Transcriptomic Analysis of Sodium-Silicate-Induced Resistance against Rhizoctonia solani AG-3 in Potato
, Dongmei Zhang 1,3, Hongli Huo 1,3, Lele Li 1, Zhijun Xiu 1,3, Chunfang Yang 1,3 and Xiaoyu Zhang 1,*
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe MS has scope to improve in the scientific writing
Author Response
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Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThe authors conducted a transcriptomic analysis of genes in Rhizoctonia solani infected potato after sodium silicate treatment. They did RNA-seq and qRT-PCR and found the pathways affected by sodium silicate. According to the genes they identified, sodium silicate treatment can activate plant physical barriers, trigger innate immunity, regulate plant hormone and phenylpropanoid compounds to affect plant resistance against R. solani. This study provides valuable information to study the Rhizoctonia solani resistance. There are a few things I recommend changing.
Major points:
The information about inoculation needs to be added to the results. The authors conducted Rhizoctonia solani inoculation on potato before collecting RNA for RNA-seq but didn’t mention the inoculation results. Since they claimed sodium silicate can improve potato resistance against R. solani, I think it’s better to add the results showing that sodium silicate treated potato does better than the control.
I have some concerns about the RNA-seq results since the gene expression of three time points are so different from each other according to figure 1b and figure 2. I want to ask are there any artificial effects for these samples? For example, was sample collection conducted by different samplers for different time points or was RNA extraction of three time points conducted by different samplers? Does the Venn diagram in figure 1b show both up-regulated genes and down-regulated genes? Since I noticed in that figure, the number of DEGs detected in all three time points is 3, but in the following text, more genes were described to show changes in the different time. For example, in the hormone transduction pathway part, PYL4, ABF, JAZ, PR-1 and ETR showed different expression level in 4, 8 and 12dpa.
Minor points:
Line 213-244 and 308-310 The expression pattern of CNGCs), CDPK and CaM / CML were mentioned twice in this paragraph (line 214-244). I recommend removing one to reduce redundancies. The expression of FLS2 was also mentioned twice in this paragraph. Please also verify the information in line 310 since the expression of FLS2 in this line is not consistent with the previous paragraph.
Line 2, 12, 14, 15, 25, 95 Rhizoctonia solani à Rhizoctonia solani
Line 108 ranged à ranged from
Line 110 provide à provides.
Line 126 Figure 1. Legend entry of down-regulated is missing. Position of (A) and title of figure 1 (A) needs to be adjusted. (B) for figure (B) is missing
Line 155-159 are assigned à were assigned.
Line 218 patterns recognition receptors à pattern recognition receptors
Line 233 calcium-dependent protein kinase (CDPKss) à calcium-dependent protein kinases (CDPKs)
Line 245 successful à successfully
Line 271-273 Table 1. The width of columns needs to be changed. It seems some words in KEGG definition column are missing.
Figure 283 Figure 8 The position of the 3 figures on the right needs to be adjusted.
Line 366 we àWe
Line 409 and 410 Please verify the concentration of sodium silicate.
Line 459-460 Version of R package
Supplementary tables: The table number of supplementary table 11-14 were mislabeled.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsI have gone through the manuscript on Transcriptomic analysis of sodium silicate-induced resistance against Rhizoctonia solani AG-3 in potato. It is written well and discussed all the findings.
How many replications for used transcriptome analysis per treatments?
In Discussion part, add one paragraph on Black scurf of potato and pathogen.
Figure 1B- increase the font size for better visibility
Figure 6 & 7- improve the quality of figure for clarity
The study was focused the role of sodium silicate for defense strategy in potatoes against R. solani infection.
The conclusion can be improved.
How you can utilize further these findings?
Author Response
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Author Response File: Author Response.pdf
Reviewer 4 Report
Comments and Suggestions for AuthorsDear Authors,
My comments:
1. The Latin name should be in italics.
2. Where was the experiment done? in greenhouse? should be written in the abstract.
3. Please change figures 6 and 7 to clear one, or increase the size of the letters. It is invisible.
4. I suggest making a separate conclusion from the discussion part. And give more information about the results in the conclusion part.
5. Please add previous studies and analog research about DEGs and pathways to the introduction.
I added my comments to the pdf file.
Good luck and thank you.
Reviewer.
Comments for author File: Comments.pdf
Author Response
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Author Response File: Author Response.pdf
Reviewer 5 Report
Comments and Suggestions for AuthorsDear Author,
I reviewed the manuscript entitled “Transcriptomic Analysis of Sodium Silicate-induced Resistance Against Rhizoctonia solani AG-3 in Potato”.
This research reveals identification of transcripts in potato using sodium silicate and expression levels of some important genes in against the Rhizoctonia solani AG-3 infection.
-Line 277-277 ‘These genes were randomly chosen for the validation analysis. These gens were randomly chosen for the validation analysis.’ Sentence repetitions should be edited.
-Statistical differences between hours should be shown in Figure 1.
- The effect of sodium silicate on preventing Rhizoctonia solani AG-3 in potatoes should be given.
- Line 406-407 No reference is given for the inoculation method; it should be added. Rhizoctonia solani does not produce spores. How was a homogeneous measurement made? It is not understood.
-Defining the effect of sodium silicate against stem canker infection in potatoes on genes related to resistance in the plant and detecting changes in important genes made the study original.
-This manuscript is written in acceptable good English.
- Significant gene differences tested should be mentioned in the abstract.
My general opinion is that the article is of a quality that can be published after minor revision. I also believe that it will receive citations as studies in this field increase.
Sincerely
Author Response
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Author Response File: Author Response.pdf
Reviewer 6 Report
Comments and Suggestions for AuthorsThis transcriptomic study investigated the genetic mechanisms underlying the resistance induction by the treatment with sodium silicate in potato against the infection of the fungus Rhizoctonia solani AG-3 . An accurate analysis of differentially expressed (up- and down-regulated) genes in treated potato plants was perofrmes.
My only criticisms are as it follows:
- Methodology.: I expected that the transcriptomic study was correlated with the phenotypic expression of the infectio; by contrast I did not find any mention of disease severity in sodium silicate-treated and not treated potato plants.
- English style: has to be improved (see text editings in the attached PDF file)
- References: According with the editorial style of the journal references in the text have to be cited with numbers in order of citation
Overall the quality and the subject of the study conform to the standard and the scope of the journal.
Comments for author File: Comments.pdf
Moderate improvement is requested
Author Response
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Author Response File: Author Response.pdf
Round 2
Reviewer 6 Report
Comments and Suggestions for AuthorsThe Authors have addressed all criticisms and filled the gap concerning the phenotypic effects of infection by R. solani AG3 by adding a supplemental file with fine pictures. The English style of the text has been improved according with the suggestions inserted as notes in the text.
