PONE-D-20-06651

Comparative transcriptome analyses in contrasting onion (Allium cepa L.) genotypes for drought stress

PLOS ONE

Dear Dr. G,

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ACADEMIC EDITOR: The reviewers make critical recommendations, but an important consideration is whether the study is technically sound and describes a significant new advance in the area. Unfortunately it appears that additional work is needed as indicated by reviewers. If these were meticulously performed, then I am sure that the MS could be reconsidered.

Manuscript require improvement in grammar, usage, and overall readability

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Kundan Kumar, PhD

Academic Editor

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

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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: 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: Though RNA-Seq based works are very common now-a-days for investigating role, discovery of candidate genes and markers and differential gene expression profiling, yet the work entitled “Comparative transcriptome analyses in contrasting onion (Allium cepa L.) genotypes for drought stress” is important in two respects, one the crop is commercially important and second, drought stress which causes huge yield loss. I commend the authors for this study, and would like some clarity on following points:

Comment 1:

“Authors performed de novo DGE analyses using aligned reads of drought-tolerant (1656C vs 1656D) and drought-sensitive (1627C vs 1627D) onion cultivars”.

I believe, the comparative analysis should have been made also between 1627D vs 1656D and 1627C vs 1656C. This could be important in better understanding the drought stress in tolerant and susceptible genotype.

Comment 2:

Why not genes were selected based on their high fold change value (negative and positive) and drought-related instead of random selection just for validation of RNA-Seq identified DGEs. Also the gene expression analysis at 6, 12, 18, 24 days should have been performed to correlate with biochemical and physiological data related to drought stress.

Comment 3:

The study comes out with a long list of drought stress-related such as genes encoding transcription factors, cytochrome P450, membrane transporters, flavonoids, and carbohydrate metabolism, etc. which showed differential expression behavior in tolerant and susceptible genotypes, it would not be much helpful in understanding the key role players. Can authors enlist few candidate genes for drought stress in onion based on present study?

Comment 4:

“Total phenol content that directly linked with the onion pungency and found to be elevated in response to drought stress”. Why none of the genes related to phenylpropanoid/Flavonoid pathway were included qRT-PCR.

Comment 5:

Discussion lacks on up-regulated genes in tolerant genotype like WAT 1 related protein, NINJA family AFP1, Methyl malonyl co-A epimerase and 21KDa Protein.

Comment 6:

Some figures labels needs clarity such as Figure 3 and Figure 5, the labels are difficult to read.

Reviewer #2: Introduction about onion is very shallow. Provide the data of onion production and loss occurs due to other stress and then mention the yield loss due to drought.

Introduction line no. 70: mention the name of the genotypes.

Introduction line no. 75-80 is the part of the result and do not need to describe here.

MM: 89: 1656 and 1627 are the cv nos? specify clearly.

MM: irrigated at 100% field capacity until they reached the 5-6 leaf stage, how come it is mentioned as field capacity, though plants are in pots.

L188: mention the name of selected genes, and site the table for the primers here.

Fig1 A: change sample as genotypes and treatments.

Morphological data should be added in main figure, shift from supplementary to main text.

L 200: significantly maintained the number of leaves, is it higher then edit the sentence as

Significantly maintained higher number of leaves

For membrane damage, authors are advised to include MDA data.

L 208, 209: incomplete sentence, please edit it: The observation recorded for leaf chlorophyll content was also in the same line 209 differing among the genotypes subjected to drought stress.

L 212: Total phenol content that directly linked with the onion pungency and found to be

elevated in response to drought stress.: and should be was

L258: , needs to be place before and after respectively.

Fig 3A-F, Fig. 5: font size is too small and is not readable.

L 305-353: data mentioned in the result section should be properly checked as at some point the fold expression has not been mentioned. Authors should uniformly mention the fold expression, where it upregulated or down regulated

L 354-359: The real time expression in the result section is written as MM part and result is missing. Pl write the result part properly. Move this write up in MM.

Prediction of SSR data does not fit relevant.

The authors are advised to correct the MS thoroughly.

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Reviewer #1: Yes: Dr. Ravi Shankar Singh

Reviewer #2: Yes: Pradeep K Agarwal

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Attachments

Attachment

Submitted filename: PONE-D-20-06651_Reviewers comments.docx

Comparative transcriptome analyses in contrasting onion (Allium cepa L.) genotypes for drought stress

PONE-D-20-06651R1

Dear Dr. G,

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.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Kundan Kumar, PhD

Academic Editor

PLOS ONE

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: Authors have responded well to the comments, and incorporated the suggestions in the manuscript.

So, the manuscript appears to be sound now and may be accepted for publication.

Reviewer #2: Authors has made all the correction properly of my comments, and now it can 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: Ravi Shankar Singh, Ph.D.

Reviewer #2: No