Review Reports

Round 1

Reviewer 1 Report

The manuscript reports result showing different expression of genes involving or/and regulating processes in two pepper lines, which have different tolerance to storage, in order to identified genes and metabolites associated with better resistance to storage, and thus help keeping of fruit quality. Using transcriptomics and metabolomics as advanced, efficient and information-rich approaches, authors found (i) that genes, related to carbohydrate metabolism, small molecule metabolism, and plant hormone signal transduction were differently expressed in the storage-resistant and non-resistant lines already at 3rd day after fruit harvest. They revealed (ii) distinctions in the biosynthesis of plant flavonoids and in glutathione, cysteine and methionine metabolism pathways between the tested lines.

The submitted manuscript fully meets the scope of ‘Horticulturae’ in particular, several major topic areas such as ‘Pre- and postharvest quality’, ‘Physiology, biochemistry, and molecular biology’, and ‘Product processing, storage, transport, and wastage’ (www.mdpi.com/journal/horticulturae). Obtained results contribute to the current knowledge of the molecular mechanism of storage tolerance of vegetables, and, in the future, could help reduce pepper post-harvest pepper losses. Materials and methods are well-described, and they allow the authors to fulfill the tasks of the investigation; the conclusions are consistent with the results.

I have no serious critical comments to the essence of this work, however, the submitted version of the manuscript should be corrected and edited prior to acceptance for publication.

Main comments and some specific suggestions are below.

1. I would recommend partial title editing. Some molecular mechanisms related to storage tolerance, which are realized in pepper fruits during a short-term storage, but not molecular mechanism of a storage itself were studied. Please consider the following title version as a possible one: ‘Investigating the molecular mechanisms of pepper fruit tolerance to storage via transcriptomics and metabolomics’.

2. Most of figures should be supplemented with more expanded explanation below captions. The general rule is that results illustrated by figures must be completely understandable to the reader when looking at them. For instance, it is necessary to clarify that A, B, A1, A2, B1, B2 (Fig. 1) indicate plant lines and days of storage. Again, clarify what the sub-figures A and B of Fig. 10 mean, and so on... It is insufficiently to mention explanatory phrases only in the text (e.g., lines 210-212, 359-365). Check this matter throughout figure captions.

3. Line 58.  Are you sure that ‘…the senescent PG in peach and tomato…’, but not ‘the PG in senescent peach and tomato’? 

4. Line 91.  Add the characteristic of lines there. E.g., in this way: ‘lines with different storage resistance, ‘A144’ (resistant to storage, named A below) and ‘A361’ (non-resistant to storage, named B), provided…’  There is a late first mention now: in Results, only in line 233.

5.  Authors should re-read the manuscript thoroughly and correct  numerous negligences (merged text – e.g., line 37 and others;  initials of the cited authors lines -115, 515; empty brackets – e.g., lines 188, 190 and others; excessive ‘ J’ in the reference list, and so on). Write Latin botanical names in italic.  Line 204.  Subsection 3.1 - what does this mean? 

Since the submitted version contains too many above-mentioned minor inaccuracies, I would strongly suggest correcting them before the proofreading stage.

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 2 Report

The manuscript entitled “Investigating the molecular mechanism of pepper storage via transcriptomics and metabolomics”, authored by Sun hao and colleagues, deals with the evaluation of the physiological examination, transcriptomic, and metabolomics mechanism under different storage resistances on peppers. The manuscript contains interesting information, but it needs an English check.

The main problem encountered during the revision of the manuscript is related to the style. It is quite clear that the revised manuscript derives from a previous submission to another journal. Authors should have carefully edit the manuscript before re-submit it. I strongly suggest the authors to read the submission instructions for authors before resubmitting again the manuscript to Horticulture (https://www.mdpi.com/journal/horticulturae/instructions).

The affiliation section should be filled as reported in author guidelines. In particular, each author's affiliation should be added. After affiliation, the email address, along with each author's acronym, should be clearly stated.

The first sentences of the abstract, in which authors explain the state of the art and the aim of the manuscript, is not very clear. Please, consider to rewrite it.

Keywords should be words not contained in the title, at most present in the abstract. Their usefulness is to make easier the searching of the article using the common scientific search engines. Since several keywords are already present in the title, and/or repeated several times in the abstract, I strongly advise the authors to add other keywords. As journal guidelines for authors clearly report, authors can provide up to 10 different keywords.

The introductory section is very well organized. It contains essential information both on the plant raw material and on the techniques used by the authors to fulfil their purposes. However, regarding the Materials and Methods section, I think that this section is very incomplete. While many of the techniques used in this manuscript are simple, well known, and widely used in different research laboratories, it is essential that the authors be more descriptive as possibile (for example, section 2.3.). Consequently, I strongly suggest that you review this section and add the missing information.

Please, distribute the Figures in the main text based on when they are first named. Moreover, remove Figure 11. References to supplementary figures should be included in the text, and not as images. Furthermore, a great many figures have never been named in the text.

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 3 Report

I think the manuscript "Investigating the molecular mechanism of pepper storage via transcriptomics and metabolomics" by Sun hao et al. is an interesting research focused on the postharvest of pepper. They used transcriptomic and metabolomic to indagate the mechanisms involved in fruit softening. 
In my opinion there are only a few aspects to fix. 

1. line 30. the scientific name of pepper needs to be written in italic style;
2. please check the spaces between words in the entire manuscript. for example: line 37 "economicvalue", line 100 "measure dim mediately".....and so on;
3. line 209. please replate figure 1 with fig 1 because later on in the manuscript you always use the abbreviation. 
4. can you add more information in the figures and tables caption (the bars are SE or SD, number of replicates, explain figure A, B...when you have more than one...)?
5. usually after Anova and post test if there is a significant difference between samples you put different letters or * on the bars. are there any significant differences in any of the data showed in figure 1 and 11?
6. can you improve the quality of figure 8, 9 and 10?
7. please remove the excel icons about supplementay materials.
8. line 533 there are 2 "that" words

Author Response

Please see the attachment.

Author Response File: Author Response.docx