PONE-D-24-60023Morphological characteristics and genome-wide association analysis among local Andrographis paniculata from Thailand under controlled environment in plant factoryPLOS ONE

Dear Dr. Chutimanukul,

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ACADEMIC EDITOR: Please insert comments here and delete this placeholder text when finished. The reviewers suggested several minor and major comments. I suggest major revisions. Kindly check the journal's technical requirements and formatting according to journal requirements.. 

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PLOS ONE

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Additional Editor Comments:

The reviewers suggested several minor and major comments. I suggest major revisions. Kindly check the journal's technical requirements and formatting according to journal requirements.

[Note: HTML markup is below. Please do not edit.]

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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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

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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: 1-As one of important parts of the paper is about GWAS analysis, it is suggested to address high quality publications about the merits of GWAS analysis in different species in including medicinal plants. Bellow, several publications about GWAs and meta-analysis can be addressed in introduction as literature review and in discussion part for comparing similar results between the publications and the submitted manuscript.

Shariatipur et al. 2021. Comparative Genomic Analysis of Quantitative Trait Loci Associated With Micronutrient Contents, Grain Quality, and Agronomic Traits in Wheat (Triticum aestivum L.). frontiers in Plant Science, //doi.org/10.3389/fpls.2021.709817

Shariatipur et al 2021. Meta-analysis of QTLome for grain zinc and iron contents in wheat (Triticum aestivum L.). Eyphytica 217, //doi.org/10.1007/s10681-021-02818-8

Shariatipour et al. 2021. Genomic analysis of ionome-related QTLs in Arabidopsis thaliana. Scientific Reports, 11. doi.org/10.1038/s41598-021-98592-7

Salami et al. 2022. Comparative profiling of polyphenols and antioxidants and analysis of antiglycation activities in rapeseed (Brassica napus L.) under different moisture regimes. Food Chemistry, 399: //doi.org/10.1016/j.foodchem.2022.133946

Salami et al. 2023. Integration of genome wide association studies (GWAS), metabolomics and transcriptomics reveals phenolic acids and flavonoids associated genes and their regulatory elements under drought stress in rapeseed flowers. Frontiers in Plant Science, 14, 10.3389/fpls.2023.1249142

Salami et al. 2024. Dissection of quantitative trait nucleotides and candidate genes associated with agronomic and yield-related traits under drought stress in rapeseed varieties: integration of genome-wide association study and transcriptomic analysis. Frontiers in Plant Sciences, 15 doi.org/10.3389/fpls.2024.1342359

Archangi et al. 2022. Assessing genetic diversity and aggregate genotype selection in a collection of cumin (Cuminum cyminum L.) accessions under drought stress: Application of BLUP and BLUE. Scientia Horticulturem 299, 11108.. //doi.org/10.1016/j.scienta.2022.111028

Archangi et al. 2019. Association between seed yield-related traits and cDNA-AFLP markers in cumin (Cuminum cyminum) under drought and irrigation regimes. Industrial Crops and Products, 133: 276-283. //doi.org/10.1016/j.indcrop.2019.03.038

Results

-Line 312: the authors stated 62 plant samples that was not consistent with the number of accessions explained in materials and methods. Overall, materials and methods are in some places confusing as the authors did not explain the experiments and number of plant samples used for different assays

-line 346: Mantel not Mental test

-line 351: one of reasons for identifying low number of linked SNP is low plant sample size used for GWAS analysis

Discussion

Comparing with other studies is poor and discussion part need more literature review and avoid stating detailed results. Fosus on main and key finding and interpret the results. Revise discussion part as suggested.

Conclusion

Conclusion is too large and should be condensed intro 2-3 sentences stating the most important finding not explain everything

Figures and tables:

Resolution of figures are too low. It is not suitable for publication

Reviewer #2: I have gone through the manuscript “Morphological characteristics and genome-wide association analysis among local Andrographis paniculata from Thailand under controlled environment in plant factory” focusing on the identification of high yielding variety based on the content of andrographolide and biomass under Plant factories with artificial lighting (PFAL) of different cultivars. I feel it’s an excellent work done by the authors because the lant which has been selected is widely used in all over the world and the objective taken in the study is really need of the hour because in the change in environment the medicinal properties may also have changed in the plants. However, I have very few suggestions on the manuscript to improve the quality and readability of the paper which are as follows.

1. What the numeral ‘1’ in the tittle. It can be removed

2. Instead of writing only ‘Andrographis’ in many places, in should be A. paniculata in all the laces where it is mentioned.

3. The morphological description has revealed the leaves are typically 2-12 cm long, this data should be rechecked. The citation should be given from where the description has been verified (Any flora book or reference book or research paper).

4. In line number 61, the ‘2’ should be in the subscript of carbon dioxide.

5. In line number 172, check the spelling of A. paniculata

6. The most important question which need to be answered in the manuscript is, phylogenetically the accessions like CR, RB, PL, and PC—are closely related to TTT but even though provided with similar conditions the TTT given higher yield. Please explain what could be the reason in the conclusion part.

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Reviewer #1: No

Reviewer #2: Yes:  Bibhuti Bhushan Champati

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Morphological characteristics and genome-wide association analysis among local Andrographis paniculata from Thailand under controlled environment in plant factory

PONE-D-24-60023R1

Dear Dr. Chutimanukul,

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,

Faham Khamesipour, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The authors have adressed all comments systematically. I agree to the changes made by the authors.

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: Yes

**********

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 comments addressed properly and this version of the manuscript is acceptable for publication. Juts check the text for possible typo errors

Reviewer #2: (No Response)

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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: Yes:  Bibhuti Bhushan Champati

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