Phenotypic quantification of root spatial distribution along circumferential direction for field paddy-wheat

Xinxin Chen; Yongli Tang; Qingfei Duan; Jianping Hu

doi:10.1371/journal.pone.0279353

Peer Review History

Original SubmissionJune 5, 2022
17 Aug 2022 Decision Letter - Umair Ashraf, Editor PONE-D-22-15992Phenotyping for circumferential expansion of field paddy-wheat root system architecturePLOS ONE Dear Dr. Hu, 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. The reviewers raised some concerns about the manuscript that must be addressed. Authors are advised to carefully revise the manuscript and address all the concerns of the reviewers and submit a revised version. Please submit your revised manuscript by Oct 01 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. 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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. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. Additional Editor Comments: The reviewers raised some concerns about the manuscript that must be addressed. Authors are advised to carefully revise the manuscript and address all the concerns of the reviewers and submit a revised version. [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: Partly Reviewer #3: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: 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 Reviewer #3: 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 Reviewer #3: 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: The manuscript has been wisely put together with very clear vision and results. The use of figures is very intelligent. Overall it reflects a strong scientific research article. The manuscript has a clear description of results with extensively defined figures. Reviewer #2: overall the manuscript is well written but major revision requires. it will be accepted after revision. NO novelty statement was nor provided and some statistical error in your manuscript. result and material method was written well. Reviewer #3: The present manuscript entitled as “Phenotyping for circumferential expansion of field paddy-wheat root system architecture” describes the findings of a field experiment on wheat under three fertilization rates and provided some new parameters to quantify the dynamics of the root system architecture along its orientations divided into eight parts with visualization technology that consists of root in situ samplings. Authors collected plant samples during growing season 2019-20. The research idea and objectives are unique and research methodology is well organized according to the objectives. However, there are some flaws and drawbacks in the present version of article. The manuscript is poorly written, there are some sentences which are not meaningful or don’t make any clear sense for the readers. So, I recommend that the current version of the submitted manuscript should be very carefully revised and upgraded. After critical and major revision in the writings, I recommend to accept this manuscript. I also, have some other major concerns which are appended below: Line 4: you used the word “hidden half” in abstract, does it indicates roots? If so then it’s better to use roots to make the sentence easy to understand. Line 11: It is not clear whether you conducted research on paddy and wheat or on wheat alone that was grown in paddy soil, make it clear. You didn’t mention Nitrogen fertilizer rate used in you treatments? Lines 11-12: You mentioned in manuscript that “we provided five new to quantify the dynamics of the root system architecture”; what did you provide new? Line 20: you didn’t mention nitrogen rate and you stated about N70 and N130 nitrogen treatment in your results, provide treatment details clearly. Line 49-51: clearly state about “angle”. Line 63: what do you mean by “Depth50 and Width50”? Line 89-90: Provide country name as well. Replace light with sunlight. Provide groundwater level if possible. Line 93-94: Make this sentence grammatically correct. Line 134-135: You didn’t mention three nitrogen rate in methodology, provide clear details of your treatments? Line 179: Check and correct spellings Line 201: Check and correct the formula. Line 234: Use superscript for mm and do same for all manuscript. Line 255-256: Provide space between words and parenthesis, do same for all manuscript. Line 351: What new indicators did you observe, write those. ****** 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: Reviewer #3: 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. Attachments Attachment Submitted filename: comments_PlosOne.docx https://doi.org/10.1371/journal.pone.0279353.r001
Revision 1
4 Oct 2022 Author Response Dear editor, Thank you very much for providing me the opportunity to revise the manuscript. We have revised the above-mentioned manuscript carefully according to the comments from the Journal and reviewers. The responses to the Journal’ requirements and reviewer’s comments and changes made are listed as follows: Journal’s Requirement 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 Responses and Changes Made: According to the PLOS ONE's style requirements, we have changed the article structure consist of abstract, introduction, materials and methods, results, discussion into abstract, introduction, materials and methods, results and discussion, conclusion. And the title_authors_affiliations were also modified in title page as required. Journal’s Requirement 2: In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Responses and Changes Made: According to the PLOS ONE's data requirements, we rewritten it in the part of the materials and methods marked with blue font (Line 135-138), also we rearranged all the relevant data and put them in the Supporting Information files (S1 Data). Reviewer #1 Comment of reviewer 1: The manuscript has been wisely put together with very clear vision and results. The use of figures is very intelligent. Overall it reflects a strong scientific research article. The manuscript has a clear description of results with extensively defined figures. Responses and Changes Made: Thanks very much for the comments of the reviewer. We will continue to work hard to present our future studies in a scientific, understandable and wise way. We hope readers in this field or other fields all can get some useful information from it. Reviewer #2 Comment 1 of Reviewer 2: overall the manuscript is well written but major revision requires. it will be accepted after revision. NO novelty statement was nor provided and some statistical error in your manuscript. result and material method was written well. The manuscript titled “Phenotyping for circumferential expansion of field paddy-wheat root systemarchitecture” emphasize on wheat root system with reference to circumferential orientations. Using three fertilization rates and experiment was designed to quantify dynamic root system architecture (RSA). With field root in situ samplings and RSA digitization, authors findings are presented in this manuscript. Introduction and material method section is written well. In result section table-2, last column is not understandable, either it is p-value or t-value. If it is p-value, that is non-significant and if it is p-value that is also non-significant. Without clarification of this aspect, this table is not able to be published. Responses and Changes Made: According to the reviewer’s comments, we revised Table 2 marked in blue font and listed the average value and coefficient of variation of each indicator as the comparison object, then we constructed the relationship function between different nitrogen application rates. The P value was not listed, but where there were significant differences, the asterisk (p<0.05) or double asterisk (p<0.01) was used to mark the corresponding R² value, and we put the data in the Supporting Information files (S2 Data). Comment 2 of Reviewer 2 Variation has not been well explained in reference to p-value, confidence level etc; so under these condition, such results are unacceptable. Author should justify the results with p-value using analysis of variance models. Responses and Changes Made: According to the reviewer’s comments, we analyzed the novel indicators with p-value using One-factorial ANOVA and justified the results in the part of Results and discussions marked with blue font (Line363-370 ). Comment 3 of Reviewer 2 In line # 243, author mentioned one-factorial anova, but I could not see that in table with p-value. Responses and Changes Made: According to the reviewer’s comments, we illustrated p<0.05 and p<0.01 with an asterisk and double asterisk, respectively ( Table 1 and Table 2). Comment 4 of Reviewer 2 The overall conclusion of the study is missing and describe the novelty of your research .Under such conditions, this study is not publishable unless the above mentioned suggestions are addressed properly. Responses and Changes Made: According to the reviewer’s comments, we supplemented the conclusion in which we described the novelty of our research in the part of the Conclusions marked with blue font (Line 376-393). Reviewer #3 Comment 1 of Reviewer 3: The present manuscript entitled as “Phenotyping for circumferential expansion of field paddy-wheat root system architecture” describes the findings of a field experiment on wheat under three fertilization rates and provided some new parameters to quantify the dynamics of the root system architecture along its orientations divided into eight parts with visualization technology that consists of root in situ samplings. Authors collected plant samples during growing season 2019-20. The research idea and objectives are unique and research methodology is well organized according to the objectives. However, there are some flaws and drawbacks in the present version of article. The manuscript is poorly written, there are some sentences which are not meaningful or don’t make any clear sense for the readers. So, I recommend that the current version of the submitted manuscript should be very carefully revised and upgraded. After critical and major revision in the writings, I recommend to accept this manuscript. I also, have some other major concerns which are appended below: Responses and Changes Made: According to the reviewer’s comments, the manuscript has been revised upgraded carefully, especially for writings. We also discussed it with a foreign assistant professor to reduce its writing problems and improve the readability. We did not to mark the above changes with colored fonts, because the whole article has been modified. For other concerns, we have made corresponding modifications and marked with blue font. Comment 2 of Reviewer 3: Line 4: you used the word “hidden half” in abstract, does it indicates roots? If so then it’s better to use roots to make the sentence easy to understand. Responses and Changes Made: According to the reviewer’s comments, we have revised "hidden half" with roots in the abstract for the word “hidden half” in abstract indicates roots, and the modified part was marked with blue font (Line 4). Comment 3 of Reviewer 3: Line 11: It is not clear whether you conducted research on paddy and wheat or on wheat alone that was grown in paddy soil, make it clear. You didn’t mention Nitrogen fertilizer rate used in you treatments? Responses and Changes Made: According to the reviewer’s comments, to clarify this problem, we illustrated it in the parts of the Materials and methods (Line 100-103) that we conducted the research on wheat alone grown in paddy soil. For the Nitrogen fertilizer rate used in our treatments, we also revised it in the parts of the Materials and methods (Line 108-111). And the modified part was marked with blue font. Comment 4 of Reviewer 3: Lines 11-12: You mentioned in manuscript that “we provided five new to quantify the dynamics of the root system architecture”; what did you provide new? Responses and Changes Made: According to the reviewer’s comments, we concluded it in the part of the Results and Discussions (Line 327-335) and Conclusions (Line376-388) marked with blue font. In short, the new indicators come from a new analysis angle combined with previous root research methods and quantitative indicators. Comment 5 of Reviewer 3: Line 20: you didn’t mention nitrogen rate and you stated about N70 and N130 nitrogen treatment in your results, provide treatment details clearly. Responses and Changes Made: According to the reviewer’s comments, we supplied the treatments of nitrogen fertilizer rates in detail in the parts of the Materials and methods marked with blue font (Line 108-111), shown as “Before sowing, the application of diammonium phosphate was 375 kg∙hm2, potassium chloride was 375 kg∙hm2, and the applications of urea were 70 kg∙hm2, 100 kg∙hm2 and 130 kg∙hm2, which represented the three N application rates and were named N70, N100, and N130 respectively.” Comment 6 of Reviewer 3: Line 49-51: clearly state about “angle”. Responses and Changes Made: According to the reviewer’s comments, we changed the angles into the root growth angles (Line 49-51) stated clearly in Line 38-41, which marked with blue font. The angle used in the manuscript implies the root growth angle between the root growth direction and the horizontal plane. Comment 7 of Reviewer 3: Line 63: what do you mean by “Depth50 and Width50”? Responses and Changes Made: According to the reviewer’s comments, we revised this problem and deleted it because it indicates a lack of use. The Depth50 and Width50 represent the vertical and horizontal centroids of root distribution, respectively [Teramoto S and Uga Y, 2020]. Comment 8 of Reviewer 3: Line 89-90: Provide country name as well. Replace light with sunlight. Provide groundwater level if possible. Responses and Changes Made: According to the reviewer’s comments, we provided the country name and replaced light with sunlight marked with blue font (Line 89-90). However, we did not find the groundwater level of this area in the authoritative data, so we did not supplement the data on the groundwater level. Comment 9 of Reviewer 3: Line 93-94: Make this sentence grammatically correct. Responses and Changes Made: According to the reviewer’s comments, we changed this sentence into “In the field, the rice-wheat rotation period is long, and a relatively hard plow bottom layer has formed at a depth of 10-12 cm soil layer due to alternating floods and droughts and mechanized operation.” Marked with blue font (Line 92-95). Comment 10 of Reviewer 3: Line 134-135: You didn’t mention three nitrogen rate in methodology, provide clear details of your treatments? Responses and Changes Made: According to the reviewer’s comments, we provided the three nitrogen fertilizer rate in detail in the parts of the Materials and methods marked with blue font (Line 108-111). Comment 11 of Reviewer 3: Line 179: Check and correct spellings Responses and Changes Made: According to the reviewer’s comments, we checked and corrected the “Convsex ” with “Convex” marked with blue font (Line 181). Comment 12 of Reviewer 3: Line 201: Check and correct the formula. Responses and Changes Made: According to the reviewer’s comments, we checked and corrected the “* ” with “x” in the formula (Line 203). Comment 13 of Reviewer 3: Line 234: Use superscript for mm and do same for all manuscript. Responses and Changes Made: According to the reviewer’s comments, we used superscript for mm and checked and did the same for all the manuscript. Comment 14 of Reviewer 3: Line 255-256: Provide space between words and parenthesis, do same for all manuscript. Responses and Changes Made: According to the reviewer’s comments, we provided space between words and parenthesis, and checked and did the same for all the manuscript. Comment 15 of Reviewer 3: Line 351: What new indicators did you observe, write those. Responses and Changes Made: According to the reviewer’s comments, we introduced them in the part of the Materials and methods (Line 166-204) and concluded them in the part of the Abstract (Line 11-22) and the Conclusions (Line 376-393). Changes made above were marked with blue font. We provided five new indicators (PRVP, CHARVP, WDRRSP, PRHP and RLSS) to quantify the dynamics of the root system architecture (RSA) along its eight-part circumferential orientations with visualization technology. And the visualization technology consists of in-situ field root samplings, RSA digitization, and reconstruction according to previous research. In short, the new indicators come from a new analysis angle combined with previous root research methods and quantitative indicators. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0279353.r002
2 Nov 2022 Decision Letter - Sudeshna Bhattacharjya, Editor PONE-D-22-15992R1Phenotyping for circumferential expansion of field paddy-wheat root system architecturePLOS ONE Dear Dr. Jianping Hu, Thank you for submitting your revised manuscript to PLOS ONE. Reviewers are optimistic about your manuscript, however some minor revisions are still required before the manuscript can be accepted for publication. Therefore, we invite you to submit a revised version of the manuscript having addressed the points raised during the review process along with a rebuttal letter. Looking forward to receive the revised manuscript soon. ============================== For Lab, Study and Registered Report Protocols: These article types are not expected to include results but may include pilot data. ============================== Please submit your revised manuscript by Dec 17 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, Sudeshna Bhattacharjya, Ph.D 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 (if provided): Dear Jianping Hu [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: All comments have been addressed Reviewer #4: 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: Yes Reviewer #4: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes Reviewer #4: 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: Yes Reviewer #4: 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: Yes Reviewer #4: 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: appreciation for authors that they incorporate all the objection carefully. This is strong enough to meet the potential to be published. i strongly recommended the publication of this paper Reviewer #4: • I have gone through the whole manuscript very thoroughly and found that the author has written it very extensively and descriptively. • The title should be reframed as it looks like a simple sentence. It should be catchy, attractive and reflective of the research hypothesis. • The abstract was written very scantily. It should be required. Therefore, please rewrite the abstract with proper hypotheses, the origin of study with clear-cut objectives, a brief methodology, and finally, results with proper justification and clarity. • The amount of rainfall received during the experimental period was important in determining crop growth and development, and no irrigation was provided during the growing seasons. You have mentioned that plant roots are essential for water and nutrient absorption, anchoring, mechanical support, metabolite storage, and interaction with the surrounding soil environment. As a result, I believe that water budgeting is necessary to justify the hypothesis because water is an important factor that influences root growth and development in field conditions. • Figure quality may be improved for more clarity. • The conclusion is very condensed; there is scope to improve it briefly as per the salient achievement of the study. Hence, it can be elaborated with final recommendations. ****** 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 #4: Yes: Dr Bharat Prakash Meena ******** [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.0279353.r003
Revision 2
14 Nov 2022 Author Response Dear editor, Thank you very much for providing me the opportunity to revise the manuscript again. We have revised the above-mentioned manuscript carefully according to the comments from the Journal and reviewers. The responses to the Journal’ requirements and reviewer’s comments and changes made are listed as follows: 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. Responses and Changes Made: According to the Journal’s requirements, we reviewed our reference list and found that the reference No. 68 has gone on the journal’s website (Chen J, Wang P, Ma ZM, Lyu XD, Liu TT, Siddique KHM. Optimum water and nitrogen supply regulates root distribution and produces high grain yields in spring wheat (Tritium aestivum L.) under permanent raised bed tillage in arid northwest China. Soil Till Res. 2018; 181:117-126.). So we removed and replaced it with a relevant current reference, also modified the corresponding context in the manuscript marked with the blue font (L361-363, Line 580-583). Reviewer #2 Comment of reviewer 2: Appreciation for authors that they incorporate all the objection carefully. This is strong enough to meet the potential to be published. i strongly recommended the publication of this paper Responses and Changes Made: Thanks very much for the comments and valuable suggestions of the reviewer for improving this manuscript. We are all glad that our manuscript revision has satisfied the reviewer. Reviewer #4: Comment 1 of Reviewer 4: I have gone through the whole manuscript very thoroughly and found that the author has written it very extensively and descriptively. Responses and Changes Made: We agree with the reviewer’s comments, and we hypothesize that the indicators describing the characteristics of root system architecture still need to be supplemented. Taking the root system of field paddy-wheat as the research object, we propose five new indicators characterizing the root spatial distribution characteristics along the circumferential directions based on the previous research methods. And the test results show that the newly proposed indicators can quantitatively describe the characteristics of spatial root distribution along the circumferential directions. However, as we mentioned in the conclusion, fewer samples, only one year of the experiment, and only one wheat variety are shortcomings in writing it very affirmatively and specifically. Comment 2 of Reviewer 4: The title should be reframed as it looks like a simple sentence. It should be catchy, attractive and reflective of the research hypothesis. Responses and Changes Made: According to the reviewer’s comments, we changed the title “Phenotyping for circumferential expansion of field paddy-wheat root system architecture” to “Phenotypic quantification of root spatial distribution along circumferential directions for field paddy-wheat” after carefully thinking and discussing. Comment 3 of Reviewer 4: The abstract was written very scantily. It should be required. Therefore, please rewrite the abstract with proper hypotheses, the origin of study with clear-cut objectives, a brief methodology, and finally, results with proper justification and clarity. Responses and Changes Made: According to the reviewer’s comments, we rewrote the abstract, supplied the hypotheses (Lines 7-8), and refined the goals and methods (Lines 11-16), all marked with blue font. We framed the abstract as background (Lines 2-6), hypotheses and illustrations (Lines 7-11), goals and methods (Lines 11-16), results (Lines 16-22), conclusions and prospects (Lines 22-25). Comment 4 of Reviewer 4: The amount of rainfall received during the experimental period was important in determining crop growth and development, and no irrigation was provided during the growing seasons. You have mentioned that plant roots are essential for water and nutrient absorption, anchoring, mechanical support, metabolite storage, and interaction with the surrounding soil environment. As a result, I believe that water budgeting is necessary to justify the hypothesis because water is an important factor that influences root growth and development in field conditions. Responses and Changes Made: Thanks for the reviewer’s comments; Nanjing locates in the middle and lower reaches of the Yangtze River, with an annual average rainfall of about 1000 mm and high groundwater levels. The growth of field wheat here mainly depends on rainfall without irrigation. And this study mainly proposes new quantitative indicators of wheat root growth distribution growing in natural conditions. The test data used belonged to the same growth cycle, so we did not consider the impact of rainfall on root growth during the experiment. Also, we did not record rainfall data or soil moisture content during sampling time. According to the reviewer’s comments, we searched the rainfall data from the government's website and list them from 2010-2019 in the below chart (http://www.jiangsu.gov.cn/col/col76741/index.html), for the rainfall data of 2020 was not published. And the data marked with red font covered the sampling time. We think it may not be essential to supply this part in the manuscript. Year Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Total 2010 18.8 115.6 117.8 197.9 56.1 62.1 343.3 142.1 181.1 32.1 7.6 24 1298.4 2011 10.8 17.2 43.2 11.6 40.6 312.9 278 284.3 12.6 28.7 21.3 15.8 1077 2012 21 73.3 79.3 56.2 62.4 17.8 176.4 198.3 68.7 54.6 42.8 66.4 917.2 2013 17.8 69.9 42.9 22.8 110.1 172.6 229.6 115.5 67 22.4 17.2 10.6 898.4 2014 20.6 121.2 68.4 97.6 26.3 111.8 263.5 158.8 89.2 32 97.9 3.8 1091.1 2015 29.9 58.1 104.8 121.6 96.1 661.5 258 187.4 63.6 61.6 110.7 12.3 1765.6 2016 62.8 31.1 40 155.4 119.6 186.2 477.3 78.7 187.4 308 95.4 65.8 1807.7 2017 59.3 38.8 55.1 117.9 83.9 309.1 99.6 217.1 176.4 81 7.4 9.5 1255.1 2018 106 44.9 120.7 61 142.8 49.1 182.3 273.6 66.2 37.5 65.6 117.4 1267.1 2019 51.5 90.4 37.6 51.5 41.1 109.2 63.9 123 51.4 1.4 41.7 59.1 721.8 Comment 5 of Reviewer 4: Figure quality may be improved for more clarity. Responses and Changes Made: The figures uploaded are compressed according to the requirements of the journal. According to the reviewer’s comments, we uploaded clearer pictures in supporting information. Comment 6 of Reviewer 4: The conclusion is very condensed; there is scope to improve it briefly as per the salient achievement of the study. Hence, it can be elaborated with final recommendations. Responses and Changes Made: According to the reviewer’s comments, we rearranged the conclusion marked with blue font (Lines 377-386). Attachments Attachment Submitted filename: Response to Reviewers.DOCX https://doi.org/10.1371/journal.pone.0279353.r004
6 Dec 2022 Decision Letter - Sudeshna Bhattacharjya, Editor Phenotypic quantification of root spatial distribution along circumferential direction for field paddy-wheat PONE-D-22-15992R2 Dear Dr. Hu, 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, Sudeshna Bhattacharjya, 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 #4: 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 #4: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #4: 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 #4: 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 #4: 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 #4: References should be in uniform style, so there is a need to check the style and format of references in the text as well as in the references list. Conclusion is written well although there is scope to improve it in briefly as per salient achievement of the study. It should be in bullet information. ****** 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 #4: No ******** https://doi.org/10.1371/journal.pone.0279353.r005
Formally Accepted
10 Jan 2023 Acceptance Letter - Sudeshna Bhattacharjya, Editor PONE-D-22-15992R2 Phenotypic quantification of root spatial distribution along circumferential direction for field paddy-wheat Dear Dr. Hu: 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. Sudeshna Bhattacharjya Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0279353.r006

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