Peer Review History
Original SubmissionJuly 5, 2019 |
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PONE-D-19-15336 Steady expression of high oleic acid in peanut bred by marker-assisted backcrossing for fatty acid desaturase mutant alleles and its effect on seed germination along with other seedling traits PLOS ONE Dear Dr. Bera, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. ============================== ACADEMIC EDITOR: You will see that both the reviewers made critical recommendations, but an important consideration is whether the study describes a technically sound research and made significant advances in the relevant area. However, as reviewers pointed out, I think that this manuscript needs additional works. Therefore, I encourage the authors to perform the revision as per the reviewer’s suggestions and if these were meticulously performed, then I am sure that the MS could be reconsidered on a later date. ============================== We would appreciate receiving your revised manuscript by Oct 11 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols Please include the following items when submitting your revised manuscript:
Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Manoj Prasad, PhD Academic Editor PLOS ONE Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. 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 http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 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: Partly Reviewer #2: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know Reviewer #2: 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: 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 ********** 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: This manuscript was well written but it may not fit well to this journal. I gave this recommendation for three clear reasons: 1. The authors tried to describe a whole process for development of high oil and high oleate cultivars. The experiment was not specifically designed for any genetic studies or chemical analysis. 2. In the title, steady expression of high oleic acid and its effect on seed germination along with other seedling traits did not match the manuscript content. The evaluation of these traits was the selection outcome and did not necessary related to high oleic acid. 3. Even before making the cross, authors did not genotype parent ICGV06100 for FAD2 genotype. On Figure 2a and b, it was so confused. The well images were so different, but they scored them into the same genotype (for example, on Figure 2a well 6 and 7 to Aa; Figure 2b well 5, 6, and 7 images are the same but scored to different genotype Bb, BB, Bb). In addition, Figure 1a, only 4 samples but the authors mentioned 1 to 5. Figure 1b image was not clear. Furthermore, in the introduction (lines79-81), the authors mistook gadoleic acid (C20:1) as saturated fatty acid. Reviewer #2: Results: Table 1 results are not included in the results section Line 274 to 282 is this data represented in one of the figures or tables? line 291 what is the p-values for Figure 3? Line 294 p-value?, Line 296 25% protein contents, should state "with no significant differences??"" and cite the p-value associated Line 298 p-value line 305 pod yield, p-value???? Line 311 shelling percentage in table 1 data, what are the stats and p-value?? Line 314 what are the p-values for the significant interaction effects?? Line 321 where is this data table??? Line 323 p-value is needed?? Line 328 p-value is needed to support statement line 351 mention significant differences if any her in detail and in table 3, state p-value Line 361 to 362 please re-word for clarity is confusing as written Table 1, table footnotes are needed, define importance of superscripts statistically, what are the p-values table 2 define in table footnote how yield mean sq was determined, describe in footnotes the 3 locations, define PC1, etc, briefly state in footnotes stats used Table 3. table footnotes, table should in p-values, also, briefly state the methods used, stats used, so that reader can more clearly understand the data Figure 1 and Figure 2 are never discussed in the results section. also if these figures are to be used they need to include figure legends with details of the methods and quantity of the DNA starting materials for amplification Figure 3, Figure 4, Figure 6. and Figure 7, figure legend is needed, p-values needed with standard error bards, bar graphs using the current colors is difficult to read, try black and white and different patterns, % of what?? % of total fatty acid, x-axis values?? Figure 5???? not sure if this data adds to the strength of the manuscript?? Figure 8 same as previous comments of Figure 3, 4, also what are the harvest times and from what three states, figure legend needed Figure 9. this figure is never discussed in the manuscript. either include and discuss in the results/discussion or remove. not sure if it adds to the strength of the manuscript. General Line 71 and "the" rest Line 73 and the "remaining on-third" Line 74 low caloric (corrected spelling) line 105, remove "in a while" line 295 space after and line 297 space after and ********** 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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. |
Revision 1 |
PONE-D-19-15336R1 Steady expression of high oleic acid in peanut bred by marker-assisted backcrossing for fatty acid desaturase mutant alleles and its effect on seed germination along with other seedling traits PLOS ONE Dear Dr. Bera, 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. ============================== Thank you for submitting your revised manuscript. You will see that one of the reviewers make critical recommendations and it appears that additional work is needed as indicated by the reviewers. If these were meticulously performed, then I am sure that the MS could be reconsidered on a later date. ============================== We would appreciate receiving your revised manuscript by Dec 20 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols Please include the following items when submitting your revised manuscript:
Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Manoj Prasad, PhD Academic Editor PLOS ONE [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: All comments have been addressed Reviewer #3: All comments have been addressed Reviewer #4: (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 Reviewer #3: Yes Reviewer #4: Partly ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: 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 #2: Yes Reviewer #3: Yes Reviewer #4: 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 Reviewer #3: Yes Reviewer #4: 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: (No Response) Reviewer #3: The authors have responded to all questions raised by the previous reviewer except the question about the title. They need to change the title because it does not reflects the contents of manuscript.The title should mention the main achievement which is the development of high oleic content line. The title might read something like this "Development of stable lines with high oleic content through marker assisted introgression of fatty acid desaturate mutant alleles and its effect on seed germination". All other questions raised by previous reviewer has been answered and have improved the quality of manuscript significantly. Reviewer #4: I feel that the title may be modified. Currently, the title seems to indicate that variations in germination frequencies and other seedling traits are primarily due to high oleic acid, which may not be the case due to various reasons including genomic reconstitution as elaborated below. It would be advisable to list these as separate features/studies of the high oleic lines. In the abstract, the authors talk about resistance to biotic stresses but there is no mention of this data in the manuscript. This portion towards the end should be deleted. Line 66: "in around" I have the following four important queries which the authors need to clarify: 1. Lines 191-195: Aren't four SSRs per linkage group too less for estimating recurrent genome reconstitution? 2. Why was backcrossing done only till BC3? Would it be sufficient to reconstitute a significant portion of the recurrent parent genome in the absence of background selection. Since background selection was not done, in conjunction to point 1 above, there could be sufficient portions of the non-recurrent parent genome remaining in the resulting selected line which could be responsible for other variations observed in seedling traits. Also, this would raise questions about the stability of the generated line. 3. Was stable inheritance of the high oleic phenotype tested using successive generations of harvested seed? This is not clearly given in the text. How was it done? Which generations of selfed progeny were used? 4. How is passport data a good approach to test for genomic reconstitution? I am not in agreement with this approach. Line 226: Shouldn't it be "111-115"? Line 260: Any references for this formula? Line 284: Should be "codified" or "named" or "termed" instead of "decoded" Line 290: (RPG) in brackets Line 292: What does "nine were amplified" imply? Did they harbor the SunOleic95R genome segments? Is there any information available on the genetic/physical distance of these 10 SSRs? Line 368-369: "However, the..........the groups" is not clear. Rephrase. Figure 1 legend: Please correct for language ********** 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: No Reviewer #3: No Reviewer #4: 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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. |
Revision 2 |
Steady expression of high oleic acid in peanut bred by marker-assisted backcrossing for fatty acid desaturase mutant alleles and its effect on seed germination along with other seedling traits PONE-D-19-15336R2 Dear Dr. Bera, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, Manoj Prasad, PhD 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 #3: All comments have been addressed Reviewer #4: 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 #3: Yes Reviewer #4: (No Response) ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #3: Yes Reviewer #4: (No Response) ********** 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 #3: Yes Reviewer #4: (No Response) ********** 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 #3: Yes Reviewer #4: (No Response) ********** 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 #3: I am surprised at stubborn attitude of authors. Three different reviewers have pointed out discrepancy in manuscript content and the title. The reasons have been cited and alternate titles have been suggested. Reviewers have been constructive in reviewing the manuscript but authors are reiterating the same comment again and again. They have not even considered what reviewers have been pointing out. Under these circumstances, I have no other comments to make and leave it to wisdom of editor to decide what will be right. I will not like to take up this manuscript for reviewing anymore. Reviewer #4: (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 #3: No Reviewer #4: No |
Formally Accepted |
PONE-D-19-15336R2 Steady expression of high oleic acid in peanut bred by marker-assisted backcrossing for fatty acid desaturase mutant alleles and its effect on seed germination along with other seedling traits Dear Dr. Bera: I am 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 notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Manoj Prasad Academic Editor PLOS ONE |
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