PONE-D-22-32759Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markersPLOS ONE

Dear Dr. Massawe,

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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

Reviewer #3: No

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

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: 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

Reviewer #3: 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

Reviewer #3: 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: The present study has been done to estimate the genetic diversity present in the Water yam (Dioscorea alata L.). 63 accessions from six different regions of Tanzania were collected and analyzed using 10 SSR markers. In this study no geographical isolation was found and the accessions shared genetic similarity with each other. The genetic diversity study of Water yam (Dioscorea alata L.) has been done with different research groups using different molecular markers such as RAPD, ISSR, AFLP. SSR and SNP markers. Since this is the first report on genetic diversity of Water yam (Dioscorea alata L.) from Tanzania therefore this study may be interesting for researchers working on this crop.

Reviewer #2: Line 36 add “cluster analysis” before UPGMA

In Table 1 accession on #54 & 55 are repetitions

Line 130 what do you mean by number of different alleles? Do you mean number of polymorphic alleles?

AMOVA only assess the genetic diversity and genetic relationship among populations not accessions

Why do you use a burn-in –period of 10 000? Some researchers use large burn-in-period.

Line 158-160: Shannon information index is a population parameter not locus parameters. It does not has any biological meaning in the case of markers i.e. Shannon information index value for Dab2E07 was 1.47, what does this implies?

Line 173: Some of the regions were not represented by sufficient samples such as Arusha (2) and Kilimanjaro (4), hence the genetic parameter values were under estimated. I suggest to either merging them together or the values should be adjusted based on number of samples per population.

Table 5: why among accession variation was not included? GenAlex can give the results even though the percentage variation is 0%. But I doubt that it won't be the case?

Figure 2: the classification of the accession is confusing. Based on PCoA 1 & 2 the accessions are classified into three potential groups. If we consider PCoA1, then the A & B classification should be completely different. So please recheck it.

Line 222: It is also ideal to report on the genetic distance between accessions since there may be a chance that the same accession given different name in different regions.

Table 7: The table legend is not informative. Specify the values as genetic distance and identity based on above and below diagonal for ease of reading

Line 135-136: How is the relationship in terms of number and patterns of clustering between the two clustering approaches i.e. PCA and the dendrogram generated using UPGMA

Figure 4: The quality of Figure 4 should be improve using Excel.

Citation style when references added at the beginning, in the middle and at the end of the sentence should be rechecked throughout the paper

Line 276: Is not clear? was the low number of alleles due to low or high allelic variants?

Line 276-278: the 97 and 273 values indicated are not the number of alleles per locus, but they are the total number of allele observed overall population.

Line 303-304: Is flowering time and pattern affected by environmental factors in Yam? If so, explain the results obtained in this study and previous studies based on environmental suitability for flowering.

Line 316-318: This might be attributed by the large number of samples collected from Kagera regions unless the values are adjusted based on number of sample per region. This is misleading.

Line 342-343: The implication is not correct since Arusha is represented by only two accessions.

Line 353-354: The results revealed the lack of wide genetic diversity but not lack of improved variety. The molecular data is all about variation at the DNA sequence level.

Reviewer #3: The MS entitled “Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markers” have been critically reviewed and comments are as follows:

In the present investigation, the authors evaluated genetic diversity among 63 accessions of the water yam using 10 SSR markers and reported moderate level of genetic diversity. The genetic diversity in this crop has been widely examined at various locations and using large number of accessions and more advance marker systems such as SNP. The present investigation does not provide any new information’s and the number of accessions and number of markers are very less. Large number of markers evenly distributed across the genome are recommend to be used to assessment of genetic diversity. Therefore, the present study could not be recommended for publication in PLOS One.

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Reviewer #1: Yes: Dr Rakesh Singh

Reviewer #2: Yes: Amelework B Assefa

Reviewer #3: Yes: Hemant Kumar Yadav

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Attachments

Attachment

Submitted filename: PONE-D-22-32759_reviewer with reviewers comment.pdf

PONE-D-22-32759R1Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markersPLOS ONE

Dear Dr. Massawe,

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 May 18 2023 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,

Mehdi Rahimi, Ph.D.

Academic Editor

PLOS ONE

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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 Author

The reviewer(s) have recommended minor revisions to your manuscript. Therefore, I invite you to respond to the reviewer(s)' comments and revise your manuscript.

With Thanks

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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: All comments have been addressed

Reviewer #2: 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

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: No

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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

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 reply to reviewers comments point-wise has not been submitted by authors. This needs to be submitted. The corrections in the manuscript needs to be done in track change mode which is missing. Therefore, authors are requested to submit the revised manuscript in the track change mode for further evaluation.

Reviewer #2: The abstract needs to be revisited. They have changed the analysis and the results were different from the original analysis, for example, the AMOVA results have been changed as among population, among individual and within individual. I have also seen few editorial issues to be addressed.

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Reviewer #1: Yes: Rakesh Singh

Reviewer #2: Yes: Amelework B. Assefa

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Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markers

PONE-D-22-32759R2

Dear Dr. Massawe,

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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Kind regards,

Mehdi Rahimi, Ph.D.

Academic Editor

PLOS ONE

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