PONE-D-23-04509Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in SpainPLOS ONE

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Authors should address the reviewer's comments and critically discuss the results, especially  why  some of the genotypes could not be separated in clusters as per their geographical distribution?.  The results would have been of more practical relevance had they included rice varieties from other countries as well.

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Additional Editor Comments:

Reviewers have found this study interesting, however they some concerns which need to be addressed by the authors.

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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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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: The present study has been done to develop an assay with a minimum number of SNP markers that can distinguish japonica rice varieties grown in Spain. For this purpose, 44 japonica rice varieties were studied with 22 KASP markers. For the selection of these distinguishing KASP markers a freely available software R was used to generate small sets of SNPs that can discriminate these varieties, by selecting markers from a larger genotyping dataset. Based on the data generated with 22 KASP markers on 44 rice varieties further R package-based algorithm identified 8 KASP markers which were sufficient to distinguish japonica rice varieties. I need a few clarifications based on the results presented by the authors

1. What was the reason that Hispalong and Puntal varieties could not get distinguished based on 22 KASP markers assay developed? This needs to be elaborated.

2. What additional effort was done to separate Hispalong and Puntal before proposing the minimal marker set (8 SNPs), this issue needs to be addressed.

3. Line no. 25 needs to be corrected because the set of 8 SNP markers could distinguish 43 varieties instead of 44.

4. This minimal set (8 SNPs) of SNP identified has very limited applicability because they can distinguish only 42 japonica rice varieties grown in Spain. This needs to be tested on another set of japonica varieties (from other countries) to prove its wider applicability.

Reviewer #2: The manuscript entitled "Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain" by Sales et al. demonstrates the use of molecular markers (SNP/ small and low-cost SNP panels) for rice variety identification and protection. They developed a user friendly bioinformatics algorithm in R software for varieties differentiation by selecting markers from a larger genotyping dataset. They applied this algorithm to discriminated the 44 widely cultivated Spain rice varieties with minimal sets of 8 SNPs. They also developed and tested 22 KASP assays for the markers included in these panels, and obtained reliable genotype patterns for rice varieties identification. The work is interesting and of greater benefits to rice breeders, seed certifiers and food inspection agencies. I recommend its publication but request the following queries/ comments to be incorporated before acceptance:

Introduction:

Line 44: Comma after "Italy"

Lines 46-48: Reframe for meaningful sentence.

Materials and methods

Line 55-58: "However, this phenotype-based ... programs are developed." needs revision.

Line 138: Italicise "in silico" and wherever it occurs.

Results

Table 3: The markers mentioned, what it stands should be captioned in the legend (like chromosomenumber_postion) for clarity to readers.

The proper results for "Marker polymorphism analysis" is missing in "Results"

Discussion

Discussion in general may be further expanded/ elaborated.

Following paper may be cited in view of the application of the presented work: https://www.nature.com/articles/s41598-019-41204-2

General comment:

Authors claim that the study attends the need of developing an efficient molecular tool for the identification/ differentiation of varieties. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779600/. The work is impressive but the R package should be submitted/ published in CRAN for the general users/researchers once it gets accepted.

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Reviewer #1: Yes: Rakesh Singh

Reviewer #2: Yes: Sarika Jaiswal

Division of Agricultural Bioinformatics

ICAR-Indian Agricultural Statistics Research Institute

Library Avenue, PUSA, New Delhi -110012 , INDIA

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Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain

PONE-D-23-04509R1

Dear Dr. Domingo

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,

Amit Kumar Singh

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

**********

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: The authors have addressed all the comments therefore the manuscript may be accepted for the publication.

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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: Yes: Dr Rakesh Singh

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