Developing functional markers for vitamin E biosynthesis in oil palm

Yajing Dou; Wei Xia; Annaliese S. Mason; Dongyi Huang; Xiwei Sun; Haikuo Fan; Yong Xiao

doi:10.1371/journal.pone.0259684

Peer Review History

Original SubmissionJuly 13, 2021
23 Sep 2021 Decision Letter - Maoteng Li, Editor PONE-D-21-22518Developing functional markers for vitamin E biosynthesis in oil palmPLOS ONE Dear Dr. Xiao, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Nov 07 2021 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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If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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 (if provided): [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: Yes 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: 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: The authors discovered an impressive research, which showing twenty oil palm accessions with distinct variation of vitamin E contents (171.30 to1258.50 ppm), leading to the identification of 37 candidate genes involved in vitamin E biosynthesis in oil palm by using the known protein sequences of A. thaliana and Z. mays. Multiplex PCR sequencing for the 37 genes found 1703 SNPs and 85 indels among the 20 oil palm accessions, with 226 SNPs located in coding regions. This study identified a number of candidate function associated markers and provided clues for further research into molecular breeding for high vitamin E content oil palm. The results look quite promising. The statistical methods used in the study are good. The language and organization of paper are standardized. I would like to recommend to accept this manuscript. Thank you. Reviewer #2: In the manuscript “Developing functional markers for vitamin E biosynthesis in oil palm”， the authors have detected 37 candidate genes associated with vitamin E synthesis in oil palm. The genes were sequenced and 134 SNPs and 7 indels were identified as functional markers that correlated with total vitamin E content. The molecular biology parts all sound. However, some revisions are still required before publication 1. The English need be edited 2. The raw data need be uploaded into the public database. 3. Line 47 change “Besides this” to “Besides” 4. Line 49 “which make palm oil be beneficial” should delete “…be..” 5. Line 63 “Such molecular markers, which are derived from polymorphic sites within genes causally involved in phenotypic trait variation, are known as functional markers and are highly efficient in marker-assisted selection”, This sentence is confusing, could you change it? 6. Line 67 “and other approaches described elsewhere” you don’t need this. Line 139 “similar sequences of potentially homologous genes in oil palm.” Delete “similar” here because you already mentioned the cut off value. 7. Line 257 “number of exons” change to “amount of exons” 8. Line 258 “same intron and exon number” change to “same amount of intron and exon” 9. Line 270 delete “each of” 10. Line 301 “each gene” change to “every gene”, there are some other lines with the same problem. 11. Line 321 ” Groups IV and V included two oil palm accessions each and averaged” change to “Both of group IV and V included two oil palm accessions and have an average of …” ****** 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: Dan Qiu Reviewer #2: Yes:** LI Dongdong [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.0259684.r001
Revision 1
11 Oct 2021 Author Response Dear editors and reviewers, Thank you very much for your comments and suggestions concerning our manuscript entitled “Developing functional markers for vitamin E biosynthesis in oil palm” (PONE-D-21-22518). Those comments are valuable and very helpful. We have made revisions according to reviewers’ comments carefully. Each comment raised by the editors and reviewers has been answered in the response sheet. I hope the revised version meets the requirements of “Plos One”. Details of how the comments have been addressed are prefixed by “>>>Response:” below the query to which they relate. Reviewer #1: The authors discovered an impressive research, which showing twenty oil palm accessions with distinct variation of vitamin E contents (171.30 to1258.50 ppm), leading to the identification of 37 candidate genes involved in vitamin E biosynthesis in oil palm by using the known protein sequences of A. thaliana and Z. mays. Multiplex PCR sequencing for the 37 genes found 1703 SNPs and 85 indels among the 20 oil palm accessions, with 226 SNPs located in coding regions. This study identified a number of candidate function associated markers and provided clues for further research into molecular breeding for high vitamin E content oil palm. The results look quite promising. The statistical methods used in the study are good. The language and organization of paper are standardized. I would like to recommend to accept this manuscript. Thank you. >>>Response：Thank you for your comments. We really appreciate your efforts in reviewing our manuscript. Thank you again for agreeing to accept our manuscript. Reviewer #2: In the manuscript “Developing functional markers for vitamin E biosynthesis in oil palm”, the authors have detected 37 candidate genes associated with vitamin E synthesis in oil palm. The genes were sequenced and 134 SNPs and 7 indels were identified as functional markers that correlated with total vitamin E content. The molecular biology parts all sound. However, some revisions are still required before publication. >>>Response：Thank you for your summary. We have revised the manuscript accordingly. Our point-by-point responses are listed below. 1. The English need be edited >>>Response：Thank you for your suggestion. We have revised the manuscript carefully to improve the grammar and readability. The changes will not influence the content and framework of the manuscript and all the changes were marked in the revised manuscript. 2. The raw data need be uploaded into the public database. >>>Response：Thank you for your suggestion. The raw datas of multiple PCR sequencing of 20 oil palm individuals have been uploaded to European Nucleotide Archive (accession number is PRJEB38216, https://www.ebi.ac.uk/ena/browser/view/PRJEB38216). Meanwhile, the raw short reads datas of 24 transcriptomes (eight sample and three biological replicates) are aslo available in this database (accession number is PRJEB38102, https://www.ebi.ac.uk/ena/browser/view/PRJEB38102). 3. Line 47 change “Besides this” to “Besides” >>>Response：Thank you for your suggestion. We have changed “Besides this” to “Besides anti-oxidant” in the revised manuscript. 4. Line 49 “which make palm oil be beneficial” should delete “…be..” >>>Response：Thank you for your suggestion. We have deleted the word “be” in this sentence in the revised manuscript. 5. Line 63 “Such molecular markers, which are derived from polymorphic sites within genes causally involved in phenotypic trait variation, are known as functional markers and are highly efficient in marker-assisted selection”, This sentence is confusing, could you change it? >>>Response：Thank you for your suggestions. We have changed this sentence as “Polymorphic sites within genes that are related to trait variation could be used to develop functional markers, which are beneficial to marker-assisted selection” in the revised manuscript. 6. Line 67 “and other approaches described elsewhere” you don’t need this. Line 139 “similar sequences of potentially homologous genes in oil palm.” Delete “similar” here because you already mentioned the cut off value. >>>Response：Thank you for your suggestions. We have deleted the sentence “and other approaches described elsewhere” and the related references. We have changed the sentence “similar sequences of potentially homologous genes in oil palm” as “the best-hit homologous genes in oil palm” in the revised manuscript. 7. Line 257 “number of exons” change to “amount of exons” >>>Response：Thank you for your suggestion. We have changed “number of exons” to “amount of exons” in the revised manuscript. 8. Line 258 “same intron and exon number” change to “same amount of intron and exon” >>>Response：Thank you for your suggestion. We have changed “same intron and exon number” to “same amount of introns and exons” in the revised manuscript. 9. Line 270 delete “each of” >>>Response：Thank you for your suggestion. We have changed the sentence “The functional domains were analyzed for each of the 37 candidate genes. All…” as “The functional domains analysis demonstrated that most candidate…” in the revised manuscript. 10. Line 301 “each gene” change to “every gene”, there are some other lines with the same problem. >>>Response：Thank you for your suggestion. We have corrected “each gene” as “every gene” in the revised manuscript. 11. Line 321 “Groups IV and V included two oil palm accessions each and averaged” change to “Both of group IV and V included two oil palm accessions and have an average of …” >>>Response：Thank you for your suggestion. We have changed “Groups IV and V included two oil palm accessions each and averaged” to “Both of group IV and V included two oil palm accessions and have an average of …” in the revised manuscript. Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0259684.r002
25 Oct 2021 Decision Letter - Maoteng Li, Editor Developing functional markers for vitamin E biosynthesis in oil palm PONE-D-21-22518R1 Dear Dr. Xiao, 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, Maoteng Li Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0259684.r003
Formally Accepted
11 Nov 2021 Acceptance Letter - Maoteng Li, Editor PONE-D-21-22518R1 Developing functional markers for vitamin E biosynthesis in oil palm Dear Dr. Xiao: 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. Maoteng Li Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0259684.r004

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