Exploring the genetic diversity and population structure of aerial yams (Dioscorea bulbifera L.) DArT-seq and agronomic traits

Eunice Ekaette; Emeka Nwofia; Peter Okocha; Ikenna Nnnabue; Kenneth Eluwa; Jude Obidiegwu; Paterne A. Agre

doi:10.1371/journal.pone.0306631

Peer Review History

Original SubmissionSeptember 13, 2023
5 Nov 2023 Decision Letter - Timothy Omara, Editor PONE-D-23-28562Exploring the Genetic Diversity and Population Structure of Aerial yams (Dioscorea bulbifera L.) DArT-seq and agronomic traits.PLOS ONE Dear Dr. Agre, 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 20 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. 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, Timothy Omara, PhD Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 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 2. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: https://pureadmin.qub.ac.uk/ws/files/470638768/world-04-00020.pdf https://www.mdpi.com/2037-0164/14/1/25/html https://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers18-12/010074472.pdf In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed. 3. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. [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: Yes 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: Introduction Language structure issues in “…popular staples in West Africa [3] while serving as important source of dietary calories thus contributing on average, more than 200 Kilocalories per person per day to ….“ the sentence could be better written as “….popular staples in West Africa [3], serving an important source of dietary calories with contribution of 200 Kilocalories on average per person per day to o…” Line 5 says “… diverse agro-ecologies of the country …”, What country? Nigeria? If West Africa please refer to it as you have not mentioned any country at this point. Methods The authors have not stated how long (days) the accessions were planted before harvesting The authors made mention of agronomic practices regularly applied to the crop, however, agronomic practices are too vague and the author should state these agronomic practices in supplementary if it will disrupt the section structure For the DNA extraction, the authors stated they use young leaves, how are the young leaves selected/identified? (i.e. was it the youngest leaves from the yam or the youngest leaves from a collar, trifoliate, etc.). This is vital to grade uniformity of the harvest tissues because if younger leaves were selected randomly in the yam from accessions to accession, then the data's reproducibility is questioned. Results In Table 3, what does the a, b, c, d … represent? does it mean how statistically different the traits are? Indicate this in the table legend. Figure 1 needs better resolution, the labels are not clearly visible Figure 2 legend needs to be detailed better The heat map section should be given careful attention, the authors need to rearrange the letter in a clear way and specify the most significant. The heat map figures need better resolution as the accession could hardly be seen. The authors may only plot the map of the top most significant variation and include the others/this as supplementary material. Discussion The discussion therein contains a detailed explanation of the results and the authors clearly identified the gap, however, the discussion section needs to be well-arranged with enough paragraphs separating different objectives and interrelating results. As it is, the discussion is vague, and if possible should have subheadings. Conclusion The conclusion is too minimal and a more robust conclusion highlighting the significant high impact of this work needs to be established. The last sentence for instance can be improved upon. Reviewer #2: The manuscript “Exploring the Genetic Diversity and Population Structure of Aerial yams (Dioscorea bulbifera L.) DArT-seq and agronomic traits” presents insightful knowledge on the diversity among the bilbifera species of yam. To make the manuscript more presentable the following comments can be taken into consideration: 1. Abstract: Very simplified but can be improved 2. Introduction: a. The introduction needs some more literature that will cut across some findings and the importance of the use of SNPs markers for diversity studies. b. The production and distribution of the yam specie used for the study should be emphasized with facts. c. Check the formatting. d. Is there any study on D. bulbifera? Some highlights can be in the introduction. e. Other minor typo errors have been indicated in the attachment. 3. Methodology: a. Kindly provide some information on the nature of the soil for the experimental site. b. Table 1: Kindly indicate the accessions that were samples from IITA and NRCRI in the table. c. Kindly indicate the number of replications used for this design. d. “A total of 7 qualitative morphological descriptors for yam was used to profile the 94 accessions” This statement can begin for the Phenotyping session. From the statement here, you indicated seven but the parameters in the table are 8. Please clarify and make the necessary adjustments. This may affect the analysis, and this must be clear in the results. e. I suggest tuber parameters should be added to give a very clear diversity in the accessions used. f. Pictures that show clear morphological variation can also be very good to show the difference observed. g. Table 2: Indicate the period in which the parameters were taken. 4. Results: a. Table 3: This table does not reflect the number of parameters in Table 2. Please clarify and make the necessary adjustments. b. In the abstract author indicated AMOVA results but that is not reflected in the results. I suggest the AMOVA results are indicated and explained. c. Figure 3. Explanations about this figure were not stated in the results. It is important to update that. d. Figures 7 and 8 must be together since they communicate the same information. e. Please note this well: To improve on the results and analysis. Further analysis can be done by combining the phenotypic and genotypic information in one analysis “dendrogram” to show the relationship and to support the information acquired for both data. That will be very good and explanatory enough. As it stands now, the phenotypic and genotypic information are separated and hanging but it will be good to blend the information from both sides together to make the study rich. 5. Discussion: a. The authors have elaborated on the required literature, however there is no discussion on the implication of the morphological observations with the marker’s information identified or vice versa. b. I suggest the authors explain more about that after combining the analysis of the results as indicated in the results session. ****** 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: PONE-D-23-28562 (1).pdf https://doi.org/10.1371/journal.pone.0306631.r001
Revision 1
23 Apr 2024 Author Response Journal Requirements: When submitting your revision, we need you to address these additional requirements. Query 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 appreciate the feedback from the editors we have formatted the manuscript to the PLOS requirement 2. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: https://pureadmin.qub.ac.uk/ws/files/470638768/world-04-00020.pdf https://www.mdpi.com/2037-0164/14/1/25/html https://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers18-12/010074472.pdf In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed. Response We have adjusted the entire manuscript to avoid any form of overlapping text. We have as well added new references 3. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. [Note: HTML markup is below. Please do not edit.] Response Thanks for the notice we have provided the correct grant number in the revised manuscript Reviewer's Responses to Questions Reviewers' comments: 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: Yes 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) Response: Thanks for providing good feedback to the manuscript. Reviewer #1: Introduction Query Language structure issues in “…popular staples in West Africa [3] while serving as important source of dietary calories thus contributing on average, more than 200 Kilocalories per person per day to ….“ the sentence could be better written as “….popular staples in West Africa [3], serving an important source of dietary calories with contribution of 200 Kilocalories on average per person per day to o…” Line 5 says “… diverse agro-ecologies of the country …”, What country? Nigeria? If West Africa please refer to it as you have not mentioned any country at this point. Response We have re-adjusted the entire introduction to make it more suitable for the readers Methods Query The authors have not stated how long (days) the accessions were planted before harvesting The authors made mention of agronomic practices regularly applied to the crop, however, agronomic practices are too vague and the author should state these agronomic practices in supplementary if it will disrupt the section structure For the DNA extraction, the authors stated they use young leaves, how are the young leaves selected/identified? (i.e. was it the youngest leaves from the yam or the youngest leaves from a collar, trifoliate, etc.). This is vital to grade uniformity of the harvest tissues because if younger leaves were selected randomly in the yam from accessions to accession, then the data's reproducibility is questioned. Response We appreciate feedback from the reviewer, we have provided all missing information in the revised manuscript. Results Query In Table 3, what does the a, b, c, d … represent? does it mean how statistically different the traits are? Indicate this in the table legend. Response These stand for the difference observed among the traits we have adjusted this and provided explanation below table 3. Query Figure 1 needs better resolution, the labels are not clearly visible Figure 2 legend needs to be detailed better Response We have provided high quality figure in the revised manuscript Query The heat map section should be given careful attention, the authors need to rearrange the letter in a clear way and specify the most significant. The heat map figures need better resolution as the accession could hardly be seen. The authors may only plot the map of the top most significant variation and include the others/this as supplementary material. Response We have removed this from the manuscript to avoid any confusing sentence Query Discussion The discussion therein contains a detailed explanation of the results and the authors clearly identified the gap, however, the discussion section needs to be well-arranged with enough paragraphs separating different objectives and interrelating results. As it is, the discussion is vague, and if possible should have subheadings. Response: Thanks for your feedback, we have corrected the entire discussion in the revised manuscript. Query Conclusion The conclusion is too minimal and a more robust conclusion highlighting the significant high impact of this work needs to be established. The last sentence for instance can be improved upon. Response We have adjusted the conclusion with more informative sentences. Reviewer #2: The manuscript “Exploring the Genetic Diversity and Population Structure of Aerial yams (Dioscorea bulbifera L.) DArT-seq and agronomic traits” presents insightful knowledge on the diversity among the bulbifera species of yam. To make the manuscript more presentable the following comments can be taken into consideration: Query 1. Abstract: Very simplified but can be improved Response We have adjusted the abstract in the revised manuscript 2. Introduction: a. The introduction needs some more literature that will cut across some findings and the importance of the use of SNPs markers for diversity studies. Response We have adjusted the introduction with genetic diversity related to yam Query b. The production and distribution of the yam specie used for the study should be emphasized with facts. Response We have provided details information about the production. However, there is no statistic attached as the crops is generally grown with additional yam with no attention Query c. Check the formatting. Response: Addressed in the revised manuscript d. Is there any study on D. bulbifera? Some highlights can be in the introduction. Response: Currently there is no available genetic study on the D. bulbifera. Some unpublished annual report from the NRCRI, Umudike Nigeria Query e. Other minor typo errors have been indicated in the attachment. Response: Thanks for the suggestions we have corrected all the errors in the revised manuscript 3. Methodology: Query a. Kindly provide some information on the nature of the soil for the experimental site. Response: We have provided response in the revised manuscript Query b. Table 1: Kindly indicate the accessions that were samples from IITA and NRCRI in the table. Response: We have provided this information in the revised manuscript Query c. Kindly indicate the number of replications used for this design. Response: We have provided this information in the revised manuscript Query d. “A total of 7 qualitative morphological descriptors for yam was used to profile the 94 accessions” This statement can begin for the Phenotyping session. From the statement here, you indicated seven but the parameters in the table are 8. Please clarify and make the necessary adjustments. This may affect the analysis, and this must be clear in the results. Response: We have adjusted all this in revised manuscript Query e. I suggest tuber parameters should be added to give a very clear diversity in the accessions used. Response: We appreciate suggestion from the reviewer. However, the main objective of this was to use molecular markers to access the diversity as the phenotypic is subjected to environmental variation. We plan to conduct another field evaluation with more traits for critical observation and those parameters will be added. Query f. Pictures that show clear morphological variation can also be very good to show the difference observed. Response: We have this documented during this cropping season when doing the trait profiling of the large collection Query g. Table 2: Indicate the period in which the parameters were taken. Response: We have added the missing information 4. Results: Query a. Table 3: This table does not reflect the number of parameters in Table 2. Please clarify and make the necessary adjustments. Response: We have adjusted the table 3 in the revised manuscript Query b. In the abstract author indicated AMOVA results but that is not reflected in the results. I suggest the AMOVA results are indicated and explained. Response: We have provided AMOVA table summary in the revised manuscript Query c. Figure 3. Explanations about this figure were not stated in the results. It is important to update that. Response: We have provided update in the revised manuscript Query d. Figures 7 and 8 must be together since they communicate the same information. Response: Thanks for the suggestion which is well appreciated. In this manuscript we prefer the two figure to stand alone for good clarity and discussion. Query e. Please note this well: To improve on the results and analysis. Further analysis can be done by combining the phenotypic and genotypic information in one analysis “dendrogram” to show the relationship and to support the information acquired for both data. That will be very good and explanatory enough. As it stands now, the phenotypic and genotypic information are separated and hanging but it will be good to blend the information from both sides together to make the study rich. Response: This is very good suggestion and as I have mentioned before we are planning for large profiling and this analysis will be conducted once we have several year data with large phenotypic data set. We have conducted similar work in some of our manuscript and this can be easily be replicated once the additional field data is ready 5. Discussion: a. The authors have elaborated on the required literature, however there is no discussion on the implication of the morphological observations with the marker’s information identified or vice versa. b. I suggest the authors explain more about that after combining the analysis of the results as indicated in the results session. Response We have adjusted the entire discussion. 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 https://doi.org/10.1371/journal.pone.0306631.r002
30 Apr 2024 Decision Letter - Timothy Omara, Editor PONE-D-23-28562R1Exploring the Genetic Diversity and Population Structure of Aerial yams (Dioscorea bulbifera L.) DArT-seq and agronomic traits.PLOS ONE Dear Dr. Agre, 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 Jun 14 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, Timothy Omara, PhD 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 #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 #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: No ****** 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 study on Exploring the Genetic Diversity and Population Structure of Aerial yams (Dioscorea bulbifera L.) DArT-seq and agronomic traits is a very extensive study which is accepted in the yam community as required to explore more genotypes for improvement study. However authors need to address the following to make the study scientifically sound for publishing. Generally, • All abbreviation should be checked and should be consistent throughout. Abstract: • This session is sound but will need some improvement pointing out some key results that are of significant importance to readers. Generalizing the results is not appropriate. Indicate some values and should be reelevate for the study. Introduction: • This session was simple and well written. Materials and methods: • Phenotyping: The use of just 7 variables seems not too extensive enough for the population in this study. Is there a reason for that? I suggest authors increase the number of variables by including flowering and some tuber characteristics. Remember that yam ontology has enough variable that can bring out the variation between these genotypes in the study. • The variables codes were not consistent in the entire study. Authors should ensure that that variable codes are consistent. • This will call for some figures and tables variable labels to be adjusted. • Authors should add phenotypic clusters to the analysis of the phenotypic data. • Genotyping analysis: Authors indicated AMOVA in the results, but the tools used for the AMOVA analysis were not indicated in the analysis section. Authors are expected to indicate that. Results: • This session needs more improvement. • Figures: figures were not well cited in text. Some were not talked about completely and others were misplaced. I suggest authors should make it a point to check the figure very well. • Clustering for phenotypic traits should be included in the results. • The PCA Biplot can be improved by showing the variation of the genotypes based on source or origin or agroecological zone. This will make the plot very informative and appreciable. • Summary genotypic statistics can be improved by indicating the Gene diversity and Call rate and other statistics to make table 5 very informative. • Results on AMOVA were not presented in the results. A separate paragraph should be developed for that. • The clustering was not explained well. I suggest a separate paragraph to be allocated for that. • Note that the method of population structure using STRUCTURE, Clustering and AMOVA are different, and each should complement each other. Having them together does not make your store interesting for the study. I suggest authors provide separate paragraphs for STRUCTURE, AMOVA, CLUSTERING and if possible, include PCoA or PCA and indicate how these methods manage the population structure. • More importantly, I suggest authors combine the results from phenotypic and genotypic to construct a cluster analysis to show the relation among them. That will be very good for this study. Discussion: • The discussion should be improved with any further analysis that is performed in the results section. ****** 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: Yes: Emmanuel Amponsah Adjei ******** [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: Comments.docx https://doi.org/10.1371/journal.pone.0306631.r003
Revision 2
19 Jun 2024 Author Response `We have reoganized the data and re-analyse evething to satify the reviewers comments and suggestions. We have improved all content of the manuscript including the discussion. We have added all types of analysis requested by the reviewers. https://doi.org/10.1371/journal.pone.0306631.r004
21 Jun 2024 Decision Letter - Timothy Omara, Editor Exploring the Genetic Diversity and Population Structure of Aerial yams (Dioscorea bulbifera L.) DArT-seq and agronomic traits. PONE-D-23-28562R2 Dear Dr. Agre, 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, Timothy Omara, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0306631.r005
Formally Accepted
9 Jul 2024 Acceptance Letter - Timothy Omara, Editor PONE-D-23-28562R2 PLOS ONE Dear Dr. Agre, 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. Timothy Omara Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0306631.r006

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