Genetic diversity of Schima superba based on physiological traits and SSR markers

Jiazhe Liu; Wenhui Shen; Zhangqiang Tan; Yu Zhong

doi:10.1371/journal.pone.0344465

Peer Review History

Original SubmissionNovember 5, 2025
15 Dec 2025 Decision Letter - Vikas Sharma, Editor Dear Dr. Tan, 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. ============================== ACADEMIC EDITOR: Please see the additional comments below ============================== Please submit your revised manuscript by Jan 29 2026 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 include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. Additional Editor Comments: The amplified products were separated and analyzed using capillary electrophoresis on an ABI 3130xl Genetic Analyzer (Applied Biosystems, USA), and allele sizes were determined using GeneMarker software. Authors have given average value of Numbers of allele as more than 15 which is very high and interesting. In this regard, authors are requested to provide a clear and representative figure illustrating the differentiation of alleles, preferably in the form of a peak (electropherogram) profile. The conclusion is very general. The authors are requested to strengthen this section by specifically highlighting the populations or accessions identified as promising for further research, based on the parameters evaluated in the study. quality of figures is not good please check that. [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? Reviewer #1: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: 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.requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.--> Reviewer #1: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes ****** Reviewer #1: This is a well-structured and scientifically sound study that effectively integrates physiological trait assessment with SSR-based genetic analysis across a substantial number of Schima superba populations. The combination of phenotypic and molecular data strengthens the study’s relevance for conservation, breeding, and adaptive management. The work provides important insights into population variability, genetic clustering, and marker–trait associations, offering valuable resources for future improvement and management programs. However, before publication, the below-mentioned minor issues must be addressed: 1. Provide all abbreviations after keywords used in the manuscript. 2. Include a discussion and figure regarding SSR based dendrogram in this genetic diversity analysis section. 3. The dendrogram generated from SSR markers needs improvement in clarity and formatting. 4. Include bootstrap values, proper clustering labels, and scale on the dendrogram. 5. Provide a more detailed discussion interpreting the clustering pattern and its biological significance. 6. AMOVA results should be presented clearly, preferably with a figure. 7. Discuss how the STRUCTURE groups correlate with geographical origin or genetic diversity. 8. Revise the conclusion section to improve. Highlight key findings, practical implications, novelty, and future directions. 9. The reference list is comprehensive; ensure consistent formatting according to journal guidelines. ****** what does this mean?). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). 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 For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our Privacy Policy..--> Reviewer #1: Yes: Neha ChaudharyNeha ChaudharyNeha ChaudharyNeha Chaudhary ******** [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 ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. Attachments Attachment Submitted filename: Schimasuperba-PlosOne.docx https://doi.org/10.1371/journal.pone.0344465.r001
Revision 1
30 Jan 2026 Author Response To Editor: 1. Comment: The amplified products were separated and analyzed using capillary electrophoresis on an ABI 3130xl Genetic Analyzer (Applied Biosystems, USA), and allele sizes were determined using GeneMarker software. Authors have given average value of Numbers of allele as more than 15 which is very high and interesting. In this regard, authors are requested to provide a clear and representative figure illustrating the differentiation of alleles, preferably in the form of a peak (electropherogram) profile. Response: Thank you for this helpful comment. We agree that a representative capillary electropherogram would improve the clarity of allele differentiation. Therefore, we have provided the electropherogram peak profiles for all SSR loci and samples in the Supplementary Material (S1 File), which clearly illustrates allele separation and sizing based on the ABI 3130xl Genetic Analyzer and GeneMarker outputs. 2. Comment: The conclusion is very general. The authors are requested to strengthen this section by specifically highlighting the populations or accessions identified as promising for further research, based on the parameters evaluated in the study. Response: Thank you for the suggestion. We strengthened the Conclusion by explicitly identifying HTHL and HBB as the most promising provenances for further utilization based on combined physiological and SSR diversity parameters, and highlighting SS30 and SS32 as SSR loci with potential value for marker-assisted selection. (Revised Manuscript with Track Changes, lines 491–502) 3. Comment: quality of figures is not good please check that. Response: Thank you for pointing this out. We have carefully checked the quality of all figures and re-uploaded high-resolution versions in the revised manuscript. In particular, Fig. 4 has been replaced with a clearer, higher-quality image with improved readability. To Reviewer: 1. Comment: Provide all abbreviations after keywords used in the manuscript. Response: We appreciate the reviewer's advice. We have inserted a table of abbreviations after the abstract section to facilitate reading. This table lists all abbreviations used in the manuscript along with their full definitions. Additionally, we confirmed that all abbreviations are fully defined when first mentioned in the text. (Revised Manuscript with Track Changes, line 30) 2. Comment: Include a discussion and figure regarding SSR based dendrogram in this genetic diversity analysis section. Response: Thank you for the suggestion. We have revised the genetic diversity analysis section by including the dendrogram (Fig 1) and adding corresponding discussion to interpret the clustering pattern and its biological significance in the revised manuscript. (Revised Manuscript with Track Changes, lines 223–231) 3. Comment: The dendrogram generated from SSR markers needs improvement in clarity and formatting. Response: Thank you for the comment. We have carefully checked and improved the clarity and formatting of the SSR-based dendrogram and all other figures. The updated high-resolution dendrogram (Fig1 and Fig 4) has been replaced in the revised manuscript to ensure optimal readability.(Revised Manuscript with Track Changes, lines 371–378) 4. Comment: Include bootstrap values, proper clustering labels, and scale on the dendrogram. Response: Thank you for this suggestion. We have updated the SSR-based dendrogram (Fig. 4) by adding bootstrap values, appropriate clustering labels, and a scale bar to improve the interpretability and presentation quality in the revised manuscript. 5. Comment: Provide a more detailed discussion interpreting the clustering pattern and its biological significance. Response: Thank you for this valuable comment. We have expanded the Discussion section by adding a more detailed interpretation of the SSR-based clustering pattern and explaining its biological significance, including the potential implications for genetic differentiation, germplasm conservation, and future utilization of S. superba populations. (Revised Manuscript with Track Changes, lines 384–396) 6. Comment: AMOVA results should be presented clearly, preferably with a figure. Response: We appreciate the reviewer’s suggestion to visualize the AMOVA results. We carefully considered converting the data into a figure; however, we found that a graphical representation (e.g., pie charts or bar plots) tends to obscure the precise statistical values, particularly the variance components, which is critical for the interpretation of our findings. Therefore, we respectfully prefer to retain Table 7, as it allows readers to access the exact numerical results directly. 7. Comment: Discuss how the STRUCTURE groups correlate with geographical origin or genetic diversity. Response: Thank you for this important suggestion. We have revised the Discussion section to further explain how the STRUCTURE-defined genetic groups correlate with geographical origins and patterns of genetic diversity among the sampled provenances, and we highlighted the potential implications for germplasm conservation and utilization in the revised manuscript. (Revised Manuscript with Track Changes, lines 392–404) 8.Comment: Revise the conclusion section to improve. Highlight key findings, practical implications, novelty, and future directions. Response: Thank you for the suggestion. We have revised the Conclusion section to better highlight the key findings, practical implications, novelty, and future directions. The revised conclusion now summarizes the major genetic diversity and population structure results, emphasizes the most promising provenances for further utilization, proposes conservation and breeding implications, and outlines future validation and application of the associated SSR loci.(Revised Manuscript with Track Changes, lines 491–502) 9. Comment: The reference list is comprehensive; ensure consistent formatting according to journal guidelines. Response: We thank the reviewer for the positive comment and the reminder regarding formatting. We have carefully double-checked the entire reference list and reformatted it to ensure strict compliance with the PLOS One’s author guidelines. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0344465.r002
23 Feb 2026 Decision Letter - Vikas Sharma, Editor Genetic diversity of Schima superba based on physiological traits and SSR markers PONE-D-25-59450R1 Dear Dr. Tan, 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. 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Kind regards, Vikas Sharma, Ph.D Academic Editor PLOS One Additional Editor Comments (optional): Authors have addressed the raised questions satisfactorily. 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??> 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.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: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ****** Reviewer #1: (No Response) Reviewer #2: (No Response) ****** what does this mean?). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). 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 For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our Privacy Policy..--> Reviewer #1: No Reviewer #2: Yes: Gopalakrishna Murty KadambariGopalakrishna Murty KadambariGopalakrishna Murty KadambariGopalakrishna Murty Kadambari ******** Attachments Attachment Submitted filename: Plos One review .pdf https://doi.org/10.1371/journal.pone.0344465.r003
Formally Accepted
Acceptance Letter - Vikas Sharma, Editor PONE-D-25-59450R1 PLOS One Dear Dr. Tan, 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 You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. 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. Vikas Sharma Academic Editor PLOS One https://doi.org/10.1371/journal.pone.0344465.r004

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