Morpho-agronomic, biochemical and molecular analysis of genetic diversity in the Mesoamerican common bean panel

Alison Fernando Nogueira; Vania Moda-Cirino; Jessica Delfini; Luriam Aparecida Brandão; Silas Mian; Leonel Vinicius Constantino; Douglas Mariani Zeffa; José dos Santos Neto; Leandro Simões Azeredo Gonçalves

doi:10.1371/journal.pone.0249858

Peer Review History

Original SubmissionNovember 9, 2020
19 Jan 2021 Decision Letter - Roberto Papa, Editor PONE-D-20-35240 Morpho-agronomic, biochemical and molecular analysis of genetic diversity in the Brazilian Mesoamerican common bean panel PLOS ONE Dear Dr. Azeredo Gonçalves, 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 Feb 14 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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Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [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: No ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A ****** 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: No 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: 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: First, I would like to highlight the importance and the need for studies involving germplasm characterization. In my opinion, this is the main stage of pre-breeding, especially when evaluations are not limited to morphological traits, as in the current study. In this sense, I would like to congratulate all authors, and the agronomy department of UEL and IAPAR, they have been developing great work for years on genetic breeding of bean crop. General considerations: The present study is about the evaluation and characterization of the genetic diversity of a set of 215 accessions, through morphological, biochemical, and molecular analyzes. A lot of work was done to obtain the data, and several analyzes were conducted. The study is of great importance for crop improvement; however, the discussion needs to be improved. The results could be much better explored, very few studies were cited, and the conclusion was generic. Specific considerations are included in the attached file. Reviewer #2: Manuscript number: PONE-D-20-35240 Title: Morpho-agronomic and molecular analysis of genetic diversity in the Brazilian Mesoamerican common bean panel Comments: • The bibliography needs to be completely revised (heavily). Each statement must be verifiable by the reader, for this, a precise reference to the sources is necessary. The form and style of the bibliographic citations are not uniform, and an inappropriate format is used. For instance, see references 18, 19, 24, 26, and 27. • English and grammar are too poor. The science is not communicated with sufficient clarity, making ambiguous understanding for some parts of the manuscript. My recommendation is to have the article edited by a mother-tongue with excellent English-writing skills. • The abstract does not meet the standard scientific requirements: here the results are presented in a disjointed ways and there is a lack of a general and effective view of the work. • The accurate interpretation of the data obtained is completely absent. For this reason, the part of the discussion requires substantial changes aimed at breaking down and contextualizing the results achieved. Moreover, the introduction is not well argued: the concepts need to be connected with each other more fluently. In light of these considerations, and taking into account the potential positive impact of this study in future breeding programs, I reject the article entitled “Morpho-agronomic and molecular analysis of genetic diversity in the Brazilian Mesoamerican common bean panel” with the possibility of re-submission, once the manuscript will be revised. ****** 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:** Caléo Panhoca Almeida 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.] 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: Reviewer Recommendation and Comments.pdf https://doi.org/10.1371/journal.pone.0249858.r001
Revision 1
15 Feb 2021 Author Response Dr. Editor-in-Chief Plos One Please find enclosed our response to the review about the manuscript entitled “Morpho-agronomic, biochemical and molecular analysis of genetic diversity in the Mesoamerican common bean panel” that we are re-submitting for consideration for publication at Plos One. We thank the Editor and the reviewers to taking the time to review our manuscript. All the suggestions were very important to the construction of our manuscript. We have accept all the suggestions directly in the text, and response the doubts in this letter. We are available for any further clarification. We kindly thank you for your time and consideration, Leandro SA Gonçalves Professor Universidade Estadual de Londrina Responses to Reviewer(s)' Comments: Reviewer #1 ABSTRACT: The summary is well written; however, a main conclusion is missing. L35 – The word "heritability" is duplicated. L43 - Delete "AFLP". Response: The suggestions were accepted. INTRODUCTION The introduction is well written and covers the main topic of the study. However, there was a lack as to the importance of using the three types of analysis (Morpho-agronomic, biochemical, and molecular). Response: This information was inserted in the manuscript. L57-L60 – The citation ([6]) does not support the first three arguments of the sentence (1° one of the world’s largest producers and consumers of beans; 2° Mesoamerican cultivars are more popular; 3° carioca and black commercial types are preferred, accounting for 85 and 11% of Brazil’s bean production). Provide references. L67 – Change “variation and potential” by “diversity”. L67 – Change “characteristics” by “traits”. L70 – Change “such accessions must be fully characterized and evaluated” by “the candidate accessions must be fully evaluated and characterized, both morphologically and molecularly.” L71 – Change “exploitation” by “exploration”. L71-74 – Maybe would look better with a sentence like that (just a suggestion): “The precise exploration of genetic diversity by the breeding programs is necessary for the development of new commercial cultivars adapted to the most diverse regions of the country. Usually, higher levels of diversity in the set used for breeding is related to a greater chance of identifying higher agronomic traits [12, 13].” L74 – Change “[12] [13]” by “[12,13]”. L75- Change “The common bean exhibits wide variation in a variety of traits” by “The common bean exhibits wide agronomic traits variation”. L82- Change “various” by “several”. L83 – Change “[12] [16]” by “[12,16]” Response: The suggestions were accepted. MATERIAL AND METHODS For a better understanding of the study, the authors should provide more details about the panel. Why were the panel accesses selected? What percentage of Cariocas, black, and colored beans? How many are commercial cultivars and how many are breeding lines? Response: This information is included in Supplementary Table S1. Another important point, based on what information is it possible to assure that the selected accessions are Mesoamerican? Response: Based on the characteristics of the seed and through the molecular analysis of accessions. This molecular characterization was carried out using the AFLP and SNPs markers. Delfini J, Cirino VM, Neto S, Ruas PM, César G, Ana S, et al. Population structure , genetic diversity and genomic selection signatures among a Brazilian common bean germplasm. Scientific Reports. 2021; 1–12. doi:10.1038/s41598-021-82437-4 The description of the “Morpho-agronomic characterization” section could be improved. Were all evaluations performed after the harvest? How many plants from the useful plot were evaluated? Response: This information was inserted in the manuscript. L94 – add “from different breeding programs and countries.” L97 – add the sowing month of the experiment. L105 – Change “([18])” by “[18]”. L153 – Change “Amplified fragment length polymorphism (AFLP)” by “AFLP”, the abbreviation has already been defined in the summary. Response: This information was inserted in the manuscript. RESULTS The results are clear and well presented. The values of Ac and h2 (YLD) need to be revised, figure 1 shows one value and the text describes another. Another point, the abbreviation “FT (total phenolic contents)” is like “TP” in figures 1, 2 and 3. Response: Abbreviations have been modified in the manuscript. L222 – Change “The Ac values were high (≥ 0.70) for most traits but relatively low (0.52) for YLD (Figure 1).” by “The Ac values were high (≥ 0.70) for all traits, except for YLD (0.52)”. L223 – Change “Meanwhile, h2 was high for DPPH, FT,224 FLA, W100, and NN, low for YLD (0.27), and intermediate (0.59–0.68) for all other traits” by “Meanwhile, h2 was high (0.98 – 0.90) for DPPH, FT, FLA, W100, and NN, intermediate (0.59–0.79) for all other traits, except for YLD (0.15).” L250 – “of the selected accessions” Which accessions were selected? Or does it refer to the panel? L268 and L272 – The IFP “cm” unit is missing. L309 and 335 – Add more details to the legend (e.g., the traits used for analysis, grouping method, and the colors of the figure) Response: The suggestions were accepted. DISCUSSION L345 – The panel was not “established”. Change by “evaluated”. L355 – Change “for DPPH, FLA, FT, W100, and NN, high ( 0.70) for SP, PL, IFP, and STL, and low for YLD.” by “and high ( 0.70) for the other traits, except YLD, which was low.” 361 – Change “The low Ac value obtained for YLD may hinder the selection of accessions. The variable was highly influenced by the environment and was reflected in the heritability” by “The low Ac value obtained for YLD is a consequence of the high influence of the environment for the trait, making it difficult to select the best accessions.” 362 – add “also” after “et al. [40]”. L386 – Change “PerseguinI’ by “Perseguini” L394, 407 and 409 – “the word "topologies" sounds strange. L410 – Change “for future genetic breeding programs” by “to be exploited by genetic breeding programs.” Response: The suggestions were accepted. REFERENCES: Response: References were checked and corrected. SUPPORTING INFORMATION Response: The suggestions were accepted. Reviewer #2 The bibliography needs to be completely revised (heavily). Each statement must be verifiable by the reader, for this, a precise reference to the sources is necessary. The form and style of the bibliographic citations are not uniform, and an inappropriate format is used. For instance, see references 18, 19, 24, 26, and 27. Response: References were checked and corrected. English and grammar are too poor. The science is not communicated with sufficient clarity, making ambiguous understanding for some parts of the manuscript. My recommendation is to have the article edited by a mother-tongue with excellent English-writing skills. Response: The manuscript was reviewed for the English language to eliminate possible grammar or spelling errors. The abstract does not meet the standard scientific requirements: here the results are presented in a disjointed ways and there is a lack of a general and effective view of the work. Response: The abstract has been corrected. The accurate interpretation of the data obtained is completely absent. For this reason, the part of the discussion requires substantial changes aimed at breaking down and contextualizing the results achieved. Moreover, the introduction is not well argued: the concepts need to be connected with each other more fluently. Response: The article was revised for a better understanding of the readers. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0249858.r002
26 Mar 2021 Decision Letter - Roberto Papa, Editor Morpho-agronomic, biochemical and molecular analysis of genetic diversity in the Mesoamerican common bean panel PONE-D-20-35240R1 Dear Dr. Azeredo Gonçalves, 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, Roberto Papa, PhD 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: N/A ****** 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: I would like to thank the authors for their detailed responses toward my concerns and congratulate Gonçalves LSA and your team for the work they have been doing in the genetic breeding of common beans, especially for the topics related to nutritional crop improvement. I still think that the study's discussion could be better explored, however, the authors made some changes. Once again, congratulations on your study! Reviewer #2: The manuscript entitled “Morpho-agronomic and molecular analysis of genetic diversity in the Brazilian Mesoamerican common bean panel” has been revised and implemented in accordance with the previous requests. ****** 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:** Caléo Panhoca Almeida Reviewer #2: No https://doi.org/10.1371/journal.pone.0249858.r003
Formally Accepted
12 Apr 2021 Acceptance Letter - Roberto Papa, Editor PONE-D-20-35240R1 Morpho-agronomic, biochemical and molecular analysis of genetic diversity in the Mesoamerican common bean panel Dear Dr. Azeredo Gonçalves: 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 Prof. Roberto Papa Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0249858.r004

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