PONE-D-23-32748Uncovering the genetic diversity and adaptability of Butuo Black Sheep through whole-genome re-sequencingPLOS ONE

Dear Dr. Yang,

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Olatunji Matthew Kolawole, Ph.D.

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

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

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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

Reviewer #1: No

Reviewer #2: Yes

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

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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: This study aimed at identifying SNPs that are specific to BBS or different from other breeds; inferring the evolutionary history and demographic dynamics of BBS and; exploring the potential adaptive significance and functional consequences of these SNPs for BBS.

The reviewer thinks the manuscript is good and will be relevant to conservation and breeding improvement efforts.

The following points may be considered to improve the manuscript

The last sentence on the introduction is not adding any information to the manuscript. Please consider removing it.

Give more details of the material and method. E.g. no information on the specific BBS used in the study. At least a brief details of the DNA extraction and resequencing shouybe provided.

What's the justification for your quality control and filtering parameters through out the manuscript? I think you should provide some references.

L127-129: "The online tool Strings (version 11.0, available at https://string-db.org/) was used to analyze

the protein-protein interactions of genes implicated in SNP and INDEL variations, revealing their

interactions." Can you give more details and references on this? Did you apply any statistics?

L14-143: It was observed that the resequencing results obtained were moderately accurate. Can you provide some references to this?

The table names are unacceptable. Use for example: Table 1. Sequencing information statistics of 33 BBS population.

The table can also have the highest and the lowest five samples followed by the mean, minimum and maximum.

L151-153: what is the measurable range? Who determines this? I think statements like this and several others in the results section explaining the implications of the results should come in discussion section. No?

L154: expand more on the valuable reference implications.

L212: Technical term abbreviations have been explained upon first use of the term. Do you really need to have this here?

Did you perform genomic resequencing of BBS using blood samples or genomic resequencing of BBS blood? This should be properly presented throughout the MS.

No reference to Table S1 in the text.

Reviewer #2: Comments

The manuscript draft entitled "Uncovering the genetic diversity and adaptability of Butuo Black Sheep through whole genome re-sequencing " has important contents worth communicating to the scientific community. The study seems scientifically sound, and the results are presented in a clear and concise manner. However, there are a few points that need to be addressed.

Abstract:

� The abstract start with the aim of the study and then the background, but it is better to present the background of the study followed by objectives.

� Line 15= SNPs (abbreviation along with full form should be written when it appears for the first time

� Lack of clarity between the significance of the study and recommendation.

� Line24-25 seem significant of the study, and the author should make appropriate recommendation

Keywords

� Keywords should be presented in alphabetical order

� Make the keyword “Black sheep” to “Buton black sheep”

� Whole genome resequencing should be a keyword

Introduction

� Line 28, make “Ovis aries” italic

� There are spacing problems on the reference citation

� Lines 50 and 52, “Single nucleotide polymorphisms (SNPs)” redundancy

� Lines 61 and 62 should be present in the material and methods part

� Lacks research question

� The objectives should come after the research question

Material and Methods

� It lacks some clarity such as study setting, study population, sample collection method, sample processing including DNA extraction

� Line 72, All tissues? Which??? Makes confusion

� The authors claimed that “the experiments were carried out following the guidelines of the animal care committee of Xichang University”, but this is not enough and ethical clearance letter should be obtained from the relevant ethical committee and the reference number of the approved letter should include.

� Line 84-85, spacing problem

� Line 91, full form of BWA required

� Line 96, full form of GATK required

� Line 99, full form of INDEL required

Results

� The authors presented the minimum, maximum and mean of each read, Hence, if there is a mean, standard deviation and/or standard error should be presented along with it.

� The Authors present simply figures such as 164,023,208. To make it clearly show the reads were nucleotides

� Line 170, again “Single nucleotide polymorphisms (SNPs)” repeated, the author should write the abbreviated form only when it appears for the second and more times

Discussion

� Needs some modification

� Spacing of reference citations

� Line 228-231 looks like justification of the study and it is better to write in the introduction part

� Better to use passive voice instead of saying “we have identified specific genes” line 232. “we have identified” line 271 etc.

� What is the relevance of writing sentences like “In cattle, variants of the GHR gene are associated with reproductive and milk production traits” line 234 or “the PGR gene's variants play a role in reproductive traits for cattle” line 236??? Instead, write the different breeds of sheep that have similar or different genes responsible for the variation or similarity.

� Line 283-286, repeated sentence of line 274-275

Conclusions:

� Lacks the recommendations

References

� Make Reference to References

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Reviewer #1: Yes: Kehinde Adewole Adeboye, Ekiti State Polytechnic, Isan, Nigeria

Reviewer #2: No

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Uncovering the genetic diversity and adaptability of Butuo Black Sheep through whole-genome re-sequencing

PONE-D-23-32748R1

Dear Dr. Yang,

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.

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Kind regards,

Olatunji Matthew Kolawole, Ph.D.

Academic Editor

PLOS ONE

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