Phenotypic ranking experiments in identifying breeding objective traits of smallholder farmers in northwestern Ethiopia

Oumer Sheriff; Kefyalew Alemayehu; Aynalem Haile

doi:10.1371/journal.pone.0248779

Peer Review History

Original SubmissionDecember 10, 2020
25 Feb 2021 Decision Letter - Dawit Tesfaye, Editor PONE-D-20-38878 Phenotypic ranking experiments in identifying breeding objective traits of smallholder farmers in northwestern Ethiopia PLOS ONE Dear Dr. Sheriff, 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 Apr 11 2021 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. 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Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please ensure that your ethics statement is included in your manuscript, as the ethics statement entered into the online submission form will not be published alongside your manuscript. 5.Thank you for stating the following in the Funding Section of your manuscript: "The financial support for this study was provided by Biotechnology Research Institute (BRI) of Bahir Dar University, Ethiopia." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: "The authors received no specific funding for this research " Please include your amended statements within your cover letter; we will change the online submission form on your behalf. [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: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes ****** 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 ****** 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: Yes ****** 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: Umer et al. investigated goat phenotype ranking schemes for identification breeding objective traits of smallholder farmers in Northwestern Ethiopia. For this, the authors looked into Own-flock ranking scheme in which the farmers ranked does based on age, number of kidding, twinning ability, number of kids born per kidding and number of kids weaned and Group-animal ranking scheme in which breeding does and bucks were randomly selected and phenotype information was gathered and then the farmers were asked to rank the animals with and without phenotype information. Accordingly, the author indicated that body size, mothering ability, twinning rate, kidding interval and temperament are prioritized traits while in group-animal ranking scheme, traits including coat color, body size and body conformation were found to be the priority of farmers. All in all, this study is relevant and a step forward to identify relevant to establish goat breeding objectives that could fit to smallholder farmers in Northwestern Ethiopia. Nevertheless, before this article is accepted for publication, the following issues should be addressed. 1. Statistical testing in the majority of results provided in tables are missing 2. Tables 3, 4 and 5 are all described as Table 3-- please correct! 3. In table 2 - Please indicate possible significant differences between 1 and 2, 1 and 3 and /or 2 and 3 rakings using letters or any convenient symbols. 3. Please describe if there is any goat trait preference differences between the Oromo and Arab smallholder goat farmers. 4. In the conclusion part of this manuscript, the authors indicated that in the own-flock ranking s scheme farmers were interested in productive, reproductive and behavioral traits whereas in the group-animal ranking scheme, farmers were interested in coat color, body size and body. conformation. It will be interesting if the authors could address this controversy. Reviewer #2: Authors carried out own-flock and group-animal ranking experiments on two goat breeds, the Arab and Oromo breeds, in northwestern Ethiopia. More than 15 productive, reproductive and behavioral traits were used to rank the animals according to the choice of the farmers. This is a very great effort in designing a breeding program at a community level. The paper is written very well. Authors need to state the result section as “result and discussion”. Moreover, supplementing a representative picture of the goats from each breed, with respect to the traits mentioned in Table 2 would enhance the manuscript. ****** 6. 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 #1: No Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0248779.r001
Revision 1
4 Mar 2021 Author Response Responses to the Editor’s and Reviewers' Comments Dear editor and reviewers, we would like to thank you for giving us a chance to revise our manuscript. We are also very thankful for your thoughtful and thorough review of our manuscript. The comments are encouraging and you appear to share our judgment that the study and its results are important. Each comment has been carefully considered point by point and responded accordingly. Please see below, in blue, our response to your comments. All line numbers given in the authors’ response refer to the revised manuscript and the revision can be seen as track changes in the manuscript. RESPONSE TO EDITOR’S COMMENTS 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Authors’ response: Dear Editor, thank you so much for providing us the link. We have read it carefully and revised our manuscript according to the guideline. 2. We suggest you thoroughly copyedit your manuscript for language usage, spelling, and grammar. If you do not know anyone who can help you do this, you may wish to consider employing a professional scientific editing service. Authors’ response: Dear, thanks for your concern. Indeed, we have tried all our best to improve the language usage, spelling, and grammar and make the manuscript clear to the readers. 3. We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For more information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. In your revised cover letter, please address the following prompts: a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. We will update your Data Availability statement on your behalf to reflect the information you provide. Authors’ response: Dear Editor, thanks for your question. All relevant data are within the manuscript and its supporting information files. 4. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please ensure that your ethics statement is included in your manuscript, as the ethics statement entered into the online submission form will not be published alongside your manuscript. Authors’ response: We thank you for your comment; we moved the ethics statement to the methods section of our manuscript. 5. Thank you for stating the following in the Funding Section of your manuscript: "The financial support for this study was provided by Biotechnology Research Institute (BRI) of Bahir Dar University, Ethiopia." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: "The authors received no specific funding for this research". Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Authors’ response: Dear Editor, thanks for the comment. We removed the funding statement that appeared in the acknowledgement section of our manuscript. On the other hand, we included our amended statements within our cover letter. RESPONSE TO REVIEWERS’ COMMENTS Reviewer’s comment: Reviewer #1: Umer et al. investigated goat phenotype ranking schemes for identification breeding objective traits of smallholder farmers in Northwestern Ethiopia. For this, the authors looked into Own-flock ranking scheme in which the farmers ranked does based on age, number of kidding, twinning ability, number of kids born per kidding and number of kids weaned and Group-animal ranking scheme in which breeding does and bucks were randomly selected and phenotype information was gathered and then the farmers were asked to rank the animals with and without phenotype information. Accordingly, the author indicated that body size, mothering ability, twinning rate, kidding interval and temperament are prioritized traits while in group-animal ranking scheme, traits including coat color, body size and body conformation were found to be the priority of farmers. All in all, this study is relevant and a step forward to identify relevant to establish goat breeding objectives that could fit to smallholder farmers in Northwestern Ethiopia. Nevertheless, before this article is accepted for publication, the following issues should be addressed. 1. Statistical testing in the majority of results provided in tables are missing Authors’ Response: Dear reviewer, thank you for your comment. We believe that statistical testing is needed and we included it in Table 2. The rest of the results in Tables 1, 3, 4 and 5 are qualitative data which, we believe, do not need any significance tests. 2. Tables 3, 4 and 5 are all described as Table 3-- please correct! Authors’ Response: We appreciate your comment. Sorry for the mistake we made. Now, we correct it and you may find the correction in the revised manuscript. 3. In table 2 - Please indicate possible significant differences between 1 and 2, 1 and 3 and /or 2 and 3 rakings using letters or any convenient symbols. Authors’ Response: Dear reviewer, we appreciate you. Based on your suggestion, we indicate the possible significant differences between the 1st and 2nd, 1st and 3rd, 1st and inferior, 2nd and 3rd, 2nd and inferior, and 3rd and inferior rakings using letters. 4. Please describe if there is any goat trait preference differences between the Oromo and Arab smallholder goat farmers. Authors’ Response: Dear reviewer, thank you so much for your comment. The goat trait preference difference between the Arab and Oromo goat keepers is not the objective of the present study. This issue is addressed in a previous study conducted by the same authors of the current study in 2019. For more information, you can refer an article entitled with “Production systems and breeding practices of Arab and Oromo goat keepers in northwestern Ethiopia: implications for community-based breeding programs” TROPICAL ANIMAL HEALTH AND PRODUCTION. 52, 1467–1478. 5. In the conclusion part of this manuscript, the authors indicated that in the own-flock ranking scheme farmers were interested in productive, reproductive and behavioral traits whereas in the group-animal ranking scheme, farmers were interested in coat color, body size and body conformation. It will be interesting if the authors could address this controversy. Authors’ Response: Yes. In the conclusion part of our manuscript, we indicated that goat keepers in the own-flock ranking experiment were interested in productive, reproductive and behavioral traits whereas in the group-animal ranking experiment, they were interested in coat color, body size and body conformation. This could be due to the reason that keepers in the own-flock ranking experiment know the animals very well since they are the owners of the goats whereas in the group-animal ranking experiment, goat keepers rank animals brought from another area, hence they did not know them. Thus, this controversy was happened due to the knowledge of the goat keepers that they had on the ranked animals (ranking either their own goats or unknown goats). This issue is addressed well in the methods section of our manuscript (i.e., own-flock ranking experiment and group animal ranking experiment). As a result of this, we believe that it would be redundant if we address this same issue in the conclusion part. Reviewer #2: Authors carried out own-flock and group-animal ranking experiments on two goat breeds, the Arab and Oromo breeds, in northwestern Ethiopia. More than 15 productive, reproductive and behavioral traits were used to rank the animals according to the choice of the farmers. This is a very great effort in designing a breeding program at a community level. The paper is written very well. Authors need to state the result section as “result and discussion”. Moreover, supplementing a representative picture of the goats from each breed, with respect to the traits mentioned in Table 2 would enhance the manuscript. Authors’ Response: We are grateful for your comment. Now, we state the result section as “Result and discussion”. Furthermore, we depicted the pictures of the goat populations in Figure 1. Best Regards, Oumer Sheriff, on behalf of the authors Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0248779.r002
5 Mar 2021 Decision Letter - Dawit Tesfaye, Editor Phenotypic ranking experiments in identifying breeding objective traits of smallholder farmers in northwestern Ethiopia PONE-D-20-38878R1 Dear Dr. Sheriff, 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 and comments raised by the academic editor. . 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. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Dawit Tesfaye Academic Editor PLOS ONE Additional Editor Comments (optional): The figure legend for figure 1 need to be revised as follows. Figure 1. Representative pictures of adult Arab doe (A), young Arab buck (B), Adult Oromo doe (C) and Adult Oromo buck (D) included in the study. Some of the pictures seem to be stretched to the left or right. Please correct it according to the instruction for authors. Reviewers' comments: https://doi.org/10.1371/journal.pone.0248779.r003
Formally Accepted
10 Mar 2021 Acceptance Letter - Dawit Tesfaye, Editor PONE-D-20-38878R1 Phenotypic ranking experiments in identifying breeding objective traits of smallholder farmers in northwestern Ethiopia Dear Dr. Sheriff: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Dawit Tesfaye Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0248779.r004

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