Quantitative Proteomics-Based Analysis Reveals Molecular Mechanisms of Chilling Tolerance in Grafted Cotton Seedlings

Round 1

Reviewer 1 Report

This manuscript provides an interesting report concerning the proteome of grafted and non-grafted cotton seedlings exposed to chilling stress. Although the main objective is very clear in the Introduction, I think it is somehow lost throughout the manuscript, which is barely descriptive and exhaustive to read. Authors obtained a large set of results and should emphasize the most significant ones, particularly those differing between grafted and non-grafted plants, so that the molecular mechanisms behind the increased tolerance provided by grafting can be highlighted. Also, the M&M needs to be improved; it is not clear what plant organs were subjected to the proteomic analysis. Also, more details concerning the number of replicates are needed. Only two replicates were considered?!

The Results section should be shortened and more focused to gain the attention of the readers. Also, the Discussion needs to be majorly revised. It is too much descriptive and does not provide any further insight into molecular networks activated or not by the chilling/grafting combination.

 

For these reasons, the MS is not suitable for publication at its present state.

Author Response

Dear Reviewer,

The authors appreciate the valuable comments by the reviewer. We have carefully considered the comments and revised the manuscript accordingly. A point-by-point response is as follows. The reviewers’ comments are in black and our responses are in blue. The modifications in the revised manuscript are in track changes. We hope these modifications are acceptable to you. We look forward to hearing from you soon. Thank you again for your time and consideration.

Author Response File: Author Response.docx

Reviewer 2 Report

Dear Authors,

Climatic changes are present all over the world and have a real result on agricultural and horticultural crops and this could be a threat to food security.

In recent years, many regions have experienced late frosts that have caused significant crop losses.

Finding viable solutions to protect crops from these high-cost climate accidents is a real challenge for researchers.

The paper is well described and the methods used are scientifically appropriate. Only a few points should be addressed by the authors:

• Line 94-95 – It is not specified how many plants were used in the experiment (number of grafted seedlings, rootstock seedlings, and scion seedlings)
• Line 96-98 – please specify how many plants the bark was collected
• Table 1 – Please insert the title of the table, on the same page, above the table
• Figure 4 – the names of the enzymes are hard to read, and the fonts are blurred. In my opinion, it will be easier to follow the figure if using some colored signs instead of codes (e.g. 2.7.7.9 – green bullet; 4.1.2.13. – red bullet, and so on)
• Line 383 – please Uppercase font at the beginning of the sentence
• Lines 244, 286, 363, 377, 396, and so on, please write the number at the beginning of the phrase

Thank you!

Author Response

Dear Reviewer,

The authors appreciate the valuable comments by the reviewer. We have carefully considered the comments and revised the manuscript accordingly. A point-by-point response is as follows. The reviewers’ comments are in black and our responses are in blue. The modifications in the revised manuscript are in track changes. We hope these modifications are acceptable to you. We look forward to hearing from you soon. Thank you again for your time and consideration.

Author Response File: Author Response.docx

Reviewer 3 Report

Dear authors,

 

The manuscripts agronomy-1665896 untitled “Quantitative proteomics-based analysis reveals molecular mechanisms of chilling tolerance in grafted cotton seedlings” revealed the differences of gene regulation and the effects of grafting after chilling stress from the protein level. It is valuable research. However, authors did not take care about the arrangement of tables and figures, I suggest authors take care of this part carefully, and some data was missing in the Table 2 on the page 6. I suggest authors check the data carefully when you upload them in this manuscript. Others comments are mentioned below.

 

Major comments

1. Line 46-55, did authors try to explain how low temperature affects normal plat growth, geographical distribution, yield, and quality? I suggest authors rewrite this part and make more readability.
2. Check all numbers of headlines and sub-headlines. For example, change “1. Materials and Methods” to “2. Materials and Methods”, and others such as “1.1. Plant materials, Growth and Sampling”, “1.2. Protein Extraction”, ………”1. Results”, “1.1. The overview of differential proteins based on categories of pathway”……..”1. Discussion”….
3. Line 198-199, so much information was lost in table 2, for example proteins detected, proteins before grouping, distinct peptides……
4. line 222-223, authors mentioned that chilling stress increased the total proteins, but it is looks like the total protein decreased depend on table 5. Are there some mistakes in Table 5, or the description of this sentence?
5. Line 264, and Table 4 on the page 11, I did not find the information for NP_187685, XP_001767949, did authors missed these data? Line 284-285, there are not upregulation after chilling stress for S compared to S’.
6. Please carefully check the name of proteins from line 294 to line 311, because I cannot find some protein names in tables but you have mentioned them in the result section. For example, in line 299, where is the Table 8? Is it Table 5 on the page 15? Please arrange the Tables and Figures carefully.
7. Line 339, line 348, I did not find table 8 in this manuscript. Authors may miss upload it.
8. Line 351-352, it is not table 4, it may be table 6 on the page 18. Line 354, I did not find table 10. Line 356, the table 10 is table 6 on the page 18?
9. Please clearly check the tables and protein names from line 376-485.

 

 

 

Minor comments

1. Line 41-42, keep space between “7.4” and “%”, between “10” and “%”, and between “losses” and “[1]”.
2. Line 58, change “impairing” to “impairs”.
3. Line 97, delete one space between “under” and “a”.
4. Line 121, delete comma after the “g”.
5. Line 125, delete the “was” before “from”.
6. Rearrange tables and figures. For example, the Line 130 on the page 4, it should be Figure 2; Change Table 1 and Table 2 to Table2 and Table 3 on the page 5 and page 6; change Figure 2 to Figure 3 on the page 9, change Table 3 to Table 6 on the page 10, change Table 4 to Table 7 in the line 250 on the page 11,……….and so on.
7. Line 135-136, rewrite the sentence “Solvent A contained……in solvent A”.
8. Line 202, what is KEGG pathway, I suggest authors mention the full name of KEGG.
9. Please arrange the sub-headlines in results section correctly.
10. Line 247, is it 18 differential proteins? I found 15 proteins related to carbohydrate mentalism in Table 7.
11. Rearrange the headlines’ number in the Discussion section.

Author Response

Dear Reviewer,

The authors appreciate the valuable comments by the reviewer. We have carefully considered the comments and revised the manuscript accordingly. A point-by-point response is as follows. The reviewers’ comments are in black and our responses are in blue. The modifications in the revised manuscript are in track changes. We hope these modifications are acceptable to you. We look forward to hearing from you soon. Thank you again for your time and consideration.

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

Dear Auhors,

I am sorry, but I cannot find the employed revisions since they are not marked. So, I suggest the authors highlight the changes so I can review them once again.

 

Yours sincerely,

Author Response

Sorry, the revised WORD manuscript we uploaded has traces of modification, but the PDF manuscript has not been uploaded. This time, we uploaded two revised versions of WORD and PDF.

Reviewer 3 Report

Dear authors

 

You have revised the manuscript agronomy-1665896-peer-review-v1 well. However, you didn’t arrange the figures well. For example, the figure 1 on the page 8 should be figure 3.

Author Response

Thank you for your careful review. It has been revised according to your comments.