Environmental impact and phenotypic stability in potato clones resistant to late blight Phytophthora infestans (Mont) de Bary, resilient to climate change in Peru

Manuel Gastelo; Carolina Bastos; Rodomiro Ortiz; Raúl Blas

doi:10.1371/journal.pone.0318255

Peer Review History

Original SubmissionOctober 10, 2024
10 Oct 2024 Author Response https://doi.org/10.1371/journal.pone.0318255.r001
13 Nov 2024 Decision Letter - Ravinder Kumar, Editor PONE-D-24-45529Environmental impact and phenotypic stability in potato clones resistant to late blight Phytophthora infestans (Mont) de Bary, resilient to climate change in PeruPLOS ONE Dear Dr. Gastelo, 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 28 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, Ravinder Kumar, Ph.D. 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. Thank you for stating the following financial disclosure: “USAID” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. [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: Dear Authors, After careful reviewing the manuscript `Environmental impact and phenotypic stability in potato clones resistant to late blight Phytophthora infestans (Mont) de Bary, resilient to climate change in Peru`, I congratulate you and kindly consider the following recommendations: - The name of Figure 1 must be translated in English. - I propose rearranging the information in Table 3. Everywhere, the same values are repeated twice. I advise you to review the results just once and note that they apply to both scenarios with and without the control. - Line 87: the source Villazón et al. 2005 isn't listed on References list. Nevertheless there is a Villamon et al. Is it the same author? Please update the list. - Line 135: the statistical `package` is actually the software you used. You didn't mentioned any package for them, so please correct the line, replace package with software. Reviewer #2: Reviewer Comments to Author: Ms. Ref. No.: PONE-D-24-45529 Ms. Full Title: Environmental impact and phenotypic stability in potato clones resistant to late blight Phytophthora infestans (Mont) de Bary, resilient to climate change in Peru The authors conducted a study on the Environmental impact and phenotypic stability in potato clones resistant to late blight. Using total tuber yield, marketable tuber yield, evolution of disease intensity over time (AUDPC, sAUDPC), they analyzed a comprehensive 30 potatoes clones for phenotypic stability and economic profitability across locations. Late blight resistance was evaluated in a trial with no chemical application while the application of chemical in controlling late blight helped in evaluation environmental impact. The study was carried out on one season across several location, which is an admirable effort. However, substantial revisions are required if the manuscript is to be considered for publication in this valued journal. Abstract: 1. Line 19. You mentioned that the cultivars Yungay, Amaryllis and Kory were used as controls. Are they controls in terms of resistance to late blight, in terms of yield stability or both? It is important to clarify 2. Line 21. You mention that fourteen clones were resistant, stable phenotypically, low environmental impact and high profitability. Are they having all those characteristics at the same level? Likely not. It is good to mention the main clones. You can mention the top five if you can’t mention all in decreasing levels Introduction: 1. In the last paragraph in the introduction part containing the aims of the study. The authors should change the objectives and project there the different hypothesis that are tested in the study emphatically. 2. The novelty of the study over published literature has to be highlighted in the last paragraph of introduction. Materials and methods: 1. Line 76. You mentioned that the 30 genotypes tested are resistant to late blight. At 850 masl altitude. What was the basis of the selection of those genotypes? Why are you screening against for the resistance? If there is any reason for that, it has to be clearly hypothesized at the introduction 2. Line 79: The controls you used: Amarilis (moderately resistant), Yungay (susceptible) and Kory (resistant). These characteristics where supposed to be the same when using those varieties at your study site? 3. Line 86: precise the precipitation, relative humidity and temperature that give these optimal conditions 4. Line 141-142. You wrote environmental Impact rate (IA) . IA is it the abbreviation? 5. Line 143: All the elements for the EIR formula are not defined. Defined PAI and NA on the formula Results: 1. Line 220, Table 4. Values for AUDPC and sAUDPC are they fixed values or means of values? If they are means of values, provides Standard Deviation so that we can appreciate the significance from the Tukey means separation test. If is fixed values, how do the Tukey test was performed? 2. Line 254: The title of Figure 1 is in Spanish, not in English. You have to harmonize 3. Line 271. Table 5. Why you dis not performed the Tukey Test for the mean separation in order to compare clones as you did with results on AUDPC and sAUDPC provided in Table 4? 4. Table 5: Can we also identify resistant clones from this Table? Are they those with less increase when controlling the disease? If so, provide a relationship between AUDPC values and increase in yield 5. Line 274. Results presented in Figure 2 look appearing in Table 5. Duplication of results. You should choose to presents those results in a Table or in Figure 6. Line 312. Table 6. Could you provide mean separation for EIR for the different genotypes? It will help differentiating the different clones Conclusion: Provide a conclusion for your research. You should come out with the most promising clones resistant to late blight, with important yield, stable across environments and with higher economic profitability ****** 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: Yes: Eric Bertrand Kouam ******** [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 notes KOUAM (Ms. Ref. No.PONE-D-24-45529.docx https://doi.org/10.1371/journal.pone.0318255.r002
Revision 1
11 Dec 2024 Author Response Response to Academic Editor and Reviewers 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 DONE 2. Thank you for stating the following financial disclosure: “USAID” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. DONE 3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. DONE Reviewer #1: After careful reviewing the manuscript `Environmental impact and phenotypic stability in potato clones resistant to late blight Phytophthora infestans (Mont) de Bary, resilient to climate change in Peru`, I congratulate you and kindly consider the following recommendations: - The name of Figure 1 must be translated in English. DONE - I propose rearranging the information in Table 3. Everywhere, the same values are repeated twice. I advise you to review the results just once and note that they apply to both scenarios with and without the control. DONE - Line 87: the source Villazón et al. 2005 isn't listed on References list. Nevertheless there is a Villamon et al. Is it the same author? Please update the list. DONE - Line 135: the statistical `package` is actually the software you used. You didn't mentioned any package for them, so please correct the line, replace package with software. DONE Reviewer #2: Ms. Full Title: Environmental impact and phenotypic stability in potato clones resistant to late blight Phytophthora infestans (Mont) de Bary, resilient to climate change in Peru The authors conducted a study on the Environmental impact and phenotypic stability in potato clones resistant to late blight. Using total tuber yield, marketable tuber yield, evolution of disease intensity over time (AUDPC, sAUDPC), they analyzed a comprehensive 30 potatoes clones for phenotypic stability and economic profitability across locations. Late blight resistance was evaluated in a trial with no chemical application while the application of chemical in controlling late blight helped in evaluation environmental impact. The study was carried out on one season across several location, which is an admirable effort. However, substantial revisions are required if the manuscript is to be considered for publication in this valued journal. Abstract: 1. Line 19. You mentioned that the cultivars Yungay, Amaryllis and Kory were used as controls. Are they controls in terms of resistance to late blight, in terms of yield stability or both? It is important to clarify This varieties were used as controls for late blight resistance and tuber yield 2. Line 21. You mention that fourteen clones were resistant, stable phenotypically, low environmental impact and high profitability. Are they having all those characteristics at the same level? Likely not. It is good to mention the main clones. You can mention the top five if you can’t mention all in decreasing levels Clones CIP316375.102, CIP316361.187, CIP316367.117, CIP316356.149, CIP316367.147 were the ones that presented the highest yields Introduction: 1. In the last paragraph in the introduction part containing the aims of the study. The authors should change the objectives and project there the different hypothesis that are tested in the study emphatically. The objective was changed according to the hypotheses of the study 2. The novelty of the study over published literature has to be highlighted in the last paragraph of introduction. DONE Materials and methods: 1. Line 76. You mentioned that the 30 genotypes tested are resistant to late blight. At 850 masl altitude. What was the basis of the selection of those genotypes? Why are you screening against for the resistance? If there is any reason for that, it has to be clearly hypothesized at the introduction The importance of controlling late blight in potato crops has been mentioned in the introduction, one way of controlling it is to use resistant varieties that will allow for increased yields, reduce environmental impact due to less use of fungicides, preserve human health and improve economic profitability for the benefit of farmers. At 850 masl, it was corrected to 1850 masl. 2. Line 79: The controls you used: Amarilis (moderately resistant), Yungay (susceptible) and Kory (resistant). These characteristics where supposed to be the same when using those varieties at your study site? Yes, these are the resistance levels under the conditions of the study sites and were determined in previous trials 3. Line 86: precise the precipitation, relative humidity and temperature that give these optimal conditions DONE 4. Line 141-142. You wrote environmental Impact rate (IA) . IA is it the abbreviation? DONE 5. Line 143: All the elements for the EIR formula are not defined. Defined PAI and NA on the formula Yes, they are defined in the formula: number of applications (NA) and percentage of active ingredient (PAI) Results: 1. Line 220, Table 4. Values for AUDPC and sAUDPC are they fixed values or means of values? If they are means of values, provides Standard Deviation so that we can appreciate the significance from the Tukey means separation test. If is fixed values, how do the Tukey test was performed? AUDPC and sAUDPC values are averages of three replicates. The standard deviation was added 2. Line 254: The title of Figure 1 is in Spanish, not in English. You have to harmonize Changed from Spanish to English 3. Line 271. Table 5. Why you dis not performed the Tukey Test for the mean separation in order to compare clones as you did with results on AUDPC and sAUDPC provided in Table 4? Tukey mean comparison test (0.05) and standard deviations were added. 4. Table 5: Can we also identify resistant clones from this Table? Are they those with less increase when controlling the disease? If so, provide a relationship between AUDPC values and increase in yield Yes, clones with a lower increase in tuber yield when the disease is controlled is due to their resistance. A correlation was made between the AUDPC values and the increases % in tuber yield. There is a high correlation between AUDPC values and marketable tuber yield increases (r = 0.735, Pearson correlation p<=0.01) 5. Line 274. Results presented in Figure 2 look appearing in Table 5. Duplication of results. You should choose to presents those results in a Table or in Figure Figure 2 was removed 6. Line 312. Table 6. Could you provide mean separation for EIR for the different genotypes? It will help differentiating the different clones The average shown in Table 6 corresponds to each clone and is the average of the EIR of Oxapampa and Huánuco. Conclusion: Provide a conclusion for your research. You should come out with the most promising clones resistant to late blight, with important yield, stable across environments and with higher economic profitability Conclusions of the study were added Attachments Attachment Submitted filename: RESPONSE TO EDITOR.docx https://doi.org/10.1371/journal.pone.0318255.r003
14 Jan 2025 Decision Letter - Ravinder Kumar, Editor <p>Environmental impact and phenotypic stability in potato clones resistant to late blight Phytophthora infestans (Mont) de Bary, resilient to climate change in Peru PONE-D-24-45529R1 Dear Dr. Gastelo, 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, Ravinder Kumar, Ph.D. Academic Editor PLOS ONE 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 #1: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ****** 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 #1: (No Response) ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean? ). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy . Reviewer #1: No ******** https://doi.org/10.1371/journal.pone.0318255.r004
Formally Accepted
Acceptance Letter - Ravinder Kumar, Editor PONE-D-24-45529R1 PLOS ONE Dear Dr. Gastelo, 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. Ravinder Kumar Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0318255.r005

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .