Selective signatures in composite MONTANA TROPICAL beef cattle reveal potential genomic regions for tropical adaptation

Camila Alves dos Santos; Joanir Pereira Eler; Elisangela Chicaroni de Mattos Oliveira; Rafael Espigolan; Gabriela Giacomini; José Bento Sterman Ferraz; Tiago do Prado Paim

doi:10.1371/journal.pone.0301937

Peer Review History

Original SubmissionOctober 16, 2023
31 Oct 2023 Decision Letter - Tzen-Yuh Chiang, Editor PONE-D-23-33836Selective signatures in composite Montana tropical® beef cattle reveal potential genomic regions for tropical adaptationPLOS ONE Dear Dr. Santos, 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 Dec 15 2023 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. 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). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. 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Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. [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: Yes 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: No 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: No 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: Please consider carefully all comments below: - I want to thank you for placing figures and tables within the text! (and not at the end of it) - but please add line numbers!! - English: overall not too bad, but check some typos and especially the many poorly constructed sentences - Methods must be described more precisely, with less ambiguity and providing as much as possible the exact calculations that you used Background ---------- P10: changing climate scenario P10: composed of P11: arose P11: succeeded P11: do you have a reference/link for the registered Montana Tropical cattle? If it's a trademark/brand, please always capitalize it (including in the title) P11: composite breed P11: based on THE crossbreeding OF four P11: "has growth traits as 70% of their selection index" please rephrase --> growth traits account for 70% of their selection index P12: I guess you refer to pedigree errors (you can find something on this in the literature, e.g. Leroy et al. 2012 Animal Genetics) P12: history of population, not of pop structure P12: rephrase to --> The population frequency of ROH can be used as a tool to identify genomic regions under selection (i.e. signatures of selection) P12: Another method to detect signals of recent selection is the integrated haplotype score ... P12: are you sure that iHS only detects recent seelction? Methods ------- P27: "At the end, it was used 3215 genotypes (HD GGP 50K Neogen, genome reference URS UCD 1.2) for the further analyses presented here.": wrongly written (it was used?), please rewrite P27: before performing P28: signatures of selection P28: , according P28: what is the completeness value? How is it calculated? P28: breed proportion P28: what is the purpose of the ECG? P28: "standardized variance relationship matrix"? What is this? Usually, PCA is performed on the matrix of genotypes, or on the matrix of genetic relationships calculated from the genotypes (in this latter case, we talk more precisely of PCoA: principal coordinates analysis) P28: how did you choose the number 10? (I guess that you used the first 10 PCs ordered by decreasing eigenvalues or transformations thereof) P29: to determine K, besides the CV error you can look also at the number of iterations needed to converge (you can see an example and explanation in rice populations from Biscarini et al. 2016, Plos One) P30: density of ONE SNP per 100 kb P30:LROH, LAUTO: ROH and AUTO should be suffixes here P30: "The incidence of common ROH was transformed to generation class frequency by dividing by the number of animals from each generation class in the analysis." This is not clear, please explain better or add the calculations that you performed (preferred option) P30: normality test of what? Which test? P30: top 0.1% of observations in terms of what? Not clear P31: what was the cM --> Mb conversion rate that you used? 1cM = 1Mb? P31: GO analysis Reviewer #2: 1. Some information (for example, the description of calculated parameters, and used software) in the Results section should be moved to Materials and Methods. 2. The captions for Figure 2 are hardly readable. 3. The authors stated that FROH showed a positive correlation with inbreeding coefficient based on pedigree. I recommend providing these calculations in the Table (or as Supplementary Table). Was the correlation significant? 4. Figure 5 should be provided in a better quality. 5. The photograph of Montana Tropical cattle wil attract attention of potential readers, who are not familiar with this breed. ****** 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.0301937.r001
Revision 1
12 Dec 2023 Author Response We appreciate the reviewer’s considerations, and we address all questions. Reviewer #1: Please consider carefully all comments below: - I want to thank you for placing figures and tables within the text! (and not at the end of it) - but please add line numbers!! - English: overall not too bad, but check some typos and especially the many poorly constructed sentences - Methods must be described more precisely, with less ambiguity and providing as much as possible the exact calculations that you used We added line numbers and performed a carefully English check. Moreover, we revised the description of methods used. Background ---------- P10: changing climate scenario – done P10: composed of – done P11: arose - done P11: succeeded - done P11: do you have a reference/link for the registered Montana Tropical cattle? If it's a trademark/brand, please always capitalize it (including in the title) – we added a citation of the Association website in line 52 P11: composite breed – done P11: based on THE crossbreeding OF four – done. P11: "has growth traits as 70% of their selection index" please rephrase --> growth traits account for 70% of their selection index – done. P12: I guess you refer to pedigree errors (you can find something on this in the literature, e.g. Leroy et al. 2012 Animal Genetics) – done, It was a missing word before the errors. P12: history of population, not of pop structure – done. P12: rephrase to --> The population frequency of ROH can be used as a tool to identify genomic regions under selection (i.e. signatures of selection) - done P12: Another method to detect signals of recent selection is the integrated haplotype score ... – done P12: are you sure that iHS only detects recent seelction? According to the Voight et al. (2006), iHS method detect more recent signal of selection compared to other methods available. To avoid any misinterpretation, we removed “recent” from the statement. L:84 Voight, B. F., Kudaravalli, S., Wen, X., & Pritchard, J. K. (2006). A map of recent positive selection in the human genome. PLoS biology, 4(3), e72. Methods ------- P27: "At the end, it was used 3215 genotypes (HD GGP 50K Neogen, genome reference URS UCD 1.2) for the further analyses presented here.": wrongly written (it was used?), please rewrite – done P27: before performing – done P28: signatures of selection – done P28: , according – done P28: what is the completeness value? How is it calculated? The completeness value is an index of pedigree completeness, which is the harmonic mean of the pedigree completeness of the parents. The relevant parameter to identify individuals with insufficient pedigree information to estimate inbreeding, however, is the PCI. This is because inbreeding can be detected only if both maternal and paternal ancestries are known. The harmonic mean ensures that the less complete paternal pedigree is weighted more heavily, so the PCI equals zero when either parent is unknown. Inbreeding coefficients can be valid despite small PCIs if the most recent founders were indeed unrelated, e.g. because they were from other breeds. L:373 MacCluer JW, Boyce AJ, Dyke B, Weitkamp LR, Pfenning DW, Parsons CJ. Inbreeding and pedigree structure in Standardbred horses. J Hered. 1983; 1;74(6):394–9. doi:10.1093/oxfordjournals.jhered.a109824. P28: breed proportion – done P28: what is the purpose of the ECG? In the bovine mating system normally occurs the overlapping of generations. As example, a 7th generation dam can be mated with a 4th generation sire. The ECG formula accounts for this overlapping and provide a result that demonstrate the relationship of the animal with the initial crossbreeding for composite formation. In our case, we considered the animal born from a crossbreeding between founder’s breed that meet Montana requirements as a 1st generation. Therefore, we used ECG as indicator of how many generations each animal has inside the composite breed. P28: "standardized variance relationship matrix"? What is this? Usually, PCA is performed on the matrix of genotypes, or on the matrix of genetic relationships calculated from the genotypes (in this latter case, we talk more precisely of PCoA: principal coordinates analysis) We performed the PCA analysis using the genetic relationship matrix. This analysis as done using PLINK default conditions. PLINK manual (https://www.cog-genomics.org/plink/1.9/strat#pca) indicates that the command “--pca” calculate the principal components of the variance-standardized relationship matrix”. We only changed the number of retained PC according to the Kaiser’s rule. L: 385 P28: how did you choose the number 10? (I guess that you used the first 10 PCs ordered by decreasing eigenvalues or transformations thereof) We followed Kaiser’s rule, thus we retained the number of components whose eigenvalues were greater than 1. We added this information in the text. L:388 Kaiser, H. F. (1991). Coefficient alpha for a principal component and the Kaiser-Guttman rule. Psychological reports, 68(3), 855-858. P29: to determine K, besides the CV error you can look also at the number of iterations needed to converge (you can see an example and explanation in rice populations from Biscarini et al. 2016, Plos One) We appreciate your suggestion. We checked the number of iterations to convergence in each run, however we still not been able to determine the best K. The minimal number of iterations was 23.3 (K=2) and the maximum was 50.7 with K = 13, then the number of iterations decreased, resulting in 40.1 iterations to converge with K=20. As mentioned by Biscarini et al. 2016 and Alexander et al. 2019, we expected that the number of iterations needed rapidly increases when the data start to support poorly the tested number of clusters (K). P30: density of ONE SNP per 100 kb – done P30: LROH, LAUTO: ROH and AUTO should be suffixes here – done P30: "The incidence of common ROH was transformed to generation class frequency by dividing by the number of animals from each generation class in the analysis." This is not clear, please explain better or add the calculations that you performed (preferred option) L:429 The animals were grouped according to generation classes - all generations, ECG<2.5, 2.5<ECG<4.5 and ECG>4.5. The incidence of common ROH was calculated to each one of these groups. P30: normality test of what? Which test? Shapiro-wilk test of normality of the ROH results. L:430 P30: top 0.1% of observations in terms of what? Not clear We calculate the threshold as top 0.1% of ROH frequency based on a gaussian distribution. In termers of the ROH frequency, this can be observed in the Manhattan plot whose the orange line represents the threshold levels of top 0.1 %. P31: what was the cM --> Mb conversion rate that you used? 1cM = 1Mb? We calculated the average of the results obtained by Arias et al. (2009) and Weng et al. (2014) to obtain the conversion rate as stated in line 444. Both studies performed a detailed analysis of the bovine recombination map. P31: GO analysis - done Reviewer #2: 1.Some information (for example, the description of calculated parameters, and used software) in the Results section should be moved to Materials and Methods. We removed most of these descriptions, however some of them we believed that it is necessary to explain the basic of what we have done to make the results understandable, as the material and methods is presented at the end of the paper. 2. The captions for Figure 2 are hardly readable. – We remade the plot increasing the size of the captions to get a more readable figure. 3.The authors stated that FROH showed a positive correlation with inbreeding coefficient based on pedigree. I recommend providing these calculations in the Table (or as Supplementary Table). Was the correlation significant? Yes, it was significant. We added these results as Supplementary Table. 4. Figure 5 should be provided in a better quality. We tried our best to provide a better quality image. 5.The photograph of Montana Tropical cattle will attract attention of potential readers, who are not familiar with this breed – We added a link to Breeder’s Association website and a photo of the animals in the text. Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0301937.r002
24 Jan 2024 Decision Letter - Tzen-Yuh Chiang, Editor PONE-D-23-33836R1Selective signatures in composite Montana tropical® beef cattle reveal potential genomic regions for tropical adaptationPLOS ONE Dear Dr. Santos, 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 Mar 09 2024 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. 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). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Tzen-Yuh Chiang Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [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: All comments have been addressed Reviewer #2: All comments have been addressed ******** 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: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes 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 #1: No Reviewer #2: 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 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 #1: Abstract -------- - "Genomic regions related to tropical adaptability are OF paramount IMPORTANCE for animal breeding nowadays, especially ... " - "Moreover, the genomic architecture of these traits MAY BE very RELEVANT FOR breeding programs." Why do you think that the genomic architecture of these traits is relevant for breeding programmes: pelase explain (also in the text of the Abstract) - " ... were used to: i) characterize the population structure: ii) identify signatures of selection with complementary approaches, i.e. Integrated Haplotype Score (iHS) and Runs of Homozygosity (ROH); and iii) understand genes and traits related to selected region" Methods ------- - I appreciated your response to my comments on "completeness value" and "ECG": please add part of those replies to the text of the manuscript Reviewer #2: The authors addressed comment raised during review process. Figure 1 is missing in the revised manuscript. Please check it before the publication. All gene names should be in italics. Check it. ****** 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: 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.0301937.r003
Revision 2
26 Feb 2024 Author Response We appreciate the reviewer’s considerations, and we address all questions. Hereinafter, we indicate the changes made point by point in red. Review Comments to the Author Reviewer #1: Abstract -------- - "Genomic regions related to tropical adaptability are OF paramount IMPORTANCE for animal breeding nowadays, especially ... " – Done - "Moreover, the genomic architecture of these traits MAY BE very RELEVANT FOR breeding programs." Why do you think that the genomic architecture of these traits is relevant for breeding programmes: pelase explain (also in the text of the Abstract) To know the genetic architecture of this regions is important for geneticists and breeding programs so they can make more informed decisions when selecting animals with objectives related to tropical adaptation trough hybridization for example. We also complement the text in the abstract. - " ... were used to: i) characterize the population structure: ii) identify signatures of selection with complementary approaches, i.e. Integrated Haplotype Score (iHS) and Runs of Homozygosity (ROH); and iii) understand genes and traits related to selected region" – Done Methods ------- - I appreciated your response to my comments on "completeness value" and "ECG": please add part of those replies to the text of the manuscript -We added part of the explanations in the text, for completeness of the pedigree L374 – L377 and for ECG L383 – L389. Reviewer #2: The authors addressed comment raised during review process. Figure 1 is missing in the revised manuscript. Please check it before the publication. - We appreciate your comment, but in our last reviewed manuscript, we choose the option to attach the figures separately in the Editorial Manager page. All gene names should be in italics. Check it. - Done Attachments Attachment Submitted filename: Response_to_rewiers.docx https://doi.org/10.1371/journal.pone.0301937.r004
4 Mar 2024 Decision Letter - Tzen-Yuh Chiang, Editor PONE-D-23-33836R2Selective signatures in composite Montana tropical® beef cattle reveal potential genomic regions for tropical adaptationPLOS ONE Dear Dr. Santos, 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 18 2024 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. 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). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Tzen-Yuh Chiang Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [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: All comments have been addressed Reviewer #2: (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: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes 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 #1: No Reviewer #2: 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 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 #1: Please carefully check the English. There are some sentences which are poorly written: I provide a couple of examples below, but there are more. L392-393: "With the harmonic mean the less complete paternal pedigree is weighted more heavily, i.e. when both parents are unknow the PCI is equal 0" This sentence is not well written: try something like "The harmonic means place a higher weight on less complete paternal pedigrees, i.e. ... " L399-400: "In the bovine mating system normally occurs the overlapping of generations": again, not well written. Try "In cattle, normally animals mate across overlapping generations" Reviewer #2: (No Response) ****** 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: 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.0301937.r005
Revision 3
16 Mar 2024 Author Response We appreciate the reviewer's considerations. We have addressed the changes and also conducted an English review of the document. We have indicated the changes made point by point in red. Reviewer #1: Please carefully check the English. There are some sentences which are poorly written: I provide a couple of examples below, but there are more. L392-393: "With the harmonic mean the less complete paternal pedigree is weighted more heavily, i.e. when both parents are unknow the PCI is equal 0" This sentence is not well written: try something like "The harmonic means place a higher weight on less complete paternal pedigrees, i.e. ... " Done. We appreciate the suggestion. L399-400: "In the bovine mating system normally occurs the overlapping of generations": again, not well written. Try "In cattle, normally animals mate across overlapping generations" Done. Attachments Attachment Submitted filename: ResponsetoReviwersV3.docx https://doi.org/10.1371/journal.pone.0301937.r006
25 Mar 2024 Decision Letter - Tzen-Yuh Chiang, Editor Selective signatures in composite Montana tropical® beef cattle reveal potential genomic regions for tropical adaptation PONE-D-23-33836R3 Dear Dr. Santos, 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. 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, 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 #1: All comments have been addressed Reviewer #2: All comments have been addressed ******** 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: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes 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 #1: No Reviewer #2: 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 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 #1: I am satisfied with the answers to my previous comments. Please though, do check carefully the English in which your article is written, as this is important for the quality of your publication. Reviewer #2: (No Response) ****** 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: No Reviewer #2: No ******** https://doi.org/10.1371/journal.pone.0301937.r007

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