PONE-D-22-33894Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breedsPLOS ONE

Dear Dr. Moradi,

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Reviewers' comments:

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Comments to the Author

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Reviewer #1: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The manuscript entitled “Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds” is interesting. In the study, the authors used OvineSNP50 Bead Chip array to estimate and compare LD, genetic diversity, effective population size and genomic inbreeding of three Iranian indigenous sheep breeds. The authors found that the Baluchi breed has higher levels of LD and haplotype blocks than other two breeds. Estimation of genomic inbreeding showed the highest inbreeding coefficient in Baluchi and the lowest in Zel breed that was explained by high pressure of artificial selection on Baluchi breed. Overall, the findings are interesting and the manuscript is well structured and well written. My only concern is that the sample size is less specially for Lori-Bakhtiari (=47) and Zel (=47) breeds. Otherwise, the manuscript has merit and may be accepted for publication.

Reviewer #2: The article entitled “Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds ” focuses on the knowledge of linkage disequilibrium, genetic structure and genetic diversity in three Iranian local sheep breeds. This study is of wide interest to the community, but I have following concerns which needs to be addressed.

1.In the introduction section, more breed information for Baluchi , Lori-Bakhtiari and Zel is needed.

2. why you state more information for QTL, GS, and LD in the introduction section?please explain it. I personally feel that the current organizational structure of the introduction section is unreasonable, and more valuable information should be provided by the author.

3.Line 92, please the name of database,or provide the accession number.

4. line 113, how many SNPs was remain? Please provide it in the text.

5. line 118, provide the author name

6.Line200-202, please rewrite this sentence.

7.Line 914, please fixed the subtitle.

8.Please write the results and discussion, respectively. The current write way is difficult for readers to clearly understand the author's intention.

9.Improve discussion and conclusion. More utility from this work should be signified.

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Reviewer #1: Yes: Arun Kumar De

Reviewer #2: No

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PONE-D-22-33894R1Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breedsPLOS ONE

Dear Dr. Moradi,

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 Jun 11 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-emailutm_source=authorlettersutm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Shamik Polley, Ph.D

Academic Editor

PLOS ONE

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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:

I appreciate the authors' corrections. Still not satisfied with the article's figures' resolution. There are a few minor corrections listed below.

Line 249: (Fig 1Error! Reference source not found.)          

-        Please check it and modify it accordingly.

Line 301: Fig 1.

-      It seems to fit in fig 3. Please check it again and correct it in the manuscript.

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Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds

PONE-D-22-33894R2

Dear Dr. Moradi,

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,

Shamik Polley, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: