PONE-D-20-25223

NTRK2 and litter size in sheep: an insight from GWAS and pathway enrichment analysis

PLOS ONE

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Additional Editor Comments (if provided):

The idea of the article is good. But the study needs to provide detailed supportive data to validate the conclusion drawn. The Introduction section needs to be edited carefully for cohesiveness and flow. Further the title should be edited and it should reflect the actual results obtained.

[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?

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: Partly

Reviewer #2: No

Reviewer #3: Partly

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

Reviewer #1: No

Reviewer #2: No

Reviewer #3: Yes

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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: No

Reviewer #2: No

Reviewer #3: Yes

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

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: 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: Reviewer Recommendation and Comments for Manuscript Number PONE-D-20-25223

• The manuscript is acceptable to be published in PLoS One with the below given modifications and additions.

Major comments:

1) The manuscript is well written and researched. Specifically, I would appreciate the authors for trying find out the genes responsible for litter size in sheep but the information provided in the manuscript and the conclusions drawn are too ambitious. There is a need for supporting tests and data, for the drawn conclusions. The conclusions need evidences through minimal wet lab experiments. The supportive data is missing.

2) The author should cite and include more data regarding NTRK2 to support their study.

Minor comments:

1. Please provide justification for the tests used in materials and methods section. Proper justification through citation is missing.

2. As it is mentioned (page 3, lines-54-55) that a previous study by Gholizadeh et al. (2014) identified two significant SNP (rs407696726 and rs412433416) on OAR10 and OAR15 in association with litter size, and in conclusion (page 15, lines-311-312) authors also claimed that they also found a one genomic region on OAR10 associated with the litter size in sheep, how this study is different or novel from the Gholizadeh et al. study?

3. Page 11, lines- 225-226, the citation number given in fig 4 doesn’t match with the reference list. Correction required.

4. Manuscript can be improved a lot in terms of content to be acceptable in Plos one.

Reviewer #2: In the manuscript, the authors described the identification of the gene variants and pathways and provides important findings which can be useful for better understanding of the mechanisms underlying in iranian baluchi sheep litter size variation.

The major concern with the manuscript is the lack of any experimental data that shows NTRK2 gene involvement in affecting the litter size in sheep. I think the authors should consider including some experimental results in the revised draft.

The other major issue with the manuscript that the title did not correlate with the purposed findings. The title must can be changed to the appropriate one.

The introduction section seems incomplete, should be re-written to provide more clear background of the study.

The methodology used for the analysis seems appropriate however, there is no detailed description of the methods for example GO and KEGG methodology should be mentioned as a different section in the Materials and Methods.

Typo-Error:

1. Page 7 line 139 "Table 3" changed it into "Table 2"

2. Page 14 line 301-302 Re-write the line " The cell junction.........connexins"

Reviewer #3: Mehdi Esmaeilifard etal, in the entitled “ NTRK2 and litter size in sheep: an insight from GWAS and pathway enrichment” manuscript, investigated the genetic mechanism that affects litter size in Iranian Baluchi Sheep. It’s indeed an interesting study to discover what genetic factor and its mechanism that contributes to litter size. By employing two-step genome wide association study and gene set enrichment analysis (with GO and KEGG databases), authors intriguingly identified two genes; namely NTRK2 and RAB4A that are associated with litter size in sheep. The function of NTRK2 in litter size homeostasis is significantly supported by the given data. Additionally, the known function of NTRK2 in oocyte development and survival process provides a direct link for NTRK2 in affecting litter size. Overall the here identified NTRK2 role in litter size is clear.

Major point

Authors showed that the second gene RAB4A significantly affects litter size, however, its known role in membrane trafficking, blood vessel formation and proliferation makes it hard to corelate RAB4A function in affecting litter size. It could be that the observed phenotype of RAB4A on litter size is an indirect effect. It is essential to explain how RAB4A is influencing litter size?

Specific point

Authors should carefully check the cited references throughout the manuscript. For example, in figure 4 the author cited Dorfman etal (28), but actually in the reference list the correct number is 29. Additionally, it's nice if author follows a standard reference style, either number or name. For example Gholizadeh et al. (2014) is cited in the text.

Figure 2: A/A has greater EBV for litter size ( n=1) than the other two A/G and G/G genotypes, it's good to show larger sample size for A/A group for statistical purpose.

Minor points

It would be good if author gives explanation of their abbreviations in the manuscript for example; EBV, SNP etc..

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Attachments

Attachment

Submitted filename: PONE-D-20-25223_reviewer comments.docx

Genome-wide association study and pathway analysis identify NTRK2 as a novel candidate gene for litter size in sheep

PONE-D-20-25223R1

Dear Dr. Esmaeilifard,

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,

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #2: All comments have been addressed

Reviewer #3: All comments have been addressed

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2. 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 #2: Yes

Reviewer #3: Yes

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

Reviewer #2: Yes

Reviewer #3: N/A

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4. 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 #2: Yes

Reviewer #3: Yes

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

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #2: Yes

Reviewer #3: Yes

**********

6. 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 #2: (No Response)

Reviewer #3: (No Response)

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7. PLOS authors have the option to publish the peer review history of their article (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: No

Reviewer #3: No