Transcriptomic Analysis and Identification of Candidate Genes Involved in Rhizome Development in Agropyron michnoi

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript "Transcriptomic Analysis and Identification of Candidate Genes Involved in Rhizome Development in Agropyron michnoi Roshev” investigates the molecular mechanisms underlying rhizome development in Agropyron michnoi, a perennial grass known for its resilience in arid environments. The study is well-structured and methodologically sound, employing different molecular techniques and clearly described experimental procedures. The authors identified 129 differentially expressed genes as rhizome-specific end pathways where these genes are involved. The manuscript represents a significant advancement in understanding the genetic basis of rhizome development. The identification of candidate genes and metabolic pathways provides a valuable resource for future breeding programs and forage quality in perennial grasses. Ethical issues do not raise concern.

Minor remarks:

Many environmental factors influence the development of the rhizome. The study does not address how these conditions affect gene expression or rhizome formation.

Species name should be italicized.

Comments on the Quality of English Language

The English language is understandable.

Author Response

Dear Reviewers,

Thank you very much for your time and professional insights in reviewing our manuscript titled “[Transcriptomic analysis and identification of candidate genes involved in rhizome development in Agropyron michnoi]”Manuscript ID: agronomy-3501402. We truly appreciate the detailed feedback, which has been extremely helpful in enhancing the quality of our work. Below, we present our point - by - point responses to your comments and suggestions.

 

The revision marks in the text are set with a green background color.

 

Response to Reviewer 1：

 

Comment 1:

Many environmental factors influence the development of the rhizome. The study does not address how these conditions affect gene expression or rhizome formation.

Response 1:

We have added content in the introduction section of the article to address the questions you raised, as follows:

Currently, research on rhizomes mainly focuses on the impact of environmental factors on plant rhizomes. Temperature, as one of the key environmental factors, can significantly regulate the growth rate and morphogenesis of rhizomes. Studies on perennial rice have found that compared with higher temperatures (28 - 30℃), lower temperatures (17 - 19℃) are more conducive to promoting the germination of axillary buds, enhancing the negative gravitropism of branches, and thus resulting in shorter rhizomes[17]. In a low temperature environment, the upward growth of branches occurs earlier than in a high temperature environment, leading to a higher frequency of short rhizomes and smaller branch angles.Water supply also plays a crucial role. Sufficient water can maintain the turgor pressure of rhizome cells and ensure the smooth progress of material transport and metabolic activities. Under water deficient conditions, rhizomes often experience growth stagnation, morphological changes and other conditions[18]. The soil nutrient status also has a profound impact on rhizome development. The contents and ratios of macronutrients such as nitrogen, phosphorus, and potassium, as well as micronutrients such as iron and zinc, will directly or indirectly act on the hormonal balance, gene expression, and metabolic pathways within the rhizomes, thereby affecting the growth, branching, and nutrient absorption capacity of rhizomes[19]. Therefore, it is of great significance to conduct research on rhizome development using molecular biology methods.

 

Comment 2:

Species name should be italicized.

Response 2:

We have checked and adjusted the species names throughout the article. The specific revisions are marked in the original text.

Finally, we would like to express our sincere gratitude to all reviewers for their invaluable comments on the paper.

 

Thanks very much.

 

Kind regards.

 

Reviewer 2 Report

Comments and Suggestions for Authors

Agropyron michnoi Roshev. is a grass plant native to Mongolia and central China. In its native habitat, it is used as livestock feed.
In this paper, RNA sequencing was used to identify genes involved in rhizome development, which I think is commendable.

1.    I don't know the sequence of the primer for RNA sequencing. I think it would be better to make a table.
2.    I don't know what DNA sequencer you used for RNA sequencing. I think it would be better to write down the equipment you used.
3.    MEGA7, which was used to analyze the phylogenetic tree, is an old software. I think it would be better to re-analyze it using the latest MEGA11.
4.    I think it would be better to include boot-strap values in the phylogenetic tree in Figure 8-(A).

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

Dear Editors and Authors,

I read the manuscript "Transcriptomic analysis and identification of candidate genes involved in rhizome development in Agropyron michnoi Roshev" with interest. In this study, the morphological comparison of rhizomes, roots and stems was made by paraffin section technique, and by using high-throughput next-generation sequencing, we sequenced the transcriptomes of different tissues (including rhizomes) in A. michnoi to identify potential candidate genes and pathways involved in rhizome development. The article's subject is important and relevant to the study area's scientific environment. Therefore, the manuscript needs some adjustments so that it can then be forwarded to the publication process. The manuscript has the potential for publication in this journal Agronomy, and needs the following adjustments:

First, review the newspaper's rules. The structure is Introduction, Material and Methods, Results,...;

TITLE

- The species name must be in italics (Agropyron michnoi).

ABSTRACT

- The objective mentioned should be similar to that mentioned in the Introduction.

What variables were analyzed? What methods were used in this research? Information about materials and methods is not present. I suggest including this information. The objective was described, and then the results of the study were presented.

- When abbreviating the scientific name of the species, it is not necessary to keep the name of the classifier together with the abbreviation (Roshev.). Review this throughout the text.

- Some abbreviations were added and were not mentioned in the text. I suggest removing the abbreviation.

- I do not suggest discussing other species, such as Arabidopsis. This discussion should be mentioned in the Discussion section.

- Replace the keywords that are repeated in the title. This will help people search for the article after it has been published.

INTRODUCTION

- Expand this section. Three paragraphs are too little.

- Some information requires references, such as "In A. michnoi, the rhizome is not uniformly developed".

- Add hypotheses before mentioning the objectives.
- "In this study, The morphological comparison of rhizomes, roots and stems was made by paraffin section technique and by using high-throughput next-generation sequencing, we sequenced the transcriptomes of different tissues (including rhizomes) in A. michnoi to identify potential candidate genes and pathways involved in rhizome development."
This objective needs to be modified. It is not necessary to detail the analyses performed in such detail.

MATERIAL AND METHODS

- Insert the geographic coordinates of the study site.
- How were these plants cultivated in three years?
- Detail how the cultivation was done and management during the cultivation of these plants, among other information.
- How old is the plant shown in Figure 3?

RESULTS

- Which study was based on the anatomical structure described in the first paragraph?
- The figures are of good quality.
- When describing the results, always mention Figures or Tables at the end of the excerpt. This was not done for some sections.
- The font size of the text in Figure 8 should be reduced.

DISCUSSION

- Some paragraphs need to be reduced or divided; for example, the paragraph continued on page 16.
- Some sections have already been mentioned in the results.
- Review this entire section.

CONCLUSION

- "In this study, the root, stem and rhizome tissues were analyzed through paraffin sections, and it was found that the rhizome had a high similarity to the root and stem."
This is not a Conclusion. I suggest removing this section.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 3 Report

Comments and Suggestions for Authors

The manuscript has been corrected.