Peer Review History
| Original SubmissionJuly 28, 2020 |
|---|
|
PONE-D-20-23535 Genotypic diversity and plasticity of root system architecture to nitrogen availability in oilseed rape PLOS ONE Dear Dr. Lecarpentier, 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 Nov 15 2020 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:
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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Mehdi Rahimi, 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 2. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 3. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. [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 Reviewer #3: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: No ********** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: No ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: 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: The aim of this study by Lecarpentier et al was to analyze the genetic diversity and plasticity of system architecture to nitrogen availability in oilseed rape using the ArchiSimple model. This study is thus of much importance and manuscript was generally well written. However, my specific comments are as follows: 1. Abstracts should have no paragraphs to my knowledge. 2. The abstract could be clearly written to explain the importance of this study and how beneficial it will be, as well as explain what the results obtained in the study will be used for in subsequent research or future purposes (If anu) 3. Sentences could be concise. Especially in the introduction section. To me, I think the introduction should be rewritten in a concise manner. As it stands now, there is too much information and seems confusing at a point. 4. The last paragraph of the introduction should be checked if possible. 5. Check manuscript for grammatical (especially subject-verb agreement) and typogragraphical errors. For example lines 13, 33, 45, 48, 50, 53, 54, 56, 58, 60, 61, 108, 179, 210, etc. 6. Line 67 - "They".. Who are the "they"? 7. The Hoagland solution was stated with no reference 8. Line 112 - "800 growing degree-days (around 30 days) after sowing and took place during approximately 150 degree-days". Please crosscheck this sentence 9. At the "trait definition section" some words were bolded. It happens in other parts but most are in this sub chapter. Kindly refer to the guide for authors and make sure the correct formatting is done. 10. Font style of reference is different. I may presume this might have been an oversight, so kindly work on that. Reviewer #2: paper is well concise but please try to make the results more clear. the discussion ins very long so try to add conclusion as well. the figures are designed very well and show good piece of information related to the paper. overall, the paper is very well written Reviewer #3: 1. In this study, author discuss about genetic diversity and plasticity of root system architecture in oilseed rape, which is suitable for it. However, number of genotype is very less to characterize root system architecture and plasticity response to nitrogen limitation of oilseed rape. 2. In material and methods; please mention the number of biological replicates which author have studied in control and two levels of availability. 3. Author please mention in manuscript text which statistical test were used for find significant effect of genotype, nitrogen and GxN effects. 4. Author mention in “Experimental design” eight seed per tube were sown and remained two plants plants per tube, please mention at which stage removed others plants from the tube. 5. In Table 1: please explain the accession type what is the meaning of “0+”, “00”, and “++“. 6. In Table1: please indicate the actual yield value or the rank based on the yield value of the accession, So readers can easily understand accession yield performance which author were selected for the study. 7. In Table 1: similarly as yield, please indicate the value of yield stability parameters which author used for stability performance of the accessions. 8. In line 108: Reference is not citing in journal format. 9. In Excavation procedure; line115: author mention that it was impossible to separate the root system of the two plants beyond 10 cm depth. Data collected beyond 10 cm depth, will show sampling error because of inappropriate data collection and will also affect the results. If author collected data of each plant separately, will show better results. 10. Author also calculates “Leaf Area Index” (LAI) based on data scanned by flatbed scanner. LAI is better to understand the dimensionless quantity that characterizes plant canopies. 11. Please do correlation analysis to find out the relationship among and between PA and RSA traits at Nitrogen level (N+ and N-), author not discussed what correlations between traits at two nitrogen level. 12. Please cite reference in manuscript for supporting on-screen root sample measurements. 13. Please write the formula in the manuscript to calculate “Nitrogen Uptake Efficiency” and Nitrogen Utilization Efficiency” and cite the references. I think equations in “Moll et al. 1982” article author can use to re-calculate NUpE and NUtP value. 14. Please prepare descriptive statistics table with mean value, cv value, SE etc. 15. In line 190 to 194: Author calculates absolute and oriented plasticity by equations, please cite the reference in manuscript if any. 16. In line 198: Author only illustrates boxplots and barplots for eight traits why not for all traits. 17. In line223: Author write “nitrogen availability had a significant effect (pvalue < 0.01) on all the nine plant allocation traits”, but in the table 3 there is 13 traits which had a significant nitrogen effect. Please re-check. 18. In line 236: Genotype x nitrogen interaction was significant for three traits only:TDB and LA, but in the Table 3 only one trait (IBD) was significant at pvalue < 0.01. 19. In line 381: Please cite the reference in journal format. 20. Please make sure all references are listed as per journal format, there is formatting error. ********** 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: Rabail Afzal Reviewer #3: 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. |
| Revision 1 |
|
Genotypic diversity and plasticity of root system architecture to nitrogen availability in oilseed rape PONE-D-20-23535R1 Dear Dr. Lecarpentier, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Mehdi Rahimi, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed Reviewer #3: 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 Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #3: 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 Reviewer #3: 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 Reviewer #3: 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: Authors have thoroughly revised the manuscript and it looks better now. Manuscript is fit to be accepted for publication. Reviewer #3: The author have been addressed all the comments in revised manuscript and ready for acceptance. All figure must be summited in required image quality for better visualization. ********** 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 Reviewer #3: Yes: Javed Akhatar, Punjab Agricultural University, Ludhiana, India |
| Formally Accepted |
|
PONE-D-20-23535R1 Genotypic diversity and plasticity of root system architecture to nitrogen availability in oilseed rape Dear Dr. Lecarpentier: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Mehdi Rahimi Academic Editor PLOS ONE |
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 .