PONE-D-24-22074Restriction site-associated DNA sequencing (RAD-seq) of tea plant (Camellia sinensis) in Sichuan province, China, provides insights into free amino acid and polyphenol contents of teaPLOS ONE

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This work was supported by Tea varieties breeding and promotion project of Sichuan (sccxtd-2023-10), Natural science Foundation of Sichuan (2023NSFSC0163), Financial independent project of Sichuan (2022ZZCX055), “The 14th Five-Year Plan” tea tree breeding project of Sichuan (2021YFYZ0025), “1 + 9” scientific and technological research project of Sichuan Academy of Agricultural Sciences.

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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: Partly

Reviewer #2: Yes

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: I Don't Know

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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: No

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: Yes

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 MS reported RAD-seq of tea plant in Sichuan province, China, providing insights into free amino acid and polyphenol contents of tea. It is acceptable for publication in PLoS One after some revisions.

1.Authoritative permission is requested to use the map in the publication.

2.The FAA content was approximately 3 µg/mL and the TP content was approximately 17 µg/mL. Please check the unit carefully, they should be 30 and 170 µg/mL, respectively. TP is a mixture of phenolic substance, it is better to analyze the main catechins. The GWAS results will be more specific and useful.

3.All tea tree to be tea plant. And tea cultivar is better than tea variety. The 139 accession is recommended to list as Supporting information.

Reviewer #2: This study on the genetic basis of the cumulation of FAAs and TP was very significant. The experiment design was reasonable and the research method was advanced too, so the conclusion was reliable.

However the following questions needs further solving.

1. In the section materials and methods, the data analysis methods of the contents of FAAs and TP needs adding. The statistical methods include ANOVA and multiple comparisons, so the section results of the contents of FAAs and Tp needs modifing accordingly.

2. It had better to transfer the figure 1A to the section materials and methods.

3. Add the important pathways of the FAAs metabolism and TP metabolism.

Reviewer #3: In general term, the manuscript titled “Restriction site-associated DNA sequencing (RAD-seq) of tea plant (Camellia sinensis) in Sichuan province, China, provides insights into free amino acid and polyphenol contents of tea” represent interesting topic and might be of interest for the broader readers of Plos One.

The authors collected 139 tea varieties from Sichuan, China and analyzed their free amino acids (FAAs) and tea polyphenols (TPs) contents and identified their variant loci using RAD. The results hold interesting data for molecular breeders in tracing their practices to the accumulated levels pf FAAs and TPs. However, the demonstration of the results is below average, and the discussion is generally lacking and superficial. Further, the quality of figures is too low, and the content is rarely readable. I would recommend accept their work after addressing these issues.

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Reviewer #1: No

Reviewer #2: Yes: Kaibing Zhou

Reviewer #3: No

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Restriction site-associated DNA sequencing (RAD-seq) of tea plant (Camellia sinensis) in Sichuan province, China, provides insights into free amino acid and polyphenol contents of tea

PONE-D-24-22074R1

Dear Dr. Wang,

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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Academic Editor

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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

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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

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

Reviewer #1: Yes

Reviewer #2: Yes

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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: (No Response)

Reviewer #2: 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

Reviewer #2: 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 R1 addressed all the concernings I raised. Please pay attention about the scientific name while proofing.

Reviewer #2: Dear authors,

This study on the genetic basis of the cumulation of FAAs and TP was very significant. The experiment design was reasonable and the research method was advanced too, so the conclusion was reliable.

Thank you for your explaination for my comments. I have no other suggestion.

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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

Reviewer #2: No

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