Genome-wide scan for selection signatures in Mexican Sardo Negro Zebu cattle

Victor Isaias Garduño López; Ricardo Martínez-Rocha; Rafael Núñez Domínguez; Rodolfo Ramírez Valverde; Joel Domínguez Viveros; Antonio Reyes Ceron; Jorge Hidalgo

doi:10.1371/journal.pone.0312453

Peer Review History

Original SubmissionMay 3, 2024
12 Aug 2024 Decision Letter - Amod Kumar, Editor PONE-D-24-17824Genome-wide scan for selection signatures in Mexican Sardo Negro Zebu cattlePLOS ONE Dear Dr. Martínez-Rocha, 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 Sep 26 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. 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(Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Manuscript_ PONE-D-24-17824 Dear editors, The manuscript: “Genome-wide scan for selection signatures in Mexican Sardo Negro zebu cattle” could provide an additional interesting piece of information on genomic selection effects in a regionally selected zebu cattle population. As this population had been selected since the fifties of the last century on pedigree basis, it provides a valuable resource for the family based inheritance on inbreeding. In the context of this report, the number of founder bulls and the proportional representation in the current population would be extremely interesting. Unfortunately, the authors did not include the information available for their sample in this report yet. Which effective family size is represented by each of the different Zebu founder genotypes in the pedigree data. On which criteria had the samples for this study been selected? How many different bull families are included and how do they represent progeny of the different founder bull genotypes of the SN in the sample selected for the SNP analysis? These data are prerequisite to evaluate the ROH and Fst data of this study. What are the phenotypic data changes for the mentioned selection criteria (morphology, body conformation, production) within the populations and compared to the reference populations / samples that had been investigated? What phenotype data for the live body weight are representative for the different samples? Are in the reference samples for the Zebu founder populations ROH for the same or different alleles in the respective regions? How many different SNPs in and between the Zebu-populations could be assigned for the ROH / Fst regions highlighted interesting on chromosomes 6, 8, 11 and 14? The manuscript should be revised including the requested information bevor considering re-review. Reviewer #2: 1. Kindly provide the rationale behind selection of only two methodologies (ROH and Fst) for this study. 2. The SN population was genotyped using Axiom platform, whereas others on the Illumina platform. How could you identify the common genetic markers for Fst method? 3. Could you explain that both SNP arrays (Axiom and Illumina) developed using the same genome assembly or not? 4. How could you decide the parameters for ROH detection? Please explain. 5. Have you identified the common genes between these two methods? 6. Kindly include nucleotide diversity method for selection signature identification, ans use DCMS methods for identification of common signals. ****** 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. 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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.0312453.r001
Revision 1
21 Aug 2024 Author Response We want to thank the two reviewers for their comments, which allowed us to improve the quality of the paper. The manuscript was modified according to the comments, and all changes will be found in a marked-up copy of our manuscript. Response to Reviewer 1 Comments Reviewer: 1 The manuscript: “Genome-wide scan for selection signatures in Mexican Sardo Negro zebu cattle” could provide an additional interesting piece of information on genomic selection effects in a regionally selected zebu cattle population. As this population had been selected since the fifties of the last century on pedigree basis, it provides a valuable resource for the family based inheritance on inbreeding. In the context of this report, the number of founder bulls and the proportional representation in the current population would be extremely interesting. Unfortunately, the authors did not include the information available for their sample in this report yet. Which effective family size is represented by each of the different Zebu founder genotypes in the pedigree data. Response 1. Thanks for the comments. The information about pedigree-based and genome-based (the same sample of the recent work) diversity already have been evaluated in previous works. This information can be found at doi.org/10.1590/0103-8478cr20210116, and doi.org/10.1016/j.livsci.2023.105267 respectively. On which criteria had the samples for this study been selected? How many different bull families are included and how do they represent progeny of the different founder bull genotypes of the SN in the sample selected for the SNP analysis? These data are prerequisite to evaluate the ROH and Fst data of this study. Response 2. Our criteria for selecting animals in the study was that the study samples were chosen randomly, and only included animals with no parent-offspring relationship. Only animals were considered if they were purebred based on pedigree and farmer interviews. What are the phenotypic data changes for the mentioned selection criteria (morphology, body conformation, production) within the populations and compared to the reference populations / samples that had been investigated? What phenotype data for the live body weight are representative for the different samples? Response 3. Thank you, we aggregated more information in the manuscript related to phenotypic information of the Sardo Negro breed. This information is already detailed in https://doi.org/10.1016/j.livsci.2020.104303. Are in the reference samples for the Zebu founder populations ROH for the same or different alleles in the respective regions? Response 4. We included ROH identified in the reference populations used in the supplementary data (S5-S8 Figs). How many different SNPs in and between the Zebu-populations could be assigned for the ROH / Fst regions highlighted interesting on chromosomes 6, 8, 11 and 14? Response 5. The information was already included in the supplementary data (S1-S2 Table). Reviewer #2: 1. Kindly provide the rationale behind selection of only two methodologies (ROH and Fst) for this study Response 1. Thanks for your feedback. We aimed to select at least one statistic within a population and one statistic across populations to visually represent signs of selection in these two ways. However, we also considered the sixth point, and we have already aggregated DCMS methods. 2. The SN population was genotyped using Axiom platform, whereas others on the Illumina platform. How could you identify the common genetic markers for Fst method? Response 2. Thank you. We didn’t clarify this point previously. We identified the common genetic markers mapping SNPs to a common assembly using SNPchiMp database (doi:10.1186/1471-2164-15-123). 3. Could you explain that both SNP arrays (Axiom and Illumina) developed using the same genome assembly or not? Axiom bovine SNP array is aligned to the Bos taurus genome assembly ARS-UCD1.2, and Illumina was developed using UMD3.1 assembly. However, we used SNPchiMp to map the SNPs from both arrays to a common reference genome. We carefully check the harmonization of alleles ensuring that the alleles are consistent between arrays. If the SNPs had different representations of alleles or different strand orientations, we used --flip and –flip-scan functions of PLINK. 4. How could you decide the parameters for ROH detection? Please explain. We decide on the minimum length of ROH of 1MB and the minimum number of 20 consecutive homozygous SNPs because, with a lower SNP density, we might detect shorter ROHs. Is known that shorter ROHs are related to ancient events in the selection signatures. We opted to set the maximum gap at 1 Mb since it's customary to permit a maximum gap of 1-2 megabases (Mb) between SNPs as a starting point. This parameter specifies the largest acceptable distance between consecutive SNPs for them to be categorized as part of the same ROH The maximum number of missing allowed genotypes was set to 1 because it results in 5% of Missing Data; a common threshold is to allow up to 5% of missing genotypes within a given ROH. 5. Have you identified the common genes between these two methods? After considering the sixth point, the common genes between the four methods is only on BTA6. That region involves the CCSER1, MMRN1, SNCA, FAM13A, HERC3, NAP1L5, PIGY, PYURF, HERC5, PPM1K, ABCG2, PKD2, SPP1, IBSP, MEPE, TRNAA-CGC, LAP3, MED28, FAM184B, NCAPG, DCAF16, LCORL, SLIT2, PACRGL, and KCNIP4 genes. 6. Kindly include nucleotide diversity method for selection signature identification, and use DCMS methods for identification of common signals. Done Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0312453.r002
8 Oct 2024 Decision Letter - Amod Kumar, Editor Genome-wide scan for selection signatures in Mexican Sardo Negro Zebu cattle PONE-D-24-17824R1 Dear Dr. Martinez-Rocha, 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, Amod Kumar, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Congratulations!!! Authors have addressed all the queries raised by the reviewers. Best Regards Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 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: Yes Reviewer #2: (No Response) ****** 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 As suggested by reviewer 1, please included references in the manuscript. Reviewer #1: Please add the two references regarding the pedigree data of the Mexican Sardo Negro Zebu cattle to this manuscript to allow forin depth information of the readers. 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: Yes: Sabine Klein, Friedrich-Loeffler-Institut, Institute of Farm Animal Genetics Mariensee Reviewer #2: No ******** https://doi.org/10.1371/journal.pone.0312453.r003
Formally Accepted
31 Oct 2024 Acceptance Letter - Amod Kumar, Editor PONE-D-24-17824R1 PLOS ONE Dear Dr. Martínez-Rocha, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, 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 customercare@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. Amod Kumar Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0312453.r004

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