. Line 130, why choose these three breeds for the research?

4. Line225, please remove the colon

5. It is recommended to adjust the format of the manuscript, such as Table 8.

6. Has the QTL identified in this study overlapped with those previously reported?

==============================

Please submit your revised manuscript by 3 Agu 2025. 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,

Lamiaa Mostafa Radwan, Ph.D.

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:

Dear Dr., Destaw Worku Worku

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Minor Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 1

This study applied the De-Correlated Composite of Multiple Selection Signals (DCMS) approach to systematically analyze genomic selection signatures in three Indian sheep breeds: Chanthangi, Garole, and Deccani. Candidate genes and QTLs associated with key traits—including growth, reproduction, disease resistance, and environmental adaptation—were successfully identified, offering novel insights into the molecular mechanisms underlying genetic improvement in Indian sheep. However, several questions remain as follows:

1.The manuscript mentions that DCMS combines five statistics including FST, H1, H12, Tajima’s D, and π, but does not elaborate on the rationale for selecting this specific combination of five indicators. Have other statistics (such as iHS and XP-EHH) been evaluated for their complementarity? How are the weights of each statistic determined in the composite calculation?

2.Line81, It is recommended to add literature citations, such as doi: 10.1038/s41467-020-16485-1, doi: 10.24272/j.issn.2095-8137.2022.124.

3. Line 130, why choose these three breeds for the research?

4. Line225, please remove the colon

5. It is recommended to adjust the format of the manuscript, such as Table 8.

6. Has the QTL identified in this study overlapped with those previously reported?

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

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #2: All comments have been addressed

Reviewer #4: (No Response)

**********

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

Reviewer #2: Yes

Reviewer #4: (No Response)

**********

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

Reviewer #2: Yes

Reviewer #4: (No Response)

**********

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

The PLOS Data policy

Reviewer #2: Yes

Reviewer #4: (No Response)

**********

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

Reviewer #2: Yes

Reviewer #4: (No Response)

**********

Reviewer #2: (No Response)

Reviewer #4: This study applied the De-Correlated Composite of Multiple Selection Signals (DCMS) approach to systematically analyze genomic selection signatures in three Indian sheep breeds: Chanthangi, Garole, and Deccani. Candidate genes and QTLs associated with key traits—including growth, reproduction, disease resistance, and environmental adaptation—were successfully identified, offering novel insights into the molecular mechanisms underlying genetic improvement in Indian sheep. However, several questions remain as follows:

1.The manuscript mentions that DCMS combines five statistics including FST, H1, H12, Tajima’s D, and π, but does not elaborate on the rationale for selecting this specific combination of five indicators. Have other statistics (such as iHS and XP-EHH) been evaluated for their complementarity? How are the weights of each statistic determined in the composite calculation?

2.Line81, It is recommended to add literature citations, such as doi: 10.1038/s41467-020-16485-1, doi: 10.24272/j.issn.2095-8137.2022.124.

3. Line 130, why choose these three breeds for the research?

4. Line225, please remove the colon

5. It is recommended to adjust the format of the manuscript, such as Table 8.

6. Has the QTL identified in this study overlapped with those previously reported?

**********

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

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Reviewer #2: Yes: Prof. (Dr.) Ananta Kumar Das, Department of Animal Genetics and Breeding, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, Kolkata-37 (IN)

Reviewer #4: No

**********

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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

Dear Dr. Worku,

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.

==============================

Dear Dr. Destaw Worku Worku

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Mainor Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer3

The manuscript has undergone slight modifications. However, there are numerous grammatical errors. In several instances, a sentence is written in the past tense, while the following one is in the future tense. For consistency, it is recommended that the Methods section be written entirely in the past tense and maintain uniformity. A thorough review of the manuscript’s grammar is also recommended and avoid overall redundancy.

In line 395, the phrase “researchers could not differentiate” is unclear. It is indistinct whether the author is referring to findings from the previously published paper by Ahmed et al. or to their own data. Recommended to rephrase this sentence to clearly convey the intended meaning.

Reviewer4

The authors have comprehensively addressed the concerns and suggestions from the initial review. The revised manuscript demonstrates notable improvements. Therefore, the manuscript can be accepted.

==============================

Please submit your revised manuscript by Oct 05 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,

Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

1. 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.

2. 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 :

Dear Dr. Destaw Worku Worku

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Mainor Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer3

The manuscript has undergone slight modifications. However, there are numerous grammatical errors. In several instances, a sentence is written in the past tense, while the following one is in the future tense. For consistency, it is recommended that the Methods section be written entirely in the past tense and maintain uniformity. A thorough review of the manuscript’s grammar is also recommended and avoid overall redundancy.

In line 395, the phrase “researchers could not differentiate” is unclear. It is indistinct whether the author is referring to findings from the previously published paper by Ahmed et al. or to their own data. Recommended to rephrase this sentence to clearly convey the intended meaning.

Reviewer4

The authors have comprehensively addressed the concerns and suggestions from the initial review. The revised manuscript demonstrates notable improvements. Therefore, the manuscript can be accepted.

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

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #3: All comments have been addressed

Reviewer #4: All comments have been addressed

**********

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

Reviewer #3: Yes

Reviewer #4: Yes

**********

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

Reviewer #3: Yes

Reviewer #4: Yes

**********

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

The PLOS Data policy

Reviewer #3: Yes

Reviewer #4: Yes

**********

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

Reviewer #3: No

Reviewer #4: Yes

**********

Reviewer #3: The manuscript has undergone slight modifications. However, there are numerous grammatical errors. In several instances, a sentence is written in the past tense, while the following one is in the future tense. For consistency, it is recommended that the Methods section be written entirely in the past tense and maintain uniformity. A thorough review of the manuscript’s grammar is also recommended and avoid overall redundancy.

In line 395, the phrase “researchers could not differentiate” is unclear. It is indistinct whether the author is referring to findings from the previously published paper by Ahmed et al. or to their own data. Recommended to rephrase this sentence to clearly convey the intended meaning.

Reviewer #4: The authors have comprehensively addressed the concerns and suggestions from the initial review. The revised manuscript demonstrates notable improvements. Therefore, the manuscript can be accepted.

**********

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 #3: No

Reviewer #4: 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

Dear Dr. Worku,

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.

==============================

Dear Dr.  Destaw Worku

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Minor Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 3

The authors has nicely addressed all the comments raised by reviewer. This study highlights important findings on QTL, which encompass significant protein-coding gene traits in Indian indigenous sheep breeds of economic interest. The study presents findings that could have a significant impact on the scientific community in time

Reviewer 5

General Comment: rewrite the entire document.

Abstract: Modify the statements such as “line 32: Natural and artificial selection shape the genomes of sheep”, “line 34: to preserve and enhance native genetic traits”, and “line 48: wide variety of characteristics”. The way of expression is not professional.

1. Give a description for each breed in the introduction section.

2. Rewrite from line: 87-90

3. A quick transition disrupts the flow of idea between paragraphs 2 and 3.

4. Line 118: “highly dense genotypes”. What does it mean? Please be sure to express the statement in professional terms.

5. Modify as 2.1 Ethics Statement and 2.2 Animal Selection and Genotyping

6. Line 246-247: 3.3.1

7. Line 282: production (9.38%). Which type of production?

8. Table 1 is not under the appropriate position because it is a common table for all breeds. You have already written the information of table 1 in text. No need of duplication.

9. In the discussion section try to elaborate on the general implication of your study, any limitation, and agreeing or disagreeing with previous reports with citations. No need of repeating the methodology or introductory information.

10. Captions of figures should be self-explanatory. So, explain each graph in detail.

==============================

Please submit your revised manuscript by Nov 30 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,

Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

1. 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.

2. 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:

Dear Dr. Destaw Worku

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Minor Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 3

The authors has nicely addressed all the comments raised by reviewer. This study highlights important findings on QTL, which encompass significant protein-coding gene traits in Indian indigenous sheep breeds of economic interest. The study presents findings that could have a significant impact on the scientific community in time

Reviewer 5

General Comment: rewrite the entire document.

Abstract: Modify the statements such as “line 32: Natural and artificial selection shape the genomes of sheep”, “line 34: to preserve and enhance native genetic traits”, and “line 48: wide variety of characteristics”. The way of expression is not professional.

1. Give a description for each breed in the introduction section.

2. Rewrite from line: 87-90

3. A quick transition disrupts the flow of idea between paragraphs 2 and 3.

4. Line 118: “highly dense genotypes”. What does it mean? Please be sure to express the statement in professional terms.

5. Modify as 2.1 Ethics Statement and 2.2 Animal Selection and Genotyping

6. Line 246-247: 3.3.1

7. Line 282: production (9.38%). Which type of production?

8. Table 1 is not under the appropriate position because it is a common table for all breeds. You have already written the information of table 1 in text. No need of duplication.

9. In the discussion section try to elaborate on the general implication of your study, any limitation, and agreeing or disagreeing with previous reports with citations. No need of repeating the methodology or introductory information.

10. Captions of figures should be self-explanatory. So, explain each graph in detail.

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

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #3: All comments have been addressed

Reviewer #5: (No Response)

**********

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

Reviewer #3: Yes

Reviewer #5: Yes

**********

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

Reviewer #3: Yes

Reviewer #5: Yes

**********

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

The PLOS Data policy

Reviewer #3: Yes

Reviewer #5: Yes

**********

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

Reviewer #3: Yes

Reviewer #5: No

**********

Reviewer #3:  The authors has nicely addressed all the comments raised by reviewer. This study highlights important findings on QTL, which encompass significant protein-coding gene traits in Indian indigenous sheep breeds of economic interest. The study presents findings that could have a significant impact on the scientific community in time.

Reviewer #5: General Comment: rewrite the entire document.

Abstract: Modify the statements such as “line 32: Natural and artificial selection shape the genomes of sheep”, “line 34: to preserve and enhance native genetic traits”, and “line 48: wide variety of characteristics”. The way of expression is not professional.

1. Give a description for each breed in the introduction section.

2. Rewrite from line: 87-90

3. A quick transition disrupts the flow of idea between paragraphs 2 and 3.

4. Line 118: “highly dense genotypes”. What does it mean? Please be sure to express the statement in professional terms.

5. Modify as 2.1 Ethics Statement and 2.2 Animal Selection and Genotyping

6. Line 246-247: 3.3.1

7. Line 282: production (9.38%). Which type of production?

8. Table 1 is not under the appropriate position because it is a common table for all breeds. You have already written the information of table 1 in text. No need of duplication.

9. In the discussion section try to elaborate on the general implication of your study, any limitation, and agreeing or disagreeing with previous reports with citations. No need of repeating the methodology or introductory information.

10. Captions of figures should be self-explanatory. So, explain each graph in detail.

**********

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 #3: No

Reviewer #5: 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

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.

Dear Dr.  Destaw Worku

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Mainor Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 3

Comments:

1. Rewrite the paragraph line no 198-204, heading 2.5.4. DCMS Estimation, with proper citation.

2. The author should revise the paragraph from lines no 344–349 with proper citation, as its current sentence is unclear and the intended meaning is difficult to understand.

3. Rewrite paragraphs of line no 353-357 with proper meaning. A clear and coherent rewrite is required.

4. Write the word ‘p-value’ and ‘q-value’ consistently throughout the manuscript.

5. The authors stated that the study identified two key candidate genes i.e. TRMT12, associated with environmental adaptation and LRRC36, associated with domestication in sheep. While Ji Yang et al. (2024) have been cited as evidence supporting the role of LRRC36 in domestication, however, no reference has been provided to substantiate the association of TRMT12 with environmental adaptation. The authors are required to cite an appropriate and relevant study demonstrating the significant association of TRMT12 with environmental adaptation. Without such supporting literature, the current claim remains unsubstantiated.

6. It is unclear why reference [20] has been cited in line 219, immediately after the section, titled 2.6 Identification of Functional Genes and QTL Regions. If information from this reference has been used, the authors should clearly rewrite the paragraph to properly reflect and justify the citation. If the reference is not relevant to the content, it should be removed.

7. Please write the full form of OAR when it is first mentioned in the manuscript and include the specific version of the OAR Rambouillet genome assembly.

8. Does OAR and CHR represent the same thing in table no 2? Does flank marker represent rsID? How does Flank marker id were obtained with rsID, as rsID of non human database are obsolete and discontinued? Author need to clarify what is meant by ‘flank marker’ in this context?

9. Please describe the significance of the p-value and q-value, specifically explaining their importance in interpreting the study’s analytical outcomes relevant to this study.

10. The manuscript requires extensive language editing and careful revision to ensure clarity and scientific accuracy, as much of the current writing is unclear and fuzzy in several sections. Additionally, the authors should remove irrelevant or nonessential content, as the paper is unnecessarily long and contains information that does not directly contribute to the study’s objectives.

Reviewer 4

the authors have comprehensively and thoroughly revised and elaborated on the core concerns and key issues raised in the initial evaluation. All the questionable points and pending problems have received clear, reasonable responses and been properly addressed.

Reviewer 5

1. Check affiliation 5

2. Remove the word “shows the” from each table caption

3. Since this study lacks experimental validation, clearly explain this limitation in the discussion and conclusion section.

==============================

Please submit your revised manuscript by Feb 05 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.

Please include the following items when submitting your revised manuscript:

• 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,

Lamiaa Mostafa Radwan, 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.

Additional Editor Comments:

Dear Dr. Destaw Worku

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Minor Revision.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 3

Comments:

1. Rewrite the paragraph line no 198-204, heading 2.5.4. DCMS Estimation, with proper citation.

2. The author should revise the paragraph from lines no 344–349 with proper citation, as its current sentence is unclear and the intended meaning is difficult to understand.

3. Rewrite paragraphs of line no 353-357 with proper meaning. A clear and coherent rewrite is required.

4. Write the word ‘p-value’ and ‘q-value’ consistently throughout the manuscript.

5. The authors stated that the study identified two key candidate genes i.e. TRMT12, associated with environmental adaptation and LRRC36, associated with domestication in sheep. While Ji Yang et al. (2024) have been cited as evidence supporting the role of LRRC36 in domestication, however, no reference has been provided to substantiate the association of TRMT12 with environmental adaptation. The authors are required to cite an appropriate and relevant study demonstrating the significant association of TRMT12 with environmental adaptation. Without such supporting literature, the current claim remains unsubstantiated.

6. It is unclear why reference [20] has been cited in line 219, immediately after the section, titled 2.6 Identification of Functional Genes and QTL Regions. If information from this reference has been used, the authors should clearly rewrite the paragraph to properly reflect and justify the citation. If the reference is not relevant to the content, it should be removed.

7. Please write the full form of OAR when it is first mentioned in the manuscript and include the specific version of the OAR Rambouillet genome assembly.

8. Does OAR and CHR represent the same thing in table no 2? Does flank marker represent rsID? How does Flank marker id were obtained with rsID, as rsID of non human database are obsolete and discontinued? Author need to clarify what is meant by ‘flank marker’ in this context?

9. Please describe the significance of the p-value and q-value, specifically explaining their importance in interpreting the study’s analytical outcomes relevant to this study.

10. The manuscript requires extensive language editing and careful revision to ensure clarity and scientific accuracy, as much of the current writing is unclear and fuzzy in several sections. Additionally, the authors should remove irrelevant or nonessential content, as the paper is unnecessarily long and contains information that does not directly contribute to the study’s objectives.

Reviewer 4

the authors have comprehensively and thoroughly revised and elaborated on the core concerns and key issues raised in the initial evaluation. All the questionable points and pending problems have received clear, reasonable responses and been properly addressed.

Reviewer 5

1. Check affiliation 5

2. Remove the word “shows the” from each table caption

3. Since this study lacks experimental validation, clearly explain this limitation in the discussion and conclusion section.

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

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #3: (No Response)

Reviewer #4: All comments have been addressed

Reviewer #5: All comments have been addressed

**********

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

Reviewer #3: Partly

Reviewer #4: Yes

Reviewer #5: Yes

**********

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

Reviewer #3: Yes

Reviewer #4: Yes

Reviewer #5: Yes

**********

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

The PLOS Data policy

Reviewer #3: Yes

Reviewer #4: Yes

Reviewer #5: Yes

**********

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

Reviewer #3: No

Reviewer #4: Yes

Reviewer #5: Yes

**********

Reviewer #3: Comments:

1. Rewrite the paragraph line no 198-204, heading 2.5.4. DCMS Estimation, with proper citation.

2. The author should revise the paragraph from lines no 344–349 with proper citation, as its current sentence is unclear and the intended meaning is difficult to understand.

3. Rewrite paragraphs of line no 353-357 with proper meaning. A clear and coherent rewrite is required.

4. Write the word ‘p-value’ and ‘q-value’ consistently throughout the manuscript.

5. The authors stated that the study identified two key candidate genes i.e. TRMT12, associated with environmental adaptation and LRRC36, associated with domestication in sheep. While Ji Yang et al. (2024) have been cited as evidence supporting the role of LRRC36 in domestication, however, no reference has been provided to substantiate the association of TRMT12 with environmental adaptation. The authors are required to cite an appropriate and relevant study demonstrating the significant association of TRMT12 with environmental adaptation. Without such supporting literature, the current claim remains unsubstantiated.

6. It is unclear why reference [20] has been cited in line 219, immediately after the section, titled 2.6 Identification of Functional Genes and QTL Regions. If information from this reference has been used, the authors should clearly rewrite the paragraph to properly reflect and justify the citation. If the reference is not relevant to the content, it should be removed.

7. Please write the full form of OAR when it is first mentioned in the manuscript and include the specific version of the OAR Rambouillet genome assembly.

8. Does OAR and CHR represent the same thing in table no 2? Does flank marker represent rsID? How does Flank marker id were obtained with rsID, as rsID of non human database are obsolete and discontinued? Author need to clarify what is meant by ‘flank marker’ in this context?

9. Please describe the significance of the p-value and q-value, specifically explaining their importance in interpreting the study’s analytical outcomes relevant to this study.

10. The manuscript requires extensive language editing and careful revision to ensure clarity and scientific accuracy, as much of the current writing is unclear and fuzzy in several sections. Additionally, the authors should remove irrelevant or nonessential content, as the paper is unnecessarily long and contains information that does not directly contribute to the study’s objectives.

Reviewer #4: the authors have comprehensively and thoroughly revised and elaborated on the core concerns and key issues raised in the initial evaluation. All the questionable points and pending problems have received clear, reasonable responses and been properly addressed.

Reviewer #5: 1. Check affiliation 5

2. Remove the word “shows the” from each table caption

3. Since this study lacks experimental validation, clearly explain this limitation in the discussion and conclusion section.

**********

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 #3: No

Reviewer #4: No

Reviewer #5: 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.

Attachments

Attachment

Submitted filename: plos review_Dec 2025.docx

Composite Selection Signal Analysis: Uncovering Candidate Genes and Quantitative Trait Loci in Indian Sheep Breeds

PONE-D-24-51732R6

Dear Dr. Destaw Worku<o:p></o:p>

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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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,

Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS One

Additional Editor Comments (optional):

Dear Dr., Destaw Worku

I am pleased to inform you that the manuscript has been accepted for publication.

Kind regards,

Prof. Lamiaa Mostafa Radwan, Ph.D.

Academic Editor

PLOS ONE

Reviewer 3

The authors adressed all the comments raised by the reviewer. however, author need to make few minor corrections..

1. put a . at the end of line no 596.

2. Write the gene name in italics throughout the manuscript.

3. in line no 409, make it 'Moreover, a gene expression study' since authors cited only one reference at the end.

Reviewer 5

Accept

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #3: All comments have been addressed

Reviewer #5: All comments have been addressed

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

Reviewer #3: Yes

Reviewer #5: Yes

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

Reviewer #3: Yes

Reviewer #5: Yes

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

The PLOS Data policy

Reviewer #3: Yes

Reviewer #5: Yes

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

Reviewer #3: Yes

Reviewer #5: Yes

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Reviewer #3: The authors adressed all the comments raised by the reviewer. however, author need to make few minor corrections..

1. put a . at the end of line no 596.

2. Write the gene name in italics throughout the manuscript.

3. in line no 409, make it 'Moreover, a gene expression study' since authors cited only one reference at the end.

Reviewer #5: (No Response)

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Reviewer #3: No

Reviewer #5: No

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