PONE-D-19-29235

Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

PLOS ONE

Dear Dr. HABIMANA,

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Tzen-Yuh Chiang

Academic Editor

PLOS ONE

Journal Requirements:

2.  Thank you for including your ethics statement:  "Ethical clearance committee of the College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda.

Ref: 031/19/DRI September 2, 2019".

Please amend your current ethics statement to confirm that your named ethics committee specifically approved this study.

For additional information about PLOS ONE submissions requirements for ethics oversight of animal work, please refer to http://journals.plos.org/plosone/s/submission-guidelines#loc-animal-research  

Once you have amended this/these statement(s) in the Methods section of the manuscript, please add the same text to the “Ethics Statement” field of the submission form (via “Edit Submission”).

3.  In your Methods section, please provide additional details regarding the chicken used in your study and ensure you have described the source. For more information regarding PLOS' policy on materials sharing and reporting, see https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-materials.

4. In your Methods section, please provide additional location information of the sampling locations, including geographic coordinates for the data set if available.

5. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the sampling locations access and, if no permits were required, a brief statement explaining why.

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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: Partly

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

Reviewer #1: Yes

Reviewer #2: No

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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: Yes

Reviewer #2: 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: No

Reviewer #2: No

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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 reports on a study of genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers. The results revealed that the considerable genetic diversity in indigenous chicken in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement. However, the manuscript requires a minor revision before it can be considered further. Overall, I think that the manuscript will need attention in the following areas:

1. The writing of the introduction is poor. The introduction section only introduces the importance of indigenous chicken, and I suggest adding some information about the recent research of microsatellite markers in chickens.

2. In the materials and methods, the twelve exotic chickens (layers and broilers) as a reference data should have a detailed information.

3. Statistical analysis methods are not clearly presented, for example, p-value is mentioned without description of what kind of test. In addition, the p-value should be written consistently in the all manuscript.

4. Line 31: “chicken” should be “chickens”.

5. Line 243: “3,31” should be “3.13”.

6. Line 243: “drift-” should be “drift”.

7. Please carefully check the format of the manuscript, and make sure it fits the journal style.

Reviewer #2: The manuscript entitled “Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers” aimed to evaluate the genetic diversity of IC in Rwanda using microsatellite markers. This is a relevant study since the knowledge of animal genetic resources has become an important issue in order to avoid the genetic erosion. Also, the local chickens are an alternative to sustainable development of livestock. The article is interesting to the journal subject area. However, some points need to be clarified to improve the manuscript understanding are listed below:

1) Introduction: The authors should reformulate the introduction in order to improve the understanding.

For example, I could not understand the sentence: “More than 40% of households keep poultry out of which approximately 80% consists of indigenous chicken (IC).” (lines 50-51).

2) M&M:

Please, specify with more details sample the collection method and the ethical permission for collection. The sentences describing the genetic groups should contain only the breed´s name, number of samples used and also, the number of regions/flocks that samples were collected. I suggest that description of phenotypic traits in a separate table, for better understanding.

3) Discussion:

In general, the discussion is basically descriptive, improving the information of the results previously showed and comparing the results of this and other papers already published. There is no discussion in terms of phylogenetic relationships or evolution, neither about the genetic distance within the breeds studied, which weakens the impact of the paper. The manuscript subject is interesting, but needs to be improved.

The English written should be improved.

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Reviewer #1: No

Reviewer #2: No

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Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

PONE-D-19-29235R1

Dear Dr. HABIMANA,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

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With kind regards,

Tzen-Yuh Chiang

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

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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

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

Reviewer #2: Yes

**********

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

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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

**********

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: Most of the suggestions were addressed and now the paper is acceptable for publication. There are some spelling errors, which could be corrected in the proofs.

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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