NP and 9311 are excellent population parents for screening QTLs of potassium-efficient rice

Tingchang Liu; Liangli Bai; Lifang Huang; Donghai Mao

doi:10.1371/journal.pone.0284510

Peer Review History

Original SubmissionSeptember 5, 2022
14 Mar 2023 Decision Letter - Rohit Joshi, Editor PONE-D-22-24710NP and 9311 are excellent population parents for screening QTLs of potassium-efficient ricePLOS ONE Dear Dr. Lifang Huang, 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 Apr 28 2023 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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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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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 by Liu et al. tested twelve high-yielding rice varieties for K efficiency under hydroponic conditions. The NP and 9311 were identified as tolerant and sensitive varieties in low potassium medium and recommended as potential parents for QTL screening based on their contrasting features. The paper consists of adequate originality, scientific quality, relevance to the field of this journal and presentation; therefore, it is suitable to publish after minor revision. My suggestion is as follows: 1. In the title of the manuscript, the authors mentioned NP and 9311 are excellent population parents for screening QTLs of K-efficient rice. Since I haven't seen any breakthrough in the QTL analysis, so I was very excited when I read the paper; however, I did not find any outcome regarding the QTLs identification. The recommendation was based only on the contrasting features of the NP and 9311 under variable K concentration. 2. In the plant materials section, the authors may incorporate some background details of the used varieties, such as origin, year of release, recommended soil type and zone for different varieties. 3. Check the spelling “lever” or “level” in the abstract. 4. Some references are missing or irregular in the text. In table 1, the author cited Ghomi et al. (2013) and YAO et al. (2005) but not indexed in the reference section. Likewise, the citation of the reference Ming-zhe et al. (2005) (lines 302-304) is missing in the manuscript’s text. Authors must follow the journal format for reference writing and could use the PLOS One template to prepare. ****** 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: Sarfraz Ahmad ******** [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. 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Revision 1
20 Mar 2023 Author Response Dear Editor: We do appreciate the time and effort you and the reviewers dedicated to providing feedback on our manuscript and are grateful for the insightful comments on our paper. We have tried to address all the raised concerns accordingly. All changes are highlighted. Here is a point-by-point response for all comments and concerns. Reviewer #1 This manuscript by Liu et al. tested twelve high-yielding rice varieties for K efficiency under hydroponic conditions. The NP and 9311 were identified as tolerant and sensitive varieties in low potassium medium and recommended as potential parents for QTL screening based on their contrasting features. The paper consists of adequate originality, scientific quality, relevance to the field of this journal and presentation; therefore, it is suitable to publish after minor revision. My suggestion is as follows: Question 1: In the title of the manuscript, the authors mentioned NP and 9311 are excellent population parents for screening QTLs of K-efficient rice. Since I haven't seen any breakthrough in the QTL analysis, so I was very excited when I read the paper; however, I did not find any outcome regarding the QTLs identification. The recommendation was based only on the contrasting features of the NP and 9311 under variable K concentration. Response: Population parents with significant phenotypic differences under low potassium levels were screened from 12 high-yield rice varieties in East Asia in this study, and a scientific and reliable method for phenotypic screening was established, which could publish as a phased result. As we know, exploring new genes in plant potassium-efficient and analyzing its mechanism are hot topics in current research, and different research teams are very competitive in this field. Based on the parents and screening methods established in our lab, we use NP as the donor parent and 9311 as the recipient parent to construct the introversion line population, and we will use the established method to identify the low potassium tolerance of the progeny lines. As the selected parents are rare combinations, it is very promising to locate the QTLs sites different from those of previous generations. We hope that later research results will be published in the journal. Question 2: In the plant materials section, the authors may incorporate some background details of the used varieties, such as origin, year of release, recommended soil type and zone for different varieties. Response: We have rewritten the Plant materials section and added the information about the 12 rice varieties used in this paper， such as origin, year of release, recommended soil type and zone for different varieties as marked with blue color. Related to this, we add the following references as marked with green color: 30. Jianhua L, Zhihai Y, Zhongyi N, Maosong H. Characteristics and key cultivation techniques of Wuyuning 8. ChinaRice. 1999;3(15). 31. Ziming W, Jiangshi Z, Weixiang Z, Chengkuan C, Guiyuan Z, Xiaolu S. Breeding of new wide compatibility strains of japonica rice. Selective Breeding. 1990:32-6. https://doi.org/10.16267/j.cnki.1005-3956 32. Chun-xiu S, Zi-lei Y, Zhi-qun Q. Physiological and Morphological Responses of the Rice TP309 to Short － term Cadmium Stress. Journal of Yichun University. 2019;41(12):5-9. 34. Gui-mao Y. A new medium rice variety Teqing No. 1 with high yield and disease resistance was successfully planted. Technology in Brief 1995:33. https://doi.org/10.14088/j.cnki.issn0439.8114 35. Shicheng L, Shao-kai M. Rice varieties and their pedigrees in China. Shanghai Science and Technology Press. 1991;(24). 36. Xiaonian W, Qiuping Y, Changming X, Chuanyong W, Linli Z. Breeding and cultivation techniques of a new two-line hybrid early rice combination 'Lingliangyou 193'. South China Agriculture. 2015;9(6):1-2. https://doi.org/10.19415/j.cnki.1673-890x Question 3: Check the spelling “lever” or “level” in the abstract. response: We sincerely thank the reviewer for careful reading. As suggested by the reviewer, we have corrected the “lever” into “level” in revised version of the manuscript as marked with red color. Question 4: Some references are missing or irregular in the text. In table 1, the author cited Ghomi et al. (2013) and YAO et al. (2005) but not indexed in the reference section. Likewise, the citation of the reference Ming-zhe et al. (2005) (lines 302-304) is missing in the manuscript’s text. Authors must follow the journal format for reference writing and could use the PLOS One template to prepare. Response: Thank you for pointing this out. We have changed the citation format of YAO et al. (2005) and Ming-zhe et al. (2005) (lines 302-304) as marked with purple color, and added the citation as marked with yellow color: 11. Ghomi K, Rabiei B, Sabouri H, Sabouri A. Mapping QTLs for traits related to salinity tolerance at seedling stage of rice (Oryza sativa L.): an agrigenomics study of an Iranian rice population. OMICS. 2013;17(5):242-51.https://doi.org/10.1089/omi.2012.0097 PMID:23638881 Attachments Attachment Submitted filename: Response to Reviewers.doc https://doi.org/10.1371/journal.pone.0284510.r002
3 Apr 2023 Decision Letter - Rohit Joshi, Editor NP and 9311 are excellent population parents for screening QTLs of potassium-efficient rice PONE-D-22-24710R1 Dear Dr. Lifang Huang, 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, Rohit Joshi, 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 ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: (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 #1: Yes: Sarfraz Ahmad ******** https://doi.org/10.1371/journal.pone.0284510.r003
Formally Accepted
6 Apr 2023 Acceptance Letter - Rohit Joshi, Editor PONE-D-22-24710R1 NP and 9311 are excellent population parents for screening QTLs of potassium-efficient rice Dear Dr. Huang: 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. Rohit Joshi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0284510.r004

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