New Andean source of resistance to anthracnose and angular leaf spot: Fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar

M. C. Gonçalves-Vidigal; T. A. S. Gilio; G. Valentini; M. Vaz-Bisneta; P. S. Vidigal Filho; Q. Song; P. R. Oblessuc; M. Melotto

doi:10.1371/journal.pone.0235215

Peer Review History

Original SubmissionJanuary 9, 2020
11 Mar 2020 Decision Letter - Reyazul Rouf Mir, Editor PONE-D-20-00761 New Andean source of resistance to anthracnose and angular leaf spot: fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar PLOS ONE Dear Dr. Maria Celeste Gonçalves-Vidigal, 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. ============================== ACADEMIC EDITOR: The manuscript was reviewed by two reviewers and both recommended the manuscript after addressing some minor changes/comments. 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We look forward to receiving your revised manuscript. Kind regards, Reyazul Rouf Mir, PhD Academic Editor PLOS ONE Additional Editor Comments (if provided): The manuscript entitled "New Andean source of resistance to anthracnose and angular leaf spot: fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar" is dealing with most important disease in common bean. The manuscript reports the fine mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar. The information will prove useful in gene cloning and use of genes in marker-assisted selection for breeding common bean cultivars with enhanced disease resistance. Based on the advise received by two reviewers, I recommend acceptance of manuscript after minor revision. The authors may consider minor comments made by the two reviewers. Journal Requirements: When submitting your revision, we need you to address these additional requirements: 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 http://www.plosone.org/attachments/PLOSOne_formatting_sample_main_body.pdf and http://www.plosone.org/attachments/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Thank you for stating the following in the Acknowledgments Section of your manuscript: "M.C. Gonçalves-Vidigal is grateful for grant from Capes number BEX 88881.170662//2018-01." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." 3. Your ethics statement must appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please also ensure that your ethics statement is included in your manuscript, as the ethics section of your online submission will not be published alongside your manuscript. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The manuscript entitled "New Andean source of resistance to anthracnose and angular leaf spot: fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar" by Gonçalves-Vidigal et al is an interesting subject and very well written. Anthracnose and angular leaf spot caused by Colletotrichum lindemuthianum and Pseudocercospora griseola , respectively, are devastating diseases of common bean around the world. The have concluded with the results by showing the fine mapping of CoPv01 CDRK / PhgPv01 CDRK loci to a smaller genomic region of 33 Kb. This information can be applied in breeding programs to develop bean cultivars with ANT and ALS resistance using marker-assisted selection. Some minor comments for authors to address arguing below Line no. 128: Please mention number of plants evaluated for non-inoculated control Line no. 148: Elaboration is required for how and where F1 hybrids seeds were selfed to obtain F2 i.e whether the procedure development of F2 from F1 was done in field conditions or in control conditions Line no. 78: Uniform style citing the reference While citing a reference in the introduction section, authors are suggested to cite only the original reference and furthermore reduce the references cited for a particular sentence. Eg in line No. 73, there are eleven references quoted by the author, better is to reduce it as minimum In the introduction and discussion sections, support your conclusions regarding fine mapping with recent published reports of 2020. Lastly authors are requested to please go through the author guidelines of the journal before submitting the final revised manuscript. Reviewer #2: The manuscript is well written and the information at Co-1 locus is well described. The new R gene and it mapping will assist development of breeding lines in the region. I therefore recommend its publication. There are few typos that need attention. L124 please mention authors L124 please check Inocula L128 rewrite L135 by [61, 62]. please add authors L135 Between change it to from L191 space after and" and , before and ****** 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: Bilal A Padder [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.0235215.r001
Revision 1
1 Apr 2020 Author Response DATE: March 28, 2020 TO: Reyazul Rouf Mir, PhD, Academic Editor PLOS ONE FROM: Maria Celeste Gonçalves-Vidigal, Corresponding Author SUBJECT: Manuscript [PONE-D-20-00761] - [EMID:c34843a9dba2cb7e] We appreciate your thoughtful comments and suggestions to improve the manuscript entitled "New Andean source of resistance to anthracnose and angular leaf spot - fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar" based on the recommendations on the cover letter. I received this communication from you on a e-mail dated Wednesday, March 11, 2020 - onbehalfof+ PloS One Editorial Office:em@editorialmanager.com We have carefully reviewed the manuscript and believe that this problem has been properly addressed in the revised manuscript. The revisions and corrections are shown in red colored font on the text of the revised manuscript and all response to the reviewer comments are provided this letter. Thank you for your collaboration and attention. Comments from the Editor and Reviewers to the Authors Reviewer #1 'The manuscript entitled "New Andean source of resistance to anthracnose and angular leaf spot: fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar" by Gonçalves-Vidigal et al isan interesting subject and very well written. Anthracnose and angular leaf spot caused by Colletotrichum lindemuthianum and Pseudocercospora griseola, respectively, are devastating diseases of common bean around the world. They have concluded with the results by showing the fine mapping of CoPv01CDRK / PhgPv01CDRKloci to a smaller genomicregion of 33 Kb. This information can be applied in breeding programs to develop bean cultivars with ANT and ALS resistance using marker-assisted selection. Some minor comments for authors to address arguing below:' Line no. 128: Please mention number of plants evaluated for non-inoculated control. Page # 6, Lines 131 to 138: All plants were inoculated and the paragraph has been rewritten: 'After the expansion of the first trifoliolate leaf, the leaflet of 10 seedlings of each line were inoculated with each race of C. lindemuthianum and the leaflet of 10 seedlings with P. griseola. Each pathogen was inoculated separately. A spore suspension containing 2.0 × 106 spores mL-1 of races 73, 2047 and 3481 of C. lindemuthianum were inoculated using a DeVilbiss number 15 atomizer powered by an electric air compressor (Schulz, SA, Joinville, Santa Catarina, Brazil). A similar procedure was employed for the inoculation with race 63-39 of P. griseola using a spore suspension of 1.2 × 104 conidia mL-1. Ten plants for resistant and susceptible control for each race were inoculated [59, 60].' Line no. 148: Elaboration is required for how and where F1 hybrids seeds were selfed to obtain F2 i.e whether the procedure development of F2 from F1 was done in field conditions or in control conditions Page #7, Lines # 156 to 162 The paragraph starting at the line 148 to 149, the paragraph has been rewritten: 'The F1 seeds were sown in polyethylene vases (48 × 30 × 11 cm) containing a mixture of the commercial substrate Plantmax®, which had been previously fertilized and sterilized. The plant vases were kept in a greenhouse until the F2 seeds were produced. The F2 individuals, obtained by selfing individual F1 plants, were used to characterize the plants for resistance to race 3481 of C. lindemuthianum. Seedlings were grown until pod maturation under natural light in greenhouses. The seedlings were maintained in a greenhouse until the first trifoliolate leaves [56] were fully expanded.' Line no. 78: Uniform style citing the reference. While citing a reference in the introduction section, authors are suggested to cite only the original reference and furthermore reduce the references cited for a particular sentence. Eg in line No. 73, there are eleven references quoted by the author, better is to reduce it as minimum. Pages # 3 and 4, Lines # 70 to 75: The number of authors in the line # 73 was reduced and they were added along of the paragraph according to the specific phrase of the author, the paragraph has been rewritten as see below : 'Resistance to ANT is conferred by independently segregating individual loci in a series named Co. Currently, the known Co genes are Co-1 and its alleles, Co-14, Co-Pa, Co-x, and Co-w on chromosome Pv01 [22, 23, 25, 27, 28, 30, 31, 32]; Co-u and CoPv02 on chromosome Pv02 [18, 22]; Co-13 and Co-17 on chromosome Pv03 [29]; Co-3, Co-32, Co-33, Co-34/Phg-3, Co-y, Co-z, and Co-RVI on chromosome Pv04 [24, 26]; Co-5, Co-6, and Co-v on chromosome Pv07; and Co-2 on chromosome Pv11 [29].' In the introduction and discussion sections, support your conclusions regarding fine mapping with recent published reports of 2020. Page # 29, Lines # 634 to 637: A new bibliographic reference was added in the Introduction on the mapping of anthracnose resistance genes in Pv01. Consequently, it was also mentioned in the Discussion 'Farooq M, Padder BA, Bhat NN, Shah MD, Shikari AB, Awale HE, Kelly JD. Temporal expression of candidate genes at the Co-1 locus and their interaction with other defense related genes in common bean. Physiol Mol Plant Pathol. 2019; 108: 101424. doi: 10.1016/j.pmpp.2019.101424.' Lastly authors are requested to please go through the author guidelines of the journal before submitting the final revised manuscript. The guidelines was checked and changes were made Reviewer #2 The manuscript is well written and the information at Co-1 locus is well described. The new R gene and it mapping will assist development of breeding lines in the region. I therefore recommend its publication. There are few typos that need attention. L124 please mention authors Page # 6, Line # 126: The authors were mentioned: 'Monosporic cultures of C. lindemuthianum and of P. griseola were prepared according to the methodologies proposed by Mathur et al. [57] and Sanglard et al. [58].' L124 please check Inocula Page # 6, Line #127: The word Inocula was replaced by Inoculum L128 rewrite Page # 6, Lines # 130 to 137, the paragraph has been rewritten as see below: 'Soon after the expansion of the first trifoliolate leaf, the leaflet of 10 seedlings of each line were inoculated with each race of C. lindemuthianum and the leaflet of 10 seedlings with P. griseola. Each pathogen was inoculated separately. A spore suspension containing 2.0 × 106 spores mL-1 of races 73, 2047 and 3481 of C. lindemuthianum were inoculated using a DeVilbiss number 15 atomizer powered by an electric air compressor (Schulz, SA, Joinville, Santa Catarina, Brazil). A similar procedure was employed for the inoculation with race 63-39 of P. griseola using a spore suspension of 1.2 × 104 conidia mL-1. Ten plants for resistant and susceptible control for each race were inoculated [59, 60].' L135 by [61, 62].please add authors L135 Between change it to from Page # 6, Line 142: The name of authors were added and the word 'from' was inserted: Pastor-Corrales et al. [61] and Inglis et al. [62]. Plants with disease reaction scores from 1 L191 space after and" and , before and Page # 9, Line # 205: The space was inserted Funding: This research was supported by Brazilian Federal Funding Institutions National Council for Scientific and Technological Development (CNPq) for financial support and scholarship grants and the Coordination for the Improvement of Higher Education Personnel (Capes). M.C. Gonçalves-Vidigal is grateful for grant from Capes number BEX 88881.170662//2018-01. We would like to thank for the suggestions from the Editor and the reviewers that have improved this manuscript. Regards, M. C. Gonçalves-Vidigal Corresponding Author https://doi.org/10.1371/journal.pone.0235215.r002
11 Jun 2020 Decision Letter - Reyazul Rouf Mir, Editor New Andean source of resistance to anthracnose and angular leaf spot: fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar PONE-D-20-00761R1 Dear Dr. Maria Celeste Gonçalves-Vidigal, 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, Reyazul Rouf Mir, 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: 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: All the queries and suggestions pointed out in the manuscript "New Andean source of resistance to anthracnose and angular leaf spot: fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar" have been well addressed and presented in the revised manuscript Reviewer #2: I have no further queries but a suggestion. Please check reference no 23, Farooq et al., After checking it I found Mahiya-Farooq on running head of the paper. So in my opinion it should be Mahiya-Farooq. ****** 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: No Reviewer #2: No https://doi.org/10.1371/journal.pone.0235215.r003
Formally Accepted
18 Jun 2020 Acceptance Letter - Reyazul Rouf Mir, Editor PONE-D-20-00761R1 New Andean source of resistance to anthracnose and angular leaf spot: fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar Dear Dr. Gonçalves-Vidigal: 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. Reyazul Rouf Mir Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0235215.r004

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