PONE-D-23-35009Genome-wide analysis of MADS-box transcription factor gene family in wild emmer wheat (Triticum turgidum subsp. dicoccoides)PLOS ONE

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Muhammad Abdul Rehman Rashid, PhD

Academic Editor

PLOS ONE

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 [GM was supported by Iran National Science Foundation (INSF) grant 99014038. The funding doesn't include publication fee.].  

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[GM was supported by Iran National Science Foundation (INSF) grant 99014038.]

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 [GM was supported by Iran National Science Foundation (INSF) grant 99014038. The funding doesn't include publication fee.]

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Reviewers' comments:

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Comments to the Author

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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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Reviewer #1: Yes

Reviewer #2: Yes

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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: In the manuscript (Genome-wide analysis of MADS-box transcription factor gene family in wild emmer wheat), The authors demonstrated that members of MADS-box gene family played an important role in the regulation of plant growth and development. A total of 117 MADS-box genes were identified in the wild emmer wheat genome, which were classified into MIKCC, MIKC and 2M types. The gene expression profiles in different tissues and developmental stages conform to the MADS-box gene subfamily classification, which is similar to common wheat and rice, suggesting that they have conserved functions. Some MADS-box genes were differentially expressed under drought stress. The response elements in the promoter region of the MADS-box gene are mainly related to light sources, but are also related to hormones, drought and low temperature. The results revealed detailed information about the MADS-box gene in wild emmer wheat. However, I think the manuscript should be revised before publication.

Major:

1. Articles cited need to be time-sensitive, the years of some published references are too long, try to refer to the literature of the past ten years.

2. The introduction part need to be polished further to highlight the background and importance of the manuscript.

3. Some of the language in the manuscript needs improvement. Some sentences should be reorganized.

4. The order of the materials and methods is somewhat chaotic, and should be elaborated in sequence according to the primary and secondary order.

5. The first paragraph of the discussion section does not highlight the important themes of the article, and the discussion needs to better clarify the importance of the current findings and how they take the field forward.

6. As an important part of the paper, the conclusion is too simple and needs to be enriched.

Minor:

1. Page 5, the part "Naming of MIKC-type MADS-box genes" should be placed in the first part of "Materials and Methods".

2. Page 12, Line 17, "Treas", should be capitalized as "TRAES".

3. Page 14, Line 6, the background color of "presence" is incorrectly used.

4. Some of the formats of the references need to be adjusted.

Reviewer #2: The purpose of the study seems somewhat sound but some major revisions need to be made before it can proceed further for proper consideration in PLoS One.

1. The ‘Introduction’ section should begin with a background to wheat and the problems its facing and then the significance of the gene family in other wheat species (in any available) or closely related species.

2. Give the ‘e-value’ for BLASTp used with HMM. Also, the reason behind using old MAFFT instead of MUSCLE as it is a medium-to-large protein multiple sequence alignment.

3. Abbreviation detail should only be given when first used. Check this throughout the manuscript.

4. Experimental verification of curated and potent MADS-box genes through qRT-PCR should be provided to enhance the quality of the results and the overall study in study.

5. The results are also not clearly written with some instances of using first person singulars (such as under the heading ‘Expression of MADS-box genes’). This should be rectified.

6. Although, the overall write-up of the manuscript is descent yet I would suggest the use of suitable punctuation (such as in abstract), break large sentences into smaller ones, italicize the scientific names and genes, and re-read the manuscript for clarity.

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Reviewer #1: Yes: Guang-Long Wang

Reviewer #2: No

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Genome-wide analysis of MADS-box transcription factor gene family in wild emmer wheat (Triticum turgidum subsp. dicoccoides)

PONE-D-23-35009R1

Dear Dr. Mirzaghaderi,

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,

Muhammad Abdul Rehman Rashid, PhD

Academic Editor

PLOS ONE

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