-->PONE-D-25-47793-->-->Population structure and diversity of common bean (Phaseolus vulgaris L.) landraces in the Peruvian Amazon-->-->PLOS ONE

Dear Dr. Ortiz,

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Academic Editor

PLOS ONE

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“This work was supported, in whole by Peruvian government funding-PROCIENCIA, E041 - Proyectos de Investigación Básica y Aplicada (PE501079155-2022), through the “Genómica del frijol Phaseolus spp. asociada con la diversidad cultural y ecosistémica en la Amazonia peruana” project. The authors are thankful to SAGA- Genetic Analysis Service for Agriculture, CIMMYT-Mexico; for their support for genotyping. Also, we thank local farmers for their cooperation and the research institutions (UNALM, UNSM, UNU) that supported this study.”

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“This work was supported, in whole by Peruvian government funding-PROCIENCIA, E041 - Proyectos de Investigación Básica y Aplicada (PE501079155-2022), through the “Genómica del frijol Phaseolus spp. asociada con la diversidad cultural y ecosistémica en la Amazonia peruana” project.”

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Additional Editor Comments:

Since authors have genotypic data and phenotypic data on multiple traits, I suggest to run the GWAS to identify genomic regions associated with traits.

Figure quality need to be improved. increase font size in Fig 6, 7 and 12.

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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

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-->2. Has the statistical analysis been performed appropriately and rigorously? -->

Reviewer #1: Yes

Reviewer #2: Yes

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-->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

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-->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

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-->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: Page 9: a. Kindly include the aim of study

b. I believe 667 accessions were collected but only 476 were analysed. Please correct this this number in the abstract, materials and method and result section

c. Kindly expand the result section to strengthen the abstract. The information on population structure and clustering is not clearly highlighted, and much of the rich detail appears to be hidden.

Kindly refer to the attached manuscript for my additional comments. Thank you. Excellent write up.

Reviewer #2: The study entitled “Population structure and diversity of common bean (Phaseolus vulgaris L.) landraces in the Peruvian Amazon” provides interesting advances in understanding the population structure and genetic diversity of common bean landraces collected from different region by utilizing both morphological and SNP markers information. However, the manuscript, in its current form, requires substantial revision before it can be considered for publication, most especially in mythology, results presentation, and conclusion. Below is the specific point to be addressed:

1. The Materials and Methods section lack essential details. Critical information such as descriptions of the recorded traits and the procedures used for data processing and analysis were insufficiently described. To ensure the reproducibility of this study, please provide a detailed description of each studied trait, rather than only indicating the number of colors or types.

2. The Results section primarily restates elements of the methodology and discussion rather than presenting the main findings in detail, and the figure quality could be improved to allow proper evaluation

3. “Despite its importance, most studies on common bean in Peru have focused on commercial varieties grown in the highlands and coastal regions, emphasizing agronomic practices and genetic improvement using both local and introduced varieties”. Please provide some references that have investigated these areas

4. The conclusion provides only a summary of the results and does not effectively address the research objective

5. “Cluster analysis based on morphological traits grouped the accessions into four major clusters

6. (Figure 3).” But Figure 3 showed Boxplot of quantitative descriptors, please verify and indicate the correct figure

7. Although the data were said to be filtered at MAF of ≥ 1%, the MAF distribution extended to 0.5 (Figure 8E). Please clarify this discrepancy

In addition to the comment above, the following suggestion would enrich the manuscript

1. Since the study was conducted at a single location, in a non-replicated trial with no appropriate experimental design, the quantitative traits may be misleading (i.e., the observed differences might not reflect the true genetic merit of the landraces under investigation). Therefore, it is recommended to include qualitative descriptors in the clustering analysis as well. The Gower distance metric is suitable for this purpose, as it can simultaneously handle both quantitative and qualitative variables.

2. Incorporating regional information into the clustering analysis will facilitate a clearer understanding of genetic flow of the accession

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-25-47793_reviewer.pdf

-->PONE-D-25-47793R1-->-->Population structure and diversity of common bean (Phaseolus vulgaris L.) landraces in the Peruvian Amazon-->-->PLOS One

Dear Dr. Ortiz,

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 06 2026 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 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,

Santosh Gudi

Academic Editor

PLOS One

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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: (No Response)

Reviewer #2: (No Response)

**********

-->2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. -->

Reviewer #1: Yes

Reviewer #2: Yes

**********

-->3. Has the statistical analysis been performed appropriately and rigorously? -->

Reviewer #1: Yes

Reviewer #2: Yes

**********

-->4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.-->

Reviewer #1: Yes

Reviewer #2: Yes

**********

-->5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.-->

Reviewer #1: Yes

Reviewer #2: Yes

**********

-->6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)-->

Reviewer #1: The author has done a good job reviewing the manuscript. However, some concerns were not addressed. Please refer to the attached manuscript.

Reviewer #2: The conclusion could be improved to address specific objectives and should be written in one paragraph

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Reviewer #1: No

Reviewer #2: Yes: Adamu Masari Abubakar

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-->

Attachments

Attachment

Submitted filename: PONE-D-25-47793_R1_reviewer.pdf

Population structure and diversity of common bean (Phaseolus vulgaris L.) landraces in the Peruvian Amazon

PONE-D-25-47793R2

Dear Dr. Ortiz,

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.

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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,

Santosh Gudi

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: (No Response)

**********

-->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: Please refer to the manuscript for review. Please avoid result inclusion in discussion. Also 100 seed weight and total grain weight were not among the traits collected, yet it is mentioned in result section. Kindly indicate clearly in materials and methods

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-->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

**********

Attachments

Attachment

Submitted filename: PONE-D-25-47793_R2_reviewer.pdf