Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars

Shigeo Takumi; Seito Mitta; Shoya Komura; Tatsuya M. Ikeda; Hitoshi Matsunaka; Kazuhiro Sato; Kentaro Yoshida; Koji Murai

doi:10.1371/journal.pone.0228397

Peer Review History

Original SubmissionNovember 14, 2019
5 Dec 2019 Decision Letter - Aimin Zhang, Editor PONE-D-19-31756 Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars PLOS ONE Dear Dr. Takumi, 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 Jan 19 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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Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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: Breeding early heading wheat cultivars could help to advance the harvest time to avoid the rainy season in Japan. Introducing the genes/QTLs in wheat relatives controlling early heading into common wheat is a effective method to improve the heading time. In this study, nine early heading lines possibly harboring the early heading-date genes from Aegilops were developed. Their agricultural traits, kernel traits and quality traits were measured and compared with their parental cultivars. RNA sequencing-based genotyping was also conducted to detect SNP between these nine lines and their parents. The results indicated that the chromosomal regions transmitted from the parental synthetic wheat might shorten the heading date. However, there still are a few points I would like to see addressed: 1.Please clarify the primers information used in this study. 2.Please unify the font size in Tables and all the manuscript. 3.Please unify the decimal reservation. Reviewer #2: The authors selected nine early heading wheat lines from the the progeny of of synthetic hexaploid wheat (AABBDD, derived from hybrid of durum wheat with Aegilops tauschii) crossed with four elite cultivars. The lines selected are useful for the improvement of early heading wheat cultivars. The manuscript was well written and organized. However, the lines used in the study were derived from only two or three times backcross with elite wheat cultivars. It's very difficult to distinguish the genes related to the early heading traits of the derived lines were from Ae. tauschii or the recombination or gene interactions between elite wheat and durum wheat, and it is proved by the fact that no shared sub-genomic D regions detected in those lines from the same cross in this study. More times backcross (>5 times) should be applied to determine D chromosomes regions related to early heading. By the way, early heading is controlled by QTLs, the chance using major gene controlling the heading date leading to overlap of the harvesting time should be few. ****** 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. https://doi.org/10.1371/journal.pone.0228397.r001
Revision 1
20 Dec 2019 Author Response Dear Editors and reviewers, Thank you very much for the reviewers’ kind comments and suggestions to our manuscript. We examined all of the comments, and revised our manuscript according to the comments as followed. Improved sentences and words were marked by red color in text and tables. In addition, we improved the format of our manuscript to fit the PLoS ONE’s style requirements. To Reviewer #1, Thank you very much for your kind review and polite comments. 1. Please clarify the primers information used in this study. <response> We made a supplementary table for the primer list and PCR conditions. 2. Please unify the font size in Tables and all the manuscript. <response> We improve the font size in Tables to 12 point. 3. Please unify the decimal reservation. <response> We improved Table 2 to unify the decimal reservation. To Reviewer #2, Thank you very much for your polite comments. 1. The lines used in the study were derived from only two or three times backcross with elite wheat cultivars. It's very difficult to distinguish the genes related to the early heading traits of the derived lines were from Ae. tauschii or the recombination or gene interactions between elite wheat and durum wheat, and it is proved by the fact that no shared sub-genomic D regions detected in those lines from the same cross in this study. More times backcross (>5 times) should be applied to determine D chromosomes regions related to early heading. <response> The objective of this research is not production of near-isogenic lines for wheat minor QTLs. As described in Introduction, this research is trial to establishment of early heading lines selected based on their phenotype and to determine the commonly shared chromosomal segments from their parental synthetic wheat hexaploid. We determined the parental synthetic wheat-derived chromosomal regions commonly shared in the selected lines. Based on the results, we discussed relationship between the chromosomal regions and presence of the QTLs for heading date in Discussion by referring to previously published reports. Surely, further researches should be required to clarify whether the identified chromosomal regions in fact control the heading date. Therefore, we added a following sentence in the fifth paragraph of Discussion; ‘Further studies to produce near isogenic lines of each minor QTL and to narrow down the introgression regions should be required to identify the causal genes for these QTLs’. 2. By the way, early heading is controlled by QTLs, the chance using major gene controlling the heading date leading to overlap of the harvesting time should be few. <response> We agree with the reviewer’s opinion. So, we think that the phenotype-based selection is important to produce early heading lines with some or several days-earliness especially via minor QTLs. Now, we can analyze the whole-genome genotypes using the next generation to identify easily the introgression regions from the parental wild wheat relatives. We think that this point is important in this study as described in Discussion. We believe that the revised manuscript is now suitable for publication. We look forward to hearing from you at your earliest convenience. Yours sincerely, Shigeo Takumi (Corresponding author) Attachments Attachment Submitted filename: ResponseToReviewer-Takumi et al-Dec19.docx https://doi.org/10.1371/journal.pone.0228397.r002
15 Jan 2020 Decision Letter - Aimin Zhang, Editor Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars PONE-D-19-31756R1 Dear Dr. Takumi, 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. 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With kind regards, Aimin Zhang, Ph.D. 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 #1: All comments have been addressed Reviewer #2: 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 #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 #1: Yes Reviewer #2: 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 #1: Yes Reviewer #2: 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 #1: The authors have adequately addressed my comments raised in a previous round of review, I have no addittional comments for the authors. and I feel that this manuscript is now acceptable for publication. Reviewer #2: The authors has made responses to all my questions and concerns. The manuscript has been carefully reversed. No more comments. ****** 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 #1: Yes: Tao Wang Reviewer #2: No https://doi.org/10.1371/journal.pone.0228397.r003
Formally Accepted
17 Jan 2020 Acceptance Letter - Aimin Zhang, Editor PONE-D-19-31756R1 Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars Dear Dr. Takumi: 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 Prof. Aimin Zhang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0228397.r004

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