Bull efficiency using dairy genetic traits

Christine E. Whitt; Loren W. Tauer; Heather Huson

doi:10.1371/journal.pone.0223436

Peer Review History

Original SubmissionJune 28, 2019
11 Aug 2019 Decision Letter - Juan J Loor, Editor PONE-D-19-18307 Efficiency of Dairy Genetic Traits PLOS ONE Dear Mrs. Whitt, 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. We would appreciate receiving your revised manuscript by Sep 25 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. 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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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No ****** 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 ****** 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 ****** 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: 1. Manuscript is technically sound and data supports the conclusions. I answered 'partly' to this question because greater rigor would have looked at the effects over time. The current study is one time point and additional time points of bull data could have strengthen the generality of conclusions. Also,a linear combination of bulls could be appropriate if one evaluated a herd of cows. The Free Disposal Hull approach would not be needed for bull selection in a herd. 2. My criticism here is not of the statistical analysis, but of the reporting of the results. Four decimals is more than can be supported based on the standard deviations or sample size of approximately 400 bulls. 3. Data is available. 4. Most of the manuscript is presented well. A few sentences are missing words. Search for 'form' and replace with 'farm' in at least one place. 'Since' should often be replaced with 'Because'. Since implies time, which is not how it was used in most places. In many of the sentences with 'there are or there were', a revision of the sentences would improve readability. 5. If my name will be associated with this review, I will advertise that I analyzed a similar data set with linear programing a few decades ago. (Shanks, R. D. and A. E. Freeman. 1979. Choosing progeny-tested Holstein sires that meet genetic goals at minimum semen costs. J. Dairy Sci. 62:1429-1434.) The market does a good job of arriving at a reasonable semen price for most bulls. When discrepancies occur, often some information not included in the data set is responsible for the outliers. ****** 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: Yes: Roger D. Shanks [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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0223436.r001
Revision 1
19 Aug 2019 Author Response 1. Manuscript is technically sound and data supports the conclusions. I answered 'partly' to this question because greater rigor would have looked at the effects over time. The current study is one time point and additional time points of bull data could have strengthen the generality of conclusions. Also, a linear combination of bulls could be appropriate if one evaluated a herd of cows. The Free Disposal Hull approach would not be needed for bull selection in a herd. We agree that analysis over time with updated bull lists would be an interesting application. In our summary, we state that analysis with an updated bull list could result in current bulls experiencing a decrease in calculated efficiencies as new bulls are added to the list. That should be expected with genetic progress. We leave that analysis for another paper. Models that investigate bull selection given the current traits in the herd with the goal of increasing certain traits could utilize linear programming to maximize the value of the herd. Our analysis simple looks at the traits of a single bull with a comparison to every other bull, thus the use of the Free Disposal Hull technique. 2. My criticism here is not of the statistical analysis, but of the reporting of the results. Four decimals is more than can be supported based on the standard deviations or sample size of approximately 400 bulls. We have made the recommended change. Now we are reporting our results with only two decimals instead of four. 3. Data is available. The data is publicly available like you mentioned 4. Most of the manuscript is presented well. A few sentences are missing words. Search for 'form' and replace with 'farm' in at least one place. 'Since' should often be replaced with 'Because'. Since implies time, which is not how it was used in most places. In many of the sentences with 'there are or there were', a revision of the sentences would improve readability. We searched the manuscript and corrected the words, ‘form to ‘farm’, and changed ‘since to because’ as you recommend and did a through read of the paper and made a few other editing changes to improve the readability of the manuscript. 5. If my name will be associated with this review, I will advertise that I analyzed a similar data set with linear programing a few decades ago. (Shanks, R. D. and A. E. Freeman. 1979. Choosing progeny-tested Holstein sires that meet genetic goals at minimum semen costs. J. Dairy Sci. 62:1429-1434.) The market does a good job of arriving at a reasonable semen price for most bulls. When discrepancies occur, often some information not included in the data set is responsible for the outliers. Thank you for your suggestion. We added a sentence in the text citing the paper. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0223436.r002
9 Sep 2019 Decision Letter - Juan J Loor, Editor PONE-D-19-18307R1 Production Efficiency of Dairy Genetic Traits PLOS ONE Dear Mrs. Whitt, 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. We would appreciate receiving your revised manuscript by Oct 24 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Juan J Loor Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] 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 #1: (No Response) ******** 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 #1: Partly ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 #1: Yes ****** 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 #1: 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 #1: Christine, Loren and Heather, Thank you for incorporating my previous comments. It was not necessary to cite my previous paper on a related topic, but your gesture was appreciated. On the revision, I was surprised by the title change. Production efficiency is not quite right for me. Within the text, you do mention bull efficiency. When I first saw the revision, I jotted down bull use efficiency. I also tried economic efficiency in the title. Because you do use the phrase in the text, please consider "Bull efficiency of dairy genetic traits" for your title. A few line specific comments follow (lines are from tracked changes version): line 69, lines 106 to 107, lines 172 to 173, line 359: How many times does Free Disposal Hull need to be defined as FDH? Unfortunately, I did not look up a PLOS ONE policy for abbreviations. Also, can an abbreviation start a sentence as in line 69? line 72: Consider replacing "efficiency" with "efficient" in this context. line 116: "predicted transmitting abilities (PTA) line 117 to 118: "genomic predicted transmitting abilities (GPTA) line 196: Is n the number of traits in this application? line 301 to 303: Profit efficiency looks to be slightly to the right of revenue efficiency distribution to me on Figure 4. Are labels correct? line 348: Delete extra "to need". lines 376 to 380: Interesting interpretation. I am not suggesting any changes, but consider that value of traits may not be solely additive with future analyses. Figure 1: If possible include a few more definitions for this figure. What is P1/P2? Is line AF perpendicular to P1/P2 line? From figure 2, I surmise that line AF should go through zero, zero and not necessarily be perpendicular. My guess is that my questions are pretty basic for the method, but I did not take the time to find the FDH reference. Interesting paper. Thanks for taking a look at this topic. Have a great day. Roger Shanks ****** 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 #1: Yes: Roger D. Shanks [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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0223436.r003
Revision 2
17 Sep 2019 Author Response You suggest the title, “Bull Efficiency of Dairy Genetic Traits” which is better than our title. However, we think that placing the word “bull” before the word “genetic” rather than “efficiency” is more correct and informative. Thus our new title is “Efficiency of Dairy Bull Genetic Traits” line 69, lines 106 to 107, lines 172 to 173, line 359: How many times does Free Disposal Hull need to be defined as FDH? Unfortunately, I did not look up a PLOS ONE policy for abbreviations. Also, can an abbreviation start a sentence as in line 69? I looked up the PLOS ONE policy for abbreviations and it states “Define abbreviations upon first appearance in the text.” I have edited the manuscript to fit the correct guidelines. line 72: Consider replacing "efficiency" with "efficient" in this context. Replacement was made. line 116: "predicted transmitting abilities (PTA) Correction made. line 117 to 118: "genomic predicted transmitting abilities (GPTA) Corrections made. line 196: Is n the number of traits in this application? I added the wording, “where i=1,…, n is the number of traits:” before equation one to address this comment. line 301 to 303: Profit efficiency looks to be slightly to the right of revenue efficiency distribution to me on Figure 4. Are labels correct? The labels are correct and I fixed my mistype from “left” to “right”. Thank you for finding this error. line 348: Delete extra "to need". Deleted as suggested. lines 376 to 380: Interesting interpretation. I am not suggesting any changes, but consider that value of traits may not be solely additive with future analyses. I included an extra sentence stating your suggestion. Figure 1: If possible include a few more definitions for this figure. What is P1/P2? Is line AF perpendicular to P1/P2 line? From figure 2, I surmise that line AF should go through zero, zero and not necessarily be perpendicular. My guess is that my questions are pretty basic for the method, but I did not take the time to find the FDH reference. I included an extra sentence at lines 181-182 where to elaborate on figure 1. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0223436.r004
23 Sep 2019 Decision Letter - Juan J Loor, Editor Bull Efficiency Using Dairy Genetic Traits PONE-D-19-18307R2 Dear Dr. Whitt, 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. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, Juan J Loor Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0223436.r005
Formally Accepted
28 Oct 2019 Acceptance Letter - Juan J Loor, Editor PONE-D-19-18307R2 Bull Efficiency Using Dairy Genetic Traits Dear Dr. Whitt: I am 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 notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Juan J Loor Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0223436.r006

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