Core collection construction and genetic diversity analysis of tea plant (Camellia sinensis [L:] O. Kuntze) accessions in Huangshan city using SSR markers

Xu Ruan; Qiong Wu; Xiaoyu Jiao; Dandan Liu; Minghui Sun; Leigang Wang; Wenjie Wang

doi:10.1371/journal.pone.0322209

Peer Review History

Original SubmissionSeptember 22, 2024
22 Sep 2024 Author Response https://doi.org/10.1371/journal.pone.0322209.r001
20 Oct 2024 Decision Letter - Mehdi Rahimi, Editor PONE-D-24-42251Core collection construction and genetic diversity analysis of tea plant (Camellia sinensis [L.] O. Kuntze) accessions in Huangshan city using SSR markersPLOS ONE Dear Dr. Wang, 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 04 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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With Thanks [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: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: It is positive to work on such large number accession. However, the number of markers used in the study is low. Moreover, we have currently in the era of NGS that can yield thousands of SNP markers. SSR markers are mainly found in areas of non coding region. Thus, have less significance in comparison to SNP markers. The main purpose of constructing core collection is to effectively address the conflict between a large number of germplasm resources in gene banks and their effective preservation, to improve the utilization rate of excellent germplasm, to promote the exploration of excellent gene and molecular markers. Core collections have to contain the largest portion of variation for certain key traits so that they would be utilizes by the breeder. Making core collection using SSR marker have shortcomings in capturing the variations/diversity in key phenotypic traits (resulted from natural or artificial selection). I strongly suggest this work to be supported by phenotypic (field) data or use more robust marker (SNP). Reviewer #2: I have thoroughly read the article. This study presents a well-structured and comprehensive analysis of tea genetic diversity, particularly in the Anhui region. The introduction effectively highlights the challenges associated with the decline of local landraces and the importance of conservation efforts. The materials and methods section is detailed and thorough, providing enough information for replication, which enhances the study's reliability. The results offer valuable insights, particularly the high genetic diversity in She County and the division of population structure into two distinct groups, supported by multiple analytical approaches. The creation of a core collection retaining 82.62% of allele richness is commendable, though further explanation on core collection selection would strengthen the findings. ****** 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. Attachments Attachment Submitted filename: Review.docx https://doi.org/10.1371/journal.pone.0322209.r002
Revision 1
29 Oct 2024 Author Response Editor Comments: 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Response: We have thoroughly rechecked the manuscript and corrected it as per the PLOS template that is provided. 2. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. Response: The plant materials for the experiment were obtained with the help of the agricultural authorities of the counties and districts of Huangshan city. We communicated sufficiently with them in the early stages, so no relevant permit was required. 3. We note that Figure 1 in your submission contain [map/satellite] images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright. We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission:1. You may seek permission from the original copyright holder of Figure 1 to publish the content specifically under the CC BY 4.0 license. We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text: “I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.” Please upload the completed Content Permission Form or other proof of granted permissions as an ""Other"" file with your submission. In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].” 2. If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only. The following resources for replacing copyrighted map figures may be helpful: USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/, The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/, Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html, NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/, Landsat: http://landsat.visibleearth.nasa.gov/, USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/#, Natural Earth (public domain): http://www.naturalearthdata.com/. Response: As we have recently learned, inserting a map into a paper is a very complex task, including surveying department review, copyright licensing, and so on. Therefore, we removed Figure 1 and replaced it with S1 Table to illustrate the accessions sampling information, and the subsequent figure number changed accordingly. 4. Please include a caption for figure 2, 3, 4. Response: We have included captions for figure 2, 3, and 4 (as figure 1 has been removed, the picture numbers have been changed to figure 1, 2, 3), and we also revised the table number. In addition, we have improved figure 2 to match figure 4 (Line 177). Reviewer comments Reviewer #1: It is positive to work on such large number accession. However, the number of markers used in the study is low. Moreover, we have currently in the era of NGS that can yield thousands of SNP markers. SSR markers are mainly found in areas of non coding region. Thus, have less significance in comparison to SNP markers. The main purpose of constructing core collection is to effectively address the conflict between a large number of germplasm resources in gene banks and their effective preservation, to improve the utilization rate of excellent germplasm, to promote the exploration of excellent gene and molecular markers. Core collections have to contain the largest portion of variation for certain key traits so that they would be utilizes by the breeder. Making core collection using SSR marker have shortcomings in capturing the variations/diversity in key phenotypic traits (resulted from natural or artificial selection). I strongly suggest this work to be supported by phenotypic (field) data or use more robust marker (SNP). Response: Thank you so much for the comments. 1. In this experiment, capillary gel electrophoresis was used. The number of samples was large, and the experiment cost was high. Therefore, considering the reasons for saving money, we selected 10 pairs of primers. However, the 10 pairs of primers were selected layer by layer from 50 pairs of primers to ensure that they could amplify and reflect the genetic diversity of the sample. 2. At present, SNP molecular marker technology has many advantages, such as a high density of distribution, a high degree of association with functional genes, and strong genetic stability. However, this experiment is carried out based on the last SSR marker experiment, and has some relevance, so we continue to select SSR markers for the experiment. Thank you very much for your strong suggestion. Next, we will try to use SNP markers combined with field phenotypic data to conduct a study on Anhui Landraces Germplasm Tea Repository, expecting more influential results. Reviewer #2: I have thoroughly read the article. This study presents a well-structured and comprehensive analysis of tea genetic diversity, particularly in the Anhui region. The introduction effectively highlights the challenges associated with the decline of local landraces and the importance of conservation efforts. The materials and methods section is detailed and thorough, providing enough information for replication, which enhances the study's reliability. The results offer valuable insights, particularly the high genetic diversity in She County and the division of population structure into two distinct groups, supported by multiple analytical approaches. The creation of a core collection retaining 82.62% of allele richness is commendable, though further explanation on core collection selection would strengthen the findings. Response: Thank you so much for the comments. We are grateful for the reviewer’s kind comments, and your encouragement will make us do better in the future. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0322209.r003
18 Mar 2025 Decision Letter - Mehdi Rahimi, Editor Core collection construction and genetic diversity analysis of tea plant (Camellia sinensis [L.] O. Kuntze) accessions in Huangshan city using SSR markers PONE-D-24-42251R1 Dear Dr. Wang, 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, Mehdi Rahimi, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0322209.r004
Formally Accepted
Acceptance Letter - Mehdi Rahimi, Editor PONE-D-24-42251R1 PLOS ONE Dear Dr. Wang, 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 Associate Prof. Mehdi Rahimi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0322209.r005

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