Transcription profiles reveal sugar and hormone signaling pathways mediating tree branch architecture in apple (Malus domestica Borkh.) grafted on different rootstocks

Yanhui Chen; Xiuhong An; Deying Zhao; Enmao Li; Renpeng Ma; Zhuang Li; Cungang Cheng

doi:10.1371/journal.pone.0236530

Peer Review History

Original SubmissionApril 6, 2020
21 May 2020 Decision Letter - Haitao Shi, Editor PONE-D-20-09821 Transcription Profiles Reveal Sugar and Hormone Signaling Pathways Mediating Tree Branch Architecture in Apple (Malus domestica Borkh.) Grafted On Different Rootstocks PLOS ONE Dear Dr. Cheng, 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. We would appreciate receiving your revised manuscript by Jul 05 2020 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. 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We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: https://link.springer.com/article/10.1007/s00344-019-09933-w https://www.frontiersin.org/articles/10.3389/fpls.2017.00654/full https://www.cell.com/trends/plant-science/fulltext/S1360-1385(15)00288-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1360138515002885%3Fshowall%3Dtrue In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed. 3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ [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: No Reviewer #2: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: No Reviewer #2: No ****** 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: Transcription Profiles Reveal Sugar and Hormone Signaling Pathways Mediating Tree Branch Architecture in Apple (Malus domestica Borkh.) Grafted On Different Rootstocks The article by Chen et al. shown the branch growth phenotypes of three combinations of ‘Fuji’ apple trees grafted on different rootstocks (VR; DIR; DSR) were investigated through transcriptomic analysis. The study is interesting and will add more reference datasets to the currently available information. The approach to understand this into plant production could be helpful at large scale. In addition, the authors have performed several other analyses such as phytohomonal analysis through HPLC, and sugar related analytics. However, in current form the manuscript is suffering from severe issues of language, grammar, and typos. The rational in the introduction creates further lack of clarity of what the authors wants to achieve from this study. In addition to that the data represented in figure format lacks any statistical support. There must be in depth statistical analysis at least one-way ANOVA or t-test to identify significance. Furthermore, the most essential part is transcriptomics. The authors have not mentioned that how many real biological replicates were used to perform this work. The author must also mention that how many total reads were obtained for each replica or each VR, DIR, DSR. How much this data is correlative to the actual gene content of Apple’s genome. Furthermore, heatmap for each kind of gene network or regulatory cycle would not help the readers. Whilst keeping in mind the low resolutions of the figures such as 5, 6 and 7. These figures are also not explained properly in the results as well as in figure captions. In current state, most of gene expression results are explained as high or low, however, there must be p value with DEG files, that is essential to add to the text. Most of the heatmaps are not well explained in the results sections. How many genes were regulated (up or down) for example in case of transcriptional factors or hormones. Why there are no explanation for certain gene that were exponentially expressed. The validated qRTPCR results are vaguely explain. I think the author should see similar papers to see how this made reader friendly. The discussion part is weaker and need more emphasis on the results. Further, the methods should be rewritten to explicitly to allow reader to reproduce Reviewer #2: Line 28: rephrase the sentence. What are the many factors ? such as !! Lines 33-40: Rearrange the information, with proper citation for the facts declared in the statements. Poorly written and not explained well. Authors are trying to compare different rootstocks in their physiological traits, but not in proper order. Overall, entire introduction section is not conveying the message leading the rationale for this study. The authors should delineate the studies in most recent literature, and, co-relate to their present studies using the root stocks studied. Methods: Line 90-92: It’s not clear about the replicates used, whether 10 or 50 ? How many biological replicates and technical replicates used ? Line 99: Use ‘briefly’ and replace in subsequent places of the MS. Results section was well described. Discussion: Discussion needs to be improved and the entire content be rephrased. Line 284-286: Authors could include the figures to show differences in length of grafted plants of all rootstocks, although the data represented in table. Line 297-300: Does not give any novel information. Line 300-302: Provide meta-analysis of the data with the support of most recent studies to show how the co-relation can contribute. Overall discussion is very verbose and loaded with too much of basic information. The authors need to focus on the results observed in this study and directly discuss the relationship between the RNA seq data and the metabolites liking to the pathways. I suggest, authors divide this section in multiple subsections and discuss individual pathways affected among the various grafts. Conclusions: Line 432-434: This sentence is redundant. The conclusions are repetitive and superfluous. Please revise and provide the novel information about the research findings made in this study. ****** 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: Ramesh katam [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. https://doi.org/10.1371/journal.pone.0236530.r001
Revision 1
5 Jul 2020 Author Response PONE-D-20-09821 Transcription profiles reveal sugar and hormone signaling pathways mediating tree branch architecture in apple (Malus domestica Borkh.) grafted on different rootstocks Reviewers' comments: Reviewer #1: The article by Chen et al. shown the branch growth phenotypes of three combinations of ‘Fuji’ apple trees grafted on different rootstocks (VR; DIR; DSR) were investigated through transcriptomic analysis. The study is interesting and will add more reference data sets to the currently available information. The approach to understand this into plant production could be helpful at large scale. In addition, the authors have performed several other analyses such as phytohomonal analysis through HPLC, and sugar related analytics. However, in current form the manuscript is suffering from severe issues of language, grammar, and typos. (1) The rational in the introduction creates further lack of clarity of what the authors wants to achieve from this study. Response: Thanks for your kind suggestion. In this study, we intended to explore the molecular determinants of tree branch architecture growth regulation induced by vigorous rootstock (VR), dwarfing interstock (DIR), and dwarfing self-rootstock (DSR). We have reedited the introduction in the revised version (Lines 27-78). (2) In addition to that the data represented in figure format lacks any statistical support. There must be in depth statistical analysis at least one-way ANOVA or t-test to identify significance. Response: Yes, we have added the statistical analysis in Figures 1, 2, 3, and 9 in the revised version. (3) Furthermore, the most essential part is transcriptomics. The authors have not mentioned that how many real biological replicates were used to perform this work. The author must also mention that how many total reads were obtained for each replica or each VR, DIR, DSR. How much this data is correlative to the actual gene content of Apple’s genome. Response: Yes, we have explained the repetition of the experimental setup in the revised version (Lines 87-91). And we have explained two other issues in detail in the revised version (Lines 206-209). (4) Furthermore, heatmap for each kind of gene network or regulatory cycle would not help the readers. Whilst keeping in mind the low resolutions of the figures such as 5, 6 and 7. These figures are also not explained properly in the results as well as in figure captions. Response: Yes, the resolution of the pictures we upload is 600 dpi. It may be that the PDF generated by the system causes the picture to become blurred. There may be an option to view the original image on the peer review system. You can find it. Thank you very much for your kind understanding. In addition, we have added more explanation for these figures in the revised version. (5) In current state, most of gene expression results are explained as high or low, however, there must be value with DEG files, that is essential to add to the text. Most of the heatmaps are not well explained in the results sections. How many genes were regulated (up or down) for example in case of transcriptional factors or hormones. Response: Yes, the information of selected DEGs in leaves of apple trees on different rootstocks were shown in supporting Tables 4-6. And we have reedited the results sections in the revised version. (6) Why there are no explanation for certain gene that were exponentially expressed. The validated qRTPCR results are vaguely explain. I think the author should see similar papers to see how this made reader friendly. Response: Thanks for your kind advice. In our sequencing data, we did not find genes whose expression was up-regulated or down-regulated sharply, probably because the overall impact of grafting different rootstocks on fruit trees was a long-term slow process rather than a rapid process. We used quantitative PCR to verify the reliability of transcriptome sequencing data. The genes analyzed in Figure 9 are important functional genes and transcription factors discussed in the results section. Therefore, in the interpretation of Figure 9, we choose to use the form of simplified description. (7) The discussion part is weaker and need more emphasis on the results. Further, the methods should be rewritten to explicitly to allow reader to reproduce. Response: Yes, we have reorganized these contents in the revised version. Reviewer #2: (1) Line 28: rephrase the sentence. What are the many factors ? such as !! Response: Thank you for your kind suggestion. We have added the factors in the revised version (Lines 28-30). (2) Lines 33-40: Rearrange the information, with proper citation for the facts declared in the statements. Poorly written and not explained well. Authors are trying to compare different rootstocks in their physiological traits, but not in proper order. Response: Yes, we have rewritten these sentences in the revised version (Lines 33-39). (3) Overall, entire introduction section is not conveying the message leading the rationale for this study. The authors should delineate the studies in most recent literature, and, co-relate to their present studies using the root stocks studied. Response: Thanks for your kind advice. We have recited several recent references in the introduction section in the revised version. And we have delineated the reasons for why we studied Malus baccata and T337 rootstocks in the revised version (Lines 59-61, 75-76 ). (4) Line 90-92: It’s not clear about the replicates used, whether 10 or 50? How many biological replicates and technical replicates used ? Response: Thanks. We have explained the repetition of the experimental setup in the revised version (Lines 87-91). (5) Line 99: Use ‘briefly’ and replace in subsequent places of the MS. Response: Yes, we have replaced them in the revised version (Lines 96 and 107). (6) Results section was well described. Response: Thank you very much for your affirmation. Your comments have benefited us a lot. (7) Discussion: Discussion needs to be improved and the entire content be rephrased. Response: Thanks for your constructive suggestions. We have divided the discussion into three sections and rearranged the contents in the revised version (Lines 289-428). (8) Line 284-286: Authors could include the figures to show differences in length of grafted plants of all rootstocks, although the data represented in table. Response: Thanks for your advice. Figures could show the differences more clearly, but we did not save appropriate photos when sampling. So we can only use statistical data to explain the differences in tree growth. We are very sorry and hope to get your understanding. (9) Line 297-300: Does not give any novel information. Response: Yes, we have deleted these repeated sentences in the revised version. (10) Line 300-302: Provide meta-analysis of the data with the support of most recent studies to show how the co-relation can contribute. Response: We are sorry that this sentence was wrong. Our intention at that time was to say that the clustering of ‘glucose metabolism’ and ‘hormone signaling’ pathways was also significantly enriched in Figure 5. We are very sorry for the inconvenience caused by our mistake. Considering that these sentences are repetitive descriptions, we have deleted them in the revised version. If you feel that this modification is incorrect, we are very willing to revise it again. (11) Overall discussion is very verbose and loaded with too much of basic information. The authors need to focus on the results observed in this study and directly discuss the relationship between the RNA seq data and the metabolites liking to the pathways. I suggest, authors divide this section in multiple subsections and discuss individual pathways affected among the various grafts. Response: Yes, thanks for your constructive suggestions. We have divided the discussion into three sections and have deleted verbose contents in the revised version (Lines 289-428). (12) Conclusions: Line 432-434: This sentence is redundant. The conclusions are repetitive and superfluous. Please revise and provide the novel information about the research findings made in this study. Response: Yes, we have deleted these lines and reedited the conclusions in the revised version (Lines 429-436). Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0236530.r002
9 Jul 2020 Decision Letter - Haitao Shi, Editor Transcription profiles reveal sugar and hormone signaling pathways mediating tree branch architecture in apple (Malus domestica Borkh.) grafted on different rootstocks PONE-D-20-09821R1 Dear Dr. Cheng, 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, Haitao Shi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0236530.r003
Formally Accepted
13 Jul 2020 Acceptance Letter - Haitao Shi, Editor PONE-D-20-09821R1 Transcription profiles reveal sugar and hormone signaling pathways mediating tree branch architecture in apple (Malus domestica Borkh.) grafted on different rootstocks Dear Dr. Cheng: 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. Haitao Shi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0236530.r004

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