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Dear Dr Raymond,

Thank you very much for submitting your Research Article entitled 'Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock' to PLOS Genetics. Your manuscript was fully evaluated at the editorial level and by an independent peer reviewer. The reviewer appreciated the attention to an important topic but identified some aspects of the manuscript that should be improved.

We therefore ask you to modify the manuscript according to the review recommendations before we can consider your manuscript for acceptance. Your revisions should address the specific points made by each reviewer.

In addition we ask that you:

1) Provide a detailed list of your responses to the review comments and a description of the changes you have made in the manuscript.

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We hope to receive your revised manuscript within the next 30 days. If you anticipate any delay in its return, we would ask you to let us know the expected resubmission date by email to plosgenetics@plos.org.

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[LINK]

Please let us know if you have any questions while making these revisions.

Yours sincerely,

Jennie Pryce

Guest Editor

PLOS Genetics

Gregory Barsh

Editor-in-Chief

PLOS Genetics

I am happy to endorse the opinion of the reviewer of this manuscript. The paper requires only very minor editing before it is ready for publication. It's a very interesting read.

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: Minor points:

line 136 –“…. no significant (p<0.05) ….” The ‘p<0.05’ is redundant as the exact p value has been reported nearby. Please remove the (p<0.05).

line 386-390 – Please be specific about the coordinates of start and end of the gene. Assuming this includes beginning of 5’UTR till the end of 3’ UTR. If so, please include in the methods description.

Figure2&3 Please make sure the y axis range is the same for both cattle and human graphs.

Table S1. Is the density of markers in datasets used the same with regards the 10K window of association with lead SNPs? There is a chance that OR of orthologue genes on chips with different marker density and genome gaps, affect the total likelihood of associations with said phenotype. Adding the marker density of the 10Kbp associated window and its average per gene in both species could clarify this issue. If there is a significant density difference (could be assessed the same way by Fisher’s exact 2x1 table) per same orthologue gene, please include that in the result section lines 149-165. This point also lends itself to the gene size-stratification analysis that has already been done using Cochran-Mantel- Haenszel in the following section.

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Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Genetics data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

Reviewer #1: Yes

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Reviewer #1: Yes: Mazdak Salavati DVM, PhD, AFHEA

Dear Dr Raymond,

We are pleased to inform you that your manuscript entitled "Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock" has been editorially accepted for publication in PLOS Genetics. Congratulations!

Before your submission can be formally accepted and sent to production you will need to complete our formatting changes, which you will receive in a follow up email. Please be aware that it may take several days for you to receive this email; during this time no action is required by you. Please note: the accept date on your published article will reflect the date of this provisional accept, but your manuscript will not be scheduled for publication until the required changes have been made.

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If you have a press-related query, or would like to know about one way to make your underlying data available (as you will be aware, this is required for publication), please see the end of this email. If your institution or institutions have a press office, please notify them about your upcoming article at this point, to enable them to help maximise its impact. Inform journal staff as soon as possible if you are preparing a press release for your article and need a publication date.

Thank you again for supporting open-access publishing; we are looking forward to publishing your work in PLOS Genetics!

Yours sincerely,

Jennie Elizabeth Pryce

Guest Editor

PLOS Genetics

Gregory Barsh

Editor-in-Chief

PLOS Genetics

www.plosgenetics.org

Twitter: @PLOSGenetics

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Comments from the reviewers (if applicable):

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Data Deposition

If you have submitted a Research Article or Front Matter that has associated data that are not suitable for deposition in a subject-specific public repository (such as GenBank or ArrayExpress), one way to make that data available is to deposit it in the Dryad Digital Repository. As you may recall, we ask all authors to agree to make data available; this is one way to achieve that. A full list of recommended repositories can be found on our website.

The following link will take you to the Dryad record for your article, so you won't have to re‐enter its bibliographic information, and can upload your files directly: 

http://datadryad.org/submit?journalID=pgenetics&manu=PGENETICS-D-20-00564R1

More information about depositing data in Dryad is available at http://www.datadryad.org/depositing. If you experience any difficulties in submitting your data, please contact help@datadryad.org for support.

Additionally, please be aware that our data availability policy requires that all numerical data underlying display items are included with the submission, and you will need to provide this before we can formally accept your manuscript, if not already present.

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