Dynamic Network Biomarker Analysis Reveals the Critical Phase Transition of Fruit Ripening in Grapevine

Round 1

Reviewer 1 Report

The manuscript entitled "Dynamic network biomarker analysis discovers the critical phase transition of fruit ripening in grapevine" analyzed the genes related to grapevine fruit ripening and identified 68 genes. The manuscript is well written, and the findings are meaningful for grape researchers.

I just have the following two minor revisions.

1. The resolution of all the figures has to be enhanced.

2. Lines 262-265 have to be deleted.

 

Author Response

Response to Reviewer #1

Comment: The manuscript is well written, and the findings are meaningful for grape researchers. I just have the following two minor revisions. 1. The resolution of all the figures has to be enhanced. 2. Lines 262-265 have to be deleted.

Response: Thanks for the positive comments and suggestions on the manuscript. We have improved the resolution of the figures and deleted the related lines in the revised manuscript according to the suggestions.   

Reviewer 2 Report

Dear Authors,  

this paper is very interesting and relevant, simply and comprehensibly written, yet a complex and modern methodology was used to obtain these valuable results. I would like to propose the paper for publication after minor revisions. Please, find comments in the attached pdf file.

Best wishes, 

Reviewer

Comments for author File: Comments.pdf

Author Response

Response to Reviewer #2

1. Comment: Figure 1 is very nice, only ensure high quality resolution for all figures.

Response: Thanks for the positive comments and suggestions. We have improved the resolution of the figures in the revised manuscript.

 

2. Comment: The results from line 246 to 252 seem very important for this study, also later in discussion and conclusions. Please if you can include more references to explain these results, e.g. is it known which kind of genes/ gene clusters are upregulated, downregulated, possibly why?, connect lower abundance of upregulated genes with conversions in berry during ripening especially this transition stage--> maybe mention source- to- sink relations in berry and photosynthetic activity, change from green (asimilate producing) to colored (asimilate consuming) berry stage, this conversion is very important and if possible need to be discussed in more details. If possible, it would be helpful for further studies to list a few best markers, most specific markers to define transition 'moment' etc.

Response: Thanks for the suggestions. We have added the GO enrichment analysis to explain the result of differential expression genes. We performed GO enrichment analysis in order to understand the function of differential expression genes before and after the key transition point of grape berry ripening. The results showed that 873 genes were assigned to GO terminology. Among them, the terms "gene expression", "macromolecular metabolic process", "carbohydrate derivative metabolic process" and "carbohydrate catabolic process" are significantly enriched in the biological process category GO terms such as "RNA binding", "oxoreductase activity", "structural molecular activity" and "organic cyclic compound binding" are significantly enriched into molecular functional categories. The second transition point upregulated 73 of the 81 genes expressed were assigned to the GO term. Among them, the biological process categories are significantly enriched: "nitrogen compound metabolism process", "cell metabolism process", "macromolecular metabolism process" and "organic matter metabolism process" and other terms. Terms such as "catechol oxidase activity", "carbohydrate derivative synthesis" and "selenium binding" are significantly enriched into molecular functional categories. In addition, terms such as "cellular component", "protein-containing complex", and "intracellular organelle" are significantly enriched into the cell component category. (Paragraph 1 Page 9)

 

3. Comment: Fig 2 scheme is very valuable and explanation clear.

Response: Thanks for the suggestions. We have revised the introduction of the scheme in Figure 2. (Paragraph 1 Page 5)

 

4. Comment: switch the numbers, 878 should be red? please clarify T4, T2, T9 and T7 in the text and figure caption.

Response: Thanks for the suggestions. We have revised the numbers in the figure and clarified these time points in the revised manuscript. (Figure 6 and Paragraph 2 Page 8)

 

5. Comment: comment for line 266 - 270: This paper dealt with concrete aims, clear and practical results obtained with new powerful methodology, directly helpful for breeding programs. Try to focus on your results and connect them with the previous results. This topic is very relevant, and poorly studied as was mentioned. However, certain amount of previous results can be connected to this study. For example, issue of epigenetic models in ripening, recently challenge models based on mutations in tomatoes etc. (Kong et al., 2019).

Response: Thanks for the comments. We have supplemented some analysis for ripening genes. (Paragraph 1 Page 8)

 

6. Comment: this part is very important, very vibrant atmosphere regarding gene activity, transcriptome, TF (transcription factors), hormon signals.

Response: Thanks for the comments. We have checked it for accuracy.  

 

7. Comment: If it is possible, it would be helpful to relate your results with the previous, e.g. ABA seems to have important/critical role for ripening of non-climacteric fruits (while ethylene for climacteric). Can you make connection with ABA related genes, or some other that were previously reported to have significant role in ripening e.g. H3K27me3 - related to ripening VviCEB1 - regulates berry size and softening, some AQPs, VvDTC 2 and 3 stronger signals in mesocarp at the onset of ripening, ABA (NCEDs) color related genes: VvPAL1, VvDFR, softening related genes and so on. if possible relate ripening your result with previously reported traits at chromosome 16 for: veraison (Topfer et al., 2011) Since this is very complex matter it also needs to be emphasised that ripening is affected by genotype, viticultural practices and environment.  references: Kong et al, Falchi et al. (2019 in The Grape Genome)

Response: Thanks for the suggestions. We have checked these papers and provided more analysis on the related genes of ripening in the revised manuscript. (Paragraph 1 Page 10)

 

8. Comment: it would be informative to highlight, out of cluster of genes in DNB peak, a few most active/informative marker genes in this process, if possible, and if relevant? Is there any signal for specific parameter that would mark the beginning of ripening, such as mentioned earlier for sweet potato ( IbNAC083)?

Response: Thanks for the comments. We have identified DNB genes as candidates for the regulation of beginning of ripening. But we didn't perform the experiments for the limitation of wet experiment in our lab. So we provided the gene list as reference for other researchers with interest.

 

9. Comment: (1) 'Vitis vinifera L.' should be in italics. (2) 'ontology' is not right. (3) second sentence in the section 3.2. maybe "obtained" instead of "resulted". (4) 'lipid' is not right. (5) here you can add: 'PSI peak', or explain which kind of peak, peak in reaching transition point in berry maturity..etc.. (6) reach, achieve or obtain? (7) instead of 'to be'. (8) and non-climacteric?

Response: Thanks for the comments. We have revised these errors in the revised manuscript.