-->PONE-D-26-11665-->-->Morphological and Molecular Characterization of Nepalese Common Bean (Phaseolus vulgaris L.) Landraces-->-->PLOS One

Dear Dr.  Thapa,

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PLOS One

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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: No

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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: No

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: No

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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: The short title on page 1 reads "Diversity in Nepalese in common bean" — correct to "Diversity in Nepalese Common Bean" or similar.

Abstract – quantitative H' range: The Shannon-Weaver index for quantitative traits is given as 0.46–0.90, but Table 1 shows values as low as 0.74 for some traits. Please verify and align.

Abstract – missing units: Add units for yield (t/ha) where first mentioned.

Keywords – repetition: "Nepalese bean landraces" repeats "Nepalese" from the title; consider simplifying to "common bean landraces".

Reference [3] appears incomplete (no title/DOI). Please check all references against PLOS ONE style.

Gene pool seed weight thresholds: The statement >40g/100 seed weight (Andean) and <25g (Mesoamerican) lacks a citation for the 40g threshold.

Nepal bean area/production data: The 2023 FAOSTAT data cited may already be outdated; consider using 2024 or 2025 data if available or note the year explicitly.

You state "augmented block design" but do not specify number of blocks or how checks were arranged. Add one sentence.

For quantitative traits, you sampled 5 plants per accession. State, whether these were technical replicates or biological replicates.

CTAB protocol: Cite the modified CTAB protocol correctly (Doyle & Doyle 1987 is listed, but "modified" needs a brief description of key changes).

PCR annealing temperatures: Annex Table 4 and Appendix 5 show conflicting annealing temps for some primers (e.g., BM143). Unify.

Table 2 – H' values: Some H' values appear duplicated (e.g., leaf shape H'=0.99, bracteole shape H'=0.99). Are these identical by chance or rounding? Please comment briefly.

PCA – eigenvalue >1: State, that you retained components with eigenvalue >1 (PC1–PC5).

Cluster V seed weight: 1236 g for thousand seed weight seems extremely high (typical max ~800 g). Check data entry or clarify if this is a misprint.

Molecular data – monomorphic markers: You had 3 monomorphic SSRs out of 15. List them or state they were excluded from further analysis.

Discussion – You state H₀ > Hₑ indicates excess heterozygotes. For a self-pollinating species, discuss possible genotyping error (e.g., null alleles) as an alternative explanation.

Conclusion – "Many landraces outperformed check varieties" – only two checks were used. Soften to "several" or specify which traits.

Some DOIs are hyperlinked, others are plain text. Make uniform.

You state data available upon request. PLOS ONE strongly prefers public deposition. Consider adding a note that data will be deposited in a public repository upon acceptance.

Reviewer #2: Comments to the authors

Your study on Phaseolus vulgaris diversity in Nepal is valuable and reflects significant research effort, particularly in combining morphological and molecular analyses. However, the manuscript in its current form does not clearly communicate the scientific contribution due to major issues in writing, organization, and methodology.

Please consider the following points:

a) Language and writing quality

The manuscript contains a lot of grammatical and stylistic errors. A thorough revision by a proficient English speaker or a professional editing service is strongly recommended.

b) Organization of the Manuscript

Results and discussion are frequently mixed; these sections should be clearly separated. Interpretations and comparisons with the literature should be moved to the Discussion section.

The overall flow from Materials and Methods to Results and Conclusion needs to be clarified and logically structured.

The manuscript editing does not follow the PLOSOne standard.

c) Methodological issues

There are important concerns regarding the methodology:

i. The formula used to calculate the diversity index appears to be incorrect and must be carefully checked and corrected.

ii. The diversity index has been calculated using quantitative data without clear categorization. Typically, diversity indices are applied to qualitative (categorical) data.

iii. If applied to quantitative data, appropriate categorization is required, and the interpretation should reflect distribution properties such as evenness or dominance. The current interpretation is therefore not appropriate and should be revised.

d) Clarity and conciseness

The manuscript contains a significant amount of unnecessary or redundant information, particularly in materials and methods results Please revise these sections to focus on essential information that directly supports the objectives and findings of the study.

Furthermore, some parts of the methodology are not clearly described; please provide clear and logically organized methodological steps. Present results clearly and separately from discussion.

e) . Referencing issues

Citations are numbered in the text, but the reference list is not correspondingly numbered. This makes it difficult to verify sources and follow the scientific argument.

Please ensure consistency and proper formatting of all references.

Final Remark: I have included detailed, specific comments directly within the annotated manuscript to guide your revision. Your study has strong potential, but substantial improvements in writing, structure, and methodological accuracy are required to make the work clear, rigorous, and suitable for publication.

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Reviewer #1: Yes: Dr. Jyoti Prakash Sahoo

Reviewer #2: Yes: Anoumaa Mariette

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Attachments

Attachment

Submitted filename: PONE-D-26-11665_Rev-AM.pdf

Attachment

Submitted filename: PONE-D-26-11665_Comments to the Editor.docx

Attachment

Submitted filename: PONE-D-26-11665_comments to author.docx

Morphological and Molecular Characterization of Nepalese Common Bean (Phaseolus vulgaris L.) Landraces

PONE-D-26-11665R1

Dear Dr. Thapa,

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.

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Kind regards,

Tzen-Yuh Chiang

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

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-->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

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-->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

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-->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

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-->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: Thank you for thoroughly addressing all the comments and suggestions from the previous review round. The manuscript has been significantly improved, and your detailed revisions have greatly enhanced its overall quality and clarity. The paper is now scientifically sound and ready for publication, pending a final round of minor grammatical and typographical corrections. I congratulate you on an excellent piece of work.

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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

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