PONE-D-20-00745

Characterizing rhizome bud dormancy in Polygonatum kingianum: chill models and mechanisms revealed by weighted correlation network analysis.

PLOS ONE

Dear Dr. Wang,

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Alexandre Fournier-Level, Ph.D.

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PLOS ONE

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Additional Editor Comments (if provided):

Dear Authors,

Thank you for submitting your article to PLoS ONE.

Your work has been reviewed by three reviewer who all find merit to your study and wish to see you work ultimately published in our journal.

However, the reviewers have pointed to a few aspects that need improvement in particular:

- Tighten the abstract and the end of the Introduction to make the aim of the study very clear (abstract and intro) and simplify/shorten the abstract to focus on the key result.

- Describe the plant material and the experimental design in greater detail using comments from Reviewers 1 and 2.

- Revise the reefernce to adhere to teh PLoS format

Please disregard comments on figure quality as the compressed version of the paper provided to the reviewer was bad but the figures you submitted are good enough.

Sincerely

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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: Yes

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

Reviewer #1: Yes

Reviewer #2: I Don't Know

Reviewer #3: Yes

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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?

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Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: 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: In this study, the authors conducted a series of experiments on the rhizome buds of Polygonatum kingianum to explore specific chill models and mechanisms for rhizome bud dormancy break. A “CUkingianum” model was deduced to describe the contribution of low temperature to the chill unit, and the rhizome bud development can be predicted through the “CASkingianum” model. Besides, weighted correlation network analysis (WGCNA) was used to study transcriptomic data of endo-, eco- and nondormant rhizome buds, and a network containing 33 modules was constructed. Those results provide insights into the mechanisms for rhizome bud dormancy break in P. kingianum, which has a certain significance for production practice. The manuscript was well written in English. However, a revision of manuscript is required before it can be accepted for publication. Please see next comments.

1. Most figures are not clear, if possible, please indicate more clear photos.

2. The dormant situation in the place of origin and environmental conditions should be provided in order to understand the main factors leading to dormancy.

3. Line157-158, the best treatments should be only one.

4. Line194-195, A, B, C and D should be shown in Fig 4.

5. Line201, “are” should be deleted.

6. Line204, “Clustering dendrogram” should be consistent with that in Fig 5, the Y axis Height should give an explanation in figure legend.

7. Line231, the title does not match what follows, it should be revised.

8. Line252-253, “The results indicated that DAG2 may bind to promoters of the hub genes to regulate bud germination in P. kingianum.” is just a speculation and lack of experimental evidence. Therefore, qRT-PCR analysis of DAG2 expressed in rhizome buds of P. kingianum during chilling and germination processes should be supplemented.

9. Line427, reference 25 (Peter LH, S. Tutorial for the WGCNA package for R: UC Los Ageles; 2014 [) is not cited correctly.

10. In Supplementary Fig. 3, “VS” should be lower case letters.

In addition, the reference format should meet the requirements of PLoS One.

Reviewer #2: Polygonatum bud dormancy has been investigated based on qRT-PCR, correlation and network analysis and few models have been proposed. Manuscript largely appears to be accepted for publication after answering following queries and implementing few suggestions:

1. Grammar needs to be thoroughly checked for example line 142.

2. Line 75 does term mean GO term?

3. Under methods section, more details about growth conditions such as humidity, watering, light intensity, duration, and weather seeds were grown in soilrite and what media was provided?

4. Line 99: Was day/night temperature same?

5. How authors classified dormancy as endo or eco or no dormancy. Provide some details.

6. Line 132: How transcription start site was determined?

7. Line 136: What tissue was used for qPCR analysis?

8. Line 139 Instead use qRT-PCR or qPCR everywhere in MS

9. Format supplementary tables and label title clearly.

Reviewer #3: Manuscript (PONE-D-20-00745) “Characterizing rhizome bud dormancy in Polygonatum kingianum: chill models and mechanisms revealed by weighted correlation network analysis” by Wang et al. presents a study about rhizome dormancy in Polygonatum. This manuscript presents a new methodology applied to one Polygonatum kingianum genotype with several cold-dormancy conditions.

The interest of the work is high due to the importance of the studied process. However this manuscript presents several deficiencies which must be revised and clarified before publication in PLoSOne Journal.

The major points for the revision of the manuscript are:

Abstract should be reduced only indicating the key information.

In the Introduction, first paragraph (lines 27-47) should be separated in at least two paragraphs to improve understanding.

Objectives of the work should be better clarified eliminating the references (page 4 line 96).

Description of methodology should be improved. The Plant material used must be clarified indicating if it is possible any reference. Description of RT-PCR must be completed. It is very important the description of the assayed genes.

Figure S2 should be incorporated to the main text, not as supplementary.

Figure 1 must be better explained in a new legend. Authors must clarify the difference between chill unit (accumulated chill?) and chilling temperature (temperature of controlled chamber?).

Legend of Figure 9 must be also clarified.

Figure 9 and 10 should be incorporated as supplementary material.

Conclusion section should be completed indicating main implications of the optained results for breeding and production.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Characterizing rhizome bud dormancy in Polygonatum kingianum : development of a novel chill models and determination of dormancy release mechanisms by weighted correlation network analysis

PONE-D-20-00745R1

Dear Dr. Wang,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

The revision now largely meets the criteria for publication in PLoS ONE. Congratulations.

However, I did notice some room for improvement as the manuscript still contains a number of typos and approximation. For example the protocol here https://www.protocols.io/view/a-method-for-motif-based-sequence-alignment-analys-bdwki7cw is full of typos and the link to meme-suite (note the hyphen) is broken. I would really appreciate you to take the time to go through the manuscript at the proofing stage very carefully and make sure you are doing justice to your hard work.

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

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With kind regards,

Alexandre Fournier-Level, Ph.D.

Academic Editor

PLOS ONE