Genetic analysis of body weight in wild populations of medaka fish from different latitudes

Tamiris I. Yassumoto; Mana Nakatsukasa; Atsushi J. Nagano; Masaki Yasugi; Takashi Yoshimura; Ai Shinomiya

doi:10.1371/journal.pone.0234803

Peer Review History

Original SubmissionJanuary 20, 2020
24 Mar 2020 Decision Letter - Christos Maravelias, Editor PONE-D-20-01808 Genetic analysis of body weight in wild populations of medaka fish from different latitudes PLOS ONE Dear Dr. Yoshimura, 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 May 08 2020 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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Thank you for stating in your Funding Statement: "This work was supported in part by a JSPS KAKENHI “Grant-in-Aid for Scientific Research (C)” (15K07163, 19K06785) to AS and “Grant-in-Aid for Specially Promoted Research” (26000013) and “Grant-in-Aid for Scientific Research (S)” (19H05643) and by the Human Frontier Science Program (RGP0030/2015) to TY. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." Please provide an amended statement that declares all the funding or sources of support (whether external or internal to your organization) received during this study, as detailed online in our guide for authors at http://journals.plos.org/plosone/s/submit-now. Please also include the statement “There was no additional external funding received for this study.” in your updated Funding Statement. Please include your amended Funding Statement 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: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 Reviewer #2: No ****** 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: 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: The articile is well-written, and the topic quite interesting with potential implications for aquaculture breeding programmes. No major modifications are required prior to publication. The only minor modification suggested is related to the introduction. In fact, while the authors recognized that their results could have implications for aquaculture, it seems not strictly related to their research the reference to human diseases and medicine science in the two paragraphs (lines 53-64). This part could be shortned or even omitted. Reviewer #2: I am unfortunately confused with the way the authors approached this subject. The content of the paper does not help much the readers to understand how the laboratory experiments and the downstream analyses were performed. More specifically: - in the abstract, the authors have at least a paragraph for obesity research. How is this relevant to the manuscript? Using medaka as a model for human health? We already know that most of these traits are polygenic. Therefore, the results of your study pointing on a single gene for growth might need more thorough reanalysis. - For the RAD approach: did you finally use both or a single enzyme? The number of SNPs you finally used (371) is much fewer than that people usually report for RAD or ddRAD approaches. You do not comment on this. - Mapping and QTL identification: with the above mentioned number of SNPs it is normal to have a very sparse linkage map with an average of only 15 markers per linkage group or chromosome. To my opinion, this number is very small to have a sound analysis. - On chromosome 4, there are only 11 markers mapped and the one showing a positive association with growth is located at the extreme; from the literature we know that sometimes it might be erroneous. - The 12 genes span a region, if I am not mistaken, of approximately 4Mb and the authors have invested a lot of effort and expenses to go for sequencing all these genes for the “source” populations (how many fish exactly?) and identify fixed differences. Very little is reported for the way you performed it; the primers, how many PCR reactions and different fragments per gene etc. ****** 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 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. 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Revision 1
9 May 2020 Author Response Response to Reviewer 1 The article is well-written, and the topic quite interesting with potential implications for aquaculture breeding programs. No major modifications are required prior to publication. The only minor modification suggested is related to the introduction. In fact, while the authors recognized that their results could have implications for aquaculture, it seems not strictly related to their research the reference to human diseases and medicine science in the two paragraphs (lines 53-64). This part could be shortened or even omitted. Response: We have shortened the two paragraphs as suggested (lines 50–57). Responses to Reviewer 2 Is the manuscript presented in an intelligible fashion and written in standard English? No Response: We used the service of an English proofreading company to improve clarity. I am unfortunately confused with the way the authors approached this subject. The content of the paper does not help much the readers to understand how the laboratory experiments and the downstream analyses were performed. Response: We have added more details to facilitate a better understanding of the experimental procedures and downstream analyses. 1.- in the abstract, the authors have at least a paragraph for obesity research. How is this relevant to the manuscript? Using medaka as a model for human health? We already know that most of these traits are polygenic. Therefore, the results of your study pointing on a single gene for growth might need more thorough reanalysis. Response: We have deleted the word “medical” from the abstract and have diminished the claim in the Introduction section. We have shortened and revised the two paragraphs that described obesity research (lines 50–57). Furthermore, we have added a description of the relevance and relationships among body weight, growth, and animal health, which affect aquaculture economics. 2.- For the RAD approach: did you finally use both or a single enzyme? The number of SNPs you finally used (371) is much fewer than that people usually report for RAD or ddRAD approaches. You do not comment on this. Response: We used both enzymes; we have added the relevant information in the Materials and Methods section (line 124). We initially obtained 5,019 RAD-sequencing markers that were genotyped in > 70% of all 155 individuals from the parental, F1, and F2 generations. In this experiment, F2 individuals originated from five parental Maizuru and Ginoza pairs. To obtain informative and reliable markers for QTL analysis, we selected markers with genotyping datasets in the parental, F1, and F2 generations with homozygous but different genotypes between all Maizuru and all Ginoza parents and a heterozygous genotype in F1. We also selected markers that were genotyped in > 80% of the F2 fish. After these selection processes, we reduced the number of markers to 371 for QTL analysis. 3. - Mapping and QTL identification: with the above mentioned number of SNPs it is normal to have a very sparse linkage map with an average of only 15 markers per linkage group or chromosome. To my opinion, this number is very small to have a sound analysis. Response: Indeed, more markers would increase the statistical power to detect more QTL and be useful for high-resolution mapping. However, we decided to use only reliable markers to minimize or avoid errors. 4. - On chromosome 4, there are only 11 markers mapped and the one showing a positive association with growth is located at the extreme; from the literature we know that sometimes it might be erroneous. Response: We designed and genotyped the new marker “ch4_0.68M,” which is located on the distal region of the medaka chromosome 4. The genetic distance between ch4_0.68M and the RAD 56900 marker supported the linkage of these two loci. Therefore, the position of 56900 and the QTL on chromosome 4 is reliable. Genotyping data on the new marker can be found in the supplemental S3 Table and in the revised manuscript (lines 209–211). 5. - The 12 genes span a region, if I am not mistaken, of approximately 4Mb and the authors have invested a lot of effort and expenses to go for sequencing all these genes for the “source” populations (how many fish exactly?) and identify fixed differences. Very little is reported for the way you performed it; the primers, how many PCR reactions and different fragments per gene etc. Response: We sequenced the whole genomes of four Maizuru and four Ginoza individuals using HiSeq 4000 (Illumina). Since these whole genome data will be published elsewhere (in preparation), the data cannot be submitted to a public database at this time. However, we showed all the SNP in the coding regions of the 12 genes in all Maizuru and Ginoza individuals included in the variant analyses in the supplemental S2 Table, lines 158–160. After reanalyzing the SNP of these Maizuru and Ginoza individuals, we added more data to Table 2. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0234803.r002
3 Jun 2020 Decision Letter - Christos Maravelias, Editor Genetic analysis of body weight in wild populations of medaka fish from different latitudes PONE-D-20-01808R1 Dear Dr. Yoshimura, 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 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, Christos Maravelias, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #2: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #2: the authors have adequately addressed the comments raised in the previous round of review and I feel that this manuscript is now acceptable for publication ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #2: No https://doi.org/10.1371/journal.pone.0234803.r003
Formally Accepted
5 Jun 2020 Acceptance Letter - Christos Maravelias, Editor PONE-D-20-01808R1 Genetic analysis of body weight in wild populations of medaka fish from different latitudes Dear Dr. Yoshimura: 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. Christos Maravelias Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0234803.r004

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