Flame resistant cotton lines generated by synergistic epistasis in a MAGIC population

Gregory N. Thyssen; Brian D. Condon; Doug J. Hinchliffe; Linghe Zeng; Marina Naoumkina; Johnie N. Jenkins; Jack C. McCarty; Ruixiu Sui; Crista Madison; Ping Li; David D. Fang

doi:10.1371/journal.pone.0278696

Peer Review History

Original SubmissionJuly 11, 2022
8 Aug 2022 Decision Letter - Yuan-Ming Zhang, Editor PONE-D-22-19253Flame resistant cotton lines generated by synergistic epistasis in a MAGIC populationPLOS ONE Dear Dr. Thyssen, 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 Sep 22 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. 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, Yuan-Ming Zhang 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. Please amend your list of authors on the manuscript to ensure that each author is linked to an affiliation. Authors’ affiliations should reflect the institution where the work was done (if authors moved subsequently, you can also list the new affiliation stating “current affiliation:….” as necessary). Additional Editor Comments: I have received two review reports. The two reviewers gave some comments and suggestions. Please address them carefully in the revision. [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: No 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: 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: In this manuscript entitled “Flame resistant cotton lines generated by synergistic epistasis in a MAGIC population” presented the identification of the lower heat release capacities textiles made from cotton fiber produced from MAGIC RILs. The flame-resistant trait of cotton germplasm has the potential to greatly reduce the costs of flame retardant additives for cotton textiles. To determine the genetic mechanism of the flame-resistant cotton by transgressive segregation, the authors used the GWAS and RNAseq methods, identified 26 loci and 13 genes were linked to the influence the HRC values in the 257 RILs. The authors showed an interesting topic, however, there are some concerns and suggestions for authors to address: 1. How about the HRC values of the eleven parents of MAGIC? The authors should to show the experiments and results in the MS. 2. Whether there is a difference in the flavonoid content between the flammable lines and FR lines? to confirm the previous suggestion that a colorless flavonoid or other natural colorless compound was responsible for the FR. And to support the GWAS and RNAseq data. 3. The GWAS and RNAseq results are too preliminary, it does not make a whole story. 4. To further focus on the 41 segregated for non-synonymous variants in the RMUP-MAGIC population among the 602 unique genes, and the 13 highly differentially expression genes within the locations, to determine the genetic mechanism of the flame-resistant cotton. Reviewer #2: The natural flame resistant is an important trait in cotton. Linkage, epistatic, GWAS and transcriptomes analysis were conducted to determine the genetic architecture in MAGIC population of cotton. Of the textiles fabricated from the five offspring of MAGIC, four exhibited the novel characteristic of inherent flame resistance. It is expected to provide guidance for breeding. This is an interesting study. But I have some concerns in statistical analysis. 1. The greatest advantages of QTL mapping using MAGIC populations come from multiple founder alleles. Many researches think that multi-allele model should be considered in the statistical analysis of MAGIC population. Multi-allele model can estimate the effect of every allele and it is beneficial to crop breeding. In this study the GWAS method was used to analyze the datasets of 11-parent MAGIC population, but all GWAS methods consider only two alleles. Please explain why the multi-allele model did not use. 2. When the GWAS method was used to analyze the dataset of MAGIC population, please consider whether the population structure should be considered. These reasons may make your results difficult to understand. For example, the loci identified in linkage analysis are apart from the loci identified by PLINK and/or mrMLM. ****** 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. https://doi.org/10.1371/journal.pone.0278696.r001
Revision 1
10 Aug 2022 Author Response August 10, 2022 Dear Dr. Yuan-Ming Zhang, Reviewers and Editorial Board of PLOS ONE: I am submitting a revised manuscript for your consideration, titled, “Flame resistant cotton lines generated by synergistic epistasis in a MAGIC population.” [PONE-D-22-19253] We appreciate your time, consideration, and valuable comments. Below we have responded to each of the comments and have made modifications to the manuscript to reflect your requests and suggestions. Sincerely, Gregory Thyssen, Ph.D. USDA-ARS Comments to the Author: 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: No RESPONSE: All p-values shown in the Tables and Supplemental Tables were computed using the default statistical methods implemented by the highly cited bioinformatic software described in the Methods. No attempt was made to artificially reduce thresholds for significance or to employ other-than-default statistical analysis. Rather than presenting just one of the genomic analyses, we present three (PLINK, mrMLM, simple linkage), which do not completely agree with each other. We agree that the genomics part of this report is preliminary, so we believe that presenting all of these data will be the most beneficial to the other researchers and breeders that will hopefully help continue this work, so that naturally flame-resistant cotton can be further characterized and used in breeding programs. Reviewer #1: In this manuscript entitled “Flame resistant cotton lines generated by synergistic epistasis in a MAGIC population” presented the identification of the lower heat release capacities textiles made from cotton fiber produced from MAGIC RILs. The flame-resistant trait of cotton germplasm has the potential to greatly reduce the costs of flame retardant additives for cotton textiles. To determine the genetic mechanism of the flame-resistant cotton by transgressive segregation, the authors used the GWAS and RNAseq methods, identified 26 loci and 13 genes were linked to the influence the HRC values in the 257 RILs. The authors showed an interesting topic, however, there are some concerns and suggestions for authors to address: 1. How about the HRC values of the eleven parents of MAGIC? The authors should show the experiments and results in the MS. RESPONSE: The HRC values of the eleven parents are represented by the vertical black lines in the histogram in Figure 1a. Now, we have added mention of the parents in the Methods and a new Supplemental Table 1 with the numerical values. 2. Whether there is a difference in the flavonoid content between the flammable lines and FR lines? to confirm the previous suggestion that a colorless flavonoid or other natural colorless compound was responsible for the FR. And to support the GWAS and RNAseq data. REPSONSE: Quantification of flavonoid compounds and other metabolites in the flame resistant and flammable lines is ongoing. Unfortunately, due to the COVID pandemic, our collaborator that was working on this has not yet been able to complete the study. We may need to grow another season for fresh material and/or replication of the experiment. Now, we have modified the manuscript to emphasize that the flavonoid mechanism remains at this point a hypothesis for future work and not a claim of a finding. As mentioned above, publication of this work will hopefully encourage other groups to test the material and develop additional samples, hypotheses, and findings. 3. The GWAS and RNAseq results are too preliminary, it does not make a whole story. RESPONSE: We agree that the genomics part of this report is preliminary. Rather than work in isolation to discover the complete mechanism, we choose to share the candidate genes and loci that we could find already by various approaches. Since the mechanism is likely the synergistic interaction of numerous small-effect loci, much further work will be required to present the whole story. However, these FR lines already have value to breeders since phenotypic selection by MCC is feasible at scale. Now, we acknowledge and further emphasize these points in the Conclusion. Again, exposure of our findings to other researchers and breeders is the fastest way for the whole story to be discovered. 4. To further focus on the 41 segregated for non-synonymous variants in the RMUP-MAGIC population among the 602 unique genes, and the 13 highly differentially expression genes within the locations, to determine the genetic mechanism of the flame-resistant cotton. RESPONSE: We do intend to further focus on our preliminary candidate genes to identify the whole story of the mechanism, and to develop genetic markers for marker assisted breeding. However, this requires another growing season, so that more stages of the developing cotton fiber tissues can be collected for RNA extraction and quantification. We are also currently developing additional informative populations to isolate and study subsets of the preliminary candidate genes. Publication of the present study will hopefully lead to study of these lines and our currently identified FR RILs at additional locations, both by our collaborators and other independent colleagues in cotton research and breeding. Reviewer #2: The natural flame resistant is an important trait in cotton. Linkage, epistatic, GWAS and transcriptomes analysis were conducted to determine the genetic architecture in MAGIC population of cotton. Of the textiles fabricated from the five offspring of MAGIC, four exhibited the novel characteristic of inherent flame resistance. It is expected to provide guidance for breeding. This is an interesting study. But I have some concerns in statistical analysis. 1. The greatest advantages of QTL mapping using MAGIC populations come from multiple founder alleles. Many researchers think that multi-allele model should be considered in the statistical analysis of MAGIC population. Multi-allele model can estimate the effect of every allele and it is beneficial to crop breeding. In this study the GWAS method was used to analyze the datasets of 11-parent MAGIC population, but all GWAS methods consider only two alleles. Please explain why the multi-allele model did not use. RESPONSE: Gossypium hirsutum cultivars have limited genetic diversity and a narrow genetic base, especially when compared to other crops like Zea mays. In this population, within the 473,000 high quality SNPs, there are no multi-allelic SNPs. Now, the manuscript has been modified to highlight this fact. Further analysis to explore the utility of a multi-allelic analysis could be achieved by first identifying haplotype blocks or regions of identity-by-descent that are large enough to include enough polymorphic SNPs to define multiple alleles of each haplotype. So far, we have not found such, but we agree with the suggestion and will continue to explore multi-allele models in future work. 2. When the GWAS method was used to analyze the dataset of MAGIC population, please consider whether the population structure should be considered. These reasons may make your results difficult to understand. For example, the loci identified in linkage analysis are apart from the loci identified by PLINK and/or mrMLM. RESPONSE: This structure of this MAGIC population has been characterized several times. First with 1,600 SSR markers, then with 6,000 SNP markers, and again with the 473,000 SNPs identified by whole genome sequencing used in the present study. [Refs 31, 32, 28 in manuscript]. These all indicated that the five cycles of bulked-pollen random mating, followed by six generations of self-pollination, was successful at creating a population with no significant population structure. We hypothesize that the discrepancies between PLINK and mrMLM are due to the inherent difficulty in identifying the mechanism of a trait that is controlled by numerous small effect loci and synergistic epistatic interactions. Since none of the parent lines possess the flame resistance phenotype, elucidation of the mechanism is not straightforward. We believe that presenting the readers with the multiple genetic analyses, though some loci differ between the approaches, is more useful for the advancement of the research by the larger cotton research community than to stretch to reconcile them, at this point. Attachments Attachment Submitted filename: Response to Reviewers-Thyssen-08102022.docx https://doi.org/10.1371/journal.pone.0278696.r002
24 Oct 2022 Decision Letter - Yuan-Ming Zhang, Editor PONE-D-22-19253R1Flame resistant cotton lines generated by synergistic epistasis in a MAGIC populationPLOS ONE Dear Dr. Thyssen, 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 08 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. 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, Yuan-Ming Zhang 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. Additional Editor Comments: I have received one additional report. Some minor revision should be addressed. Look forward to receiving your further revision soon! [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) Reviewer #3: (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: (No Response) Reviewer #3: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: (No Response) 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 #2: (No Response) 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 #2: (No Response) 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 #2: (No Response) Reviewer #3: 1. Line 92: remove ref 31. 2. Line 159-162: can you explain more how you did linkage analyses using 4 RILs? It is an haplotype analyses to compare the 4 lines? 3. Line 249-254: In table S4, could you add those loci within a few Mb from PLINK or mrMLM? 4. Line 256-264: could you describe more about any of those 13 genes are potential candidates or consistent with any other published research? I understand that the flammable traits may not have may published results. Candidate for any traits highly correlated with it? You mentioned some in the discussion but you may want to explain more in the main text. 5. Line 290: using highest or lowest HRC values instead of worst. 6. Line 327: remove “Found among”, and “were lines that”. 7. Line 335: remove “already”. ****** 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: Yes: Shuyu Liu ******** [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. https://doi.org/10.1371/journal.pone.0278696.r003
Revision 2
8 Nov 2022 Author Response November 7, 2022 Dear Dr. Yuan-Ming Zhang, Reviewers and Editorial Board of PLOS ONE: I am submitting a twice revised manuscript for your consideration, titled, “Flame resistant cotton lines generated by synergistic epistasis in a MAGIC population.” [PONE-D-22-19253] We appreciate your time, consideration, and valuable comments. Below we have responded to each of the new comments and have made additional modifications to the manuscript to reflect your requests and suggestions. Sincerely, Gregory Thyssen, Ph.D. Computational Biologist Cotton Chemistry and Utilization Unit & Cotton Fiber Bioscience Unit USDA-ARS Reviewer #3: 1. Line 92: remove ref 31. >>Done. 2. Line 159-162: can you explain more how you did linkage analyses using 4 RILs? It is an haplotype analyses to compare the 4 lines? >>Added: “Analysis of the whole genome sequencing was used to identify these common haplotypes by comparing variant call files (VCF), that were generated by samtools and bcftools mpileup software, with bedtools intersect software [39]." 3. Line 249-254: In table S4, could you add those loci within a few Mb from PLINK or mrMLM? >>We have added a new Table S5 that includes all the RNAseq expression data for every annotated gene with any detectible expression (>0 RPKM) (N=41,746) in the 8 RILs at developmental stages of 8-DPA and 16-DPA. 4. Line 256-264: could you describe more about any of those 13 genes are potential candidates or consistent with any other published research? I understand that the flammable traits may not have may published results. Candidate for any traits highly correlated with it? You mentioned some in the discussion but you may want to explain more in the main text. >>The supplemental Tables S5-S10 contain the gene descriptions and identification of the Arabidopsis orthologs for the candidate genes, differentially expressed genes and all expressed genes. The first version of this manuscript did include more speculation in the discussion and main text about flavonoid biosynthesis genes among the candidates, (a pathway we previously found to be relevant in brown cotton with natural flame retardance) but the previous reviewers at PLOS One suggested that we reduce that speculation. 5. Line 290: using highest or lowest HRC values instead of worst. >>Done. 6. Line 327: remove “Found among”, and “were lines that”. >>Done. 7. Line 335: remove “already”. >>Done. Attachments Attachment Submitted filename: Response to Reviewers-Thyssen-11072022.pdf https://doi.org/10.1371/journal.pone.0278696.r004
22 Nov 2022 Decision Letter - Yuan-Ming Zhang, Editor Flame resistant cotton lines generated by synergistic epistasis in a MAGIC population PONE-D-22-19253R2 Dear Dr. Thyssen, 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, Yuan-Ming Zhang Academic Editor PLOS ONE Additional Editor Comments (optional): I have no further comments. 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) 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 #2: (No Response) Reviewer #3: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: (No Response) 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 #2: (No Response) 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 #2: (No Response) 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 #2: (No Response) Reviewer #3: (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 #2: No Reviewer #3: Yes: Shuyu Liu ******** https://doi.org/10.1371/journal.pone.0278696.r005
Formally Accepted
2 Dec 2022 Acceptance Letter - Yuan-Ming Zhang, Editor PONE-D-22-19253R2 Flame resistant cotton lines generated by synergistic epistasis in a MAGIC population Dear Dr. Thyssen: 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. Yuan-Ming Zhang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0278696.r006

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 .