Exploring genotype by environment interaction on cassava yield and yield related traits using classical statistical methods

Moshood A. Bakare; Siraj Ismail Kayondo; Cynthia I. Aghogho; Marnin D. Wolfe; Elizabeth Y. Parkes; Peter Kulakow; Chiedozie Egesi; Ismail Yusuf Rabbi; Jean-Luc Jannink

doi:10.1371/journal.pone.0268189

Peer Review History

Original SubmissionDecember 20, 2021
7 Mar 2022 Decision Letter - Muhammad Amjad Ali, Editor PONE-D-21-40030Exploring genotype by environment interaction on cassava yield and yield related traits using classical statistical methodsPLOS ONE Dear Dr. Jannink, 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 Apr 21 2022 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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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. 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments: Dear Authors, We have received the review reports on your manuscript "Exploring genotype by environment interaction on cassava yield and yield related traits using classical statistical methods " from the renowned reviewers in the field. As you can see the comments, they have asked for revisions. Please go through the comments and revise the manuscript inline with the comments and suggestions. Regards, Muhammad Amjad Ali [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: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: I Don't Know ****** 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: I have reviewed the manuscript # PONE-D-21-40030, Title “Exploring genotype by environment interaction on cassava yield and yield related traits using classical statistical methods”. I am glad to express that the manuscript is well written, and the message is clearly presented. The standard of language is also good. The introduction is good and clearly describes the background of the study. The analytical methods used, and the conclusions drawn are satisfactory. Although the research seems more of regional importance rather than international, but I think it’s still good enough to contribute to the global knowledge. The statistical methods also look conventional. But keeping in mind the current situation of lack of facilities for advanced genomics tools for every researcher, the guidelines provided for conventional methods will be of valuable importance to make genetic gains on a very important problem of GxE in cassava. Having said that, I still want to suggest some improvements to improve the manuscript, such as 1. There are a few minor typo errors, I have mentioned them as sticky notes on the attached pdf document. 2. In materials and methods section, please add some salient features/background information of the clones/genotypes used in the study, to indicate why they were selected for the experiment. The relevant information can be added to Table 1, the table also needs improvement in formatting. 3. In materials and methods section, it is suggested that instead of showing coordinates of study sites in tabular form (Table 2) they can be displayed in a form of a map with study sites displayed as dots. 4. Similarly in materials and methods section, the weather data in Table 2 can be displayed in a graphical form for a clear understanding of readers. 5. The experimental material is designated with 2 different terms in various section of the manuscript such as a. “clones” in abstract and material & methods sections b. “genotypes” in results & discussion sections. It should be consistent throughout 6. I suggest that conclusion should be reconsidered so that it can show that based on the results all the objectives of the study were achieved. To summarise it, I recommend that the manuscript may be considered suitable for publication with minor revisions. Reviewer #2: In this study, author have investigated the dissection of the existing patterns of GEI using linear-bilinear models such as Finlay-Wilkinson, additive main effect and multiplicative interaction, and genotype and genotype by environment interaction models are critical in defining the target population of environments for future testing, selection, and advancement. Study is well designed but i have some suggestion Methods and results section is very long. I suggest you should make it little short. While, discussion section is very short. Please discuss results in detail and add appropriate references. ****** 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: Yes:** Shahid Iqbal Awan Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: Review PONE-D-21-40030.docx Attachment Submitted filename: PONE-D-21-40030.pdf https://doi.org/10.1371/journal.pone.0268189.r001
Revision 1
21 Apr 2022 Author Response 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: Partly 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: I Don't Know 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: I have reviewed the manuscript # PONE-D-21-40030, Title “Exploring genotype by environment interaction on cassava yield and yield related traits using classical statistical methods”. I am glad to express that the manuscript is well written, and the message is clearly presented. The standard of language is also good. The introduction is good and clearly describes the background of the study. The analytical methods used, and the conclusions drawn are satisfactory. Although the research seems more of regional importance rather than international, but I think it’s still good enough to contribute to the global knowledge. The statistical methods also look conventional. But keeping in mind the current situation of lack of facilities for advanced genomics tools for every researcher, the guidelines provided for conventional methods will be of valuable importance to make genetic gains on a very important problem of GxE in cassava. Having said that, I still want to suggest some improvements to improve the manuscript, such as 1. There are a few minor typo errors, I have mentioned them as sticky notes on the attached pdf document. Response The typo errors have been rectified. Meanwhile, the first sticker note is not the author name italicized but the botanical name of cassava (Manihot esculenta Crantz) as in line 72. Line 172 abbreviation IITA has been rectified to Internatiional Institute of Tropical Agriculture 2. In materials and methods section, please add some salient features/background information of the clones/genotypes used in the study, to indicate why they were selected for the experiment. The relevant information can be added to Table 1, the table also needs improvement in formatting. Response We have provided short description about where the clones were derived from and how they were screened for diseases, quality and agronomic traits of interest over different breeding stages of evaluation. This can be found from Line 174-178 of revised document. In addition, we added the cycle each clone belongs and the year of cloning as in Table 1 line 182. We further formatted the tables by bolding the table title and aligning the text within each column. 3. In materials and methods section, it is suggested that instead of showing coordinates of study sites in tabular form (Table 2) they can be displayed in a form of a map with study sites displayed as dots. Response We have reproduced a Nigerian map as Fig 1 showing the testing locations for the field trials and the agro-ecological zone each belongs to as in line 202 of revised manuscript with track changes. 4. Similarly in materials and methods section, the weather data in Table 2 can be displayed in a graphical form for a clear understanding of readers. Response A line graph named Fig 2 has been produced showing the trend of average minimum and maximum temperature, total precipitation, and mean relative humidity across the testing environments as in line 221 of revised manuscript with track changes. 5. The experimental material is designated with 2 different terms in various section of the manuscript such as a. “clones” in abstract and material & methods sections b. “genotypes” in results & discussion sections. It should be consistent throughout Response Every occurrence of “cassava genotypes” which represents the treatment in the abstract, material and methods, and result and discussion sections have been replaced with the word “clones” to be consistent. 6. I suggest that conclusion should be reconsidered so that it can show that based on the results all the objectives of the study were achieved. Response We have updated the conclusion to reflect that all research objectives as outlined in this study were achieved based on the outcome of the study. This can be found as from line 1039 to 1045 of revised manuscript with track changes. . To summarise it, I recommend that the manuscript may be considered suitable for publication with minor revisions. Reviewer #2: In this study, author have investigated the dissection of the existing patterns of GEI using linear-bilinear models such as Finlay-Wilkinson, additive main effect and multiplicative interaction, and genotype and genotype by environment interaction models are critical in defining the target population of environments for future testing, selection, and advancement. Study is well designed but i have some suggestion Methods and results section is very long. I suggest you should make it little short. While, discussion section is very short. Please discuss results in detail and add appropriate references. Response We revised both the materials and method and result sections by taking out some redundant statements as shown in a marked-up copy of the revised document. We have discussed the findings in this study and related them to findings from references such as Dixon et al, Tumuhimbise et al, Benesi et al, and Nduwumuremyi et al. 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: Yes: Shahid Iqbal Awan Reviewer #2: No Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0268189.r002
25 Apr 2022 Decision Letter - Muhammad Amjad Ali, Editor Exploring genotype by environment interaction on cassava yield and yield related traits using classical statistical methods PONE-D-21-40030R1 Dear Dr. Jannink, 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, Muhammad Amjad Ali, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0268189.r003
Formally Accepted
28 Apr 2022 Acceptance Letter - Muhammad Amjad Ali, Editor PONE-D-21-40030R1 Exploring genotype by environment interaction on cassava yield and yield related traits using classical statistical methods Dear Dr. Jannink: 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. Muhammad Amjad Ali Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0268189.r004

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