Transcriptome Analysis of Apricot Kernel Pistils Reveals the Mechanisms Underlying ROS-Mediated Freezing Resistance

Round 1

Reviewer 1 Report

The manuscript is potentially a good study but it needs to be extensively revised before a proper revision can be made. Many sentences lack verbs, and the meaning of the text is very hard to follow. Many ideas are very awkward and they seem to be a direct translation. For instance, “kernel apricots” should rather be apricot kernels. That is obviously very simple to understand and a simple swap can be made in the text but there are other meanings and sections in the text that are not comprehensive at all.

 

Scientifically, I have the following comments:

-          The introduction is very poorly written. It fails to proper address the aims of this paper and the mechanisms beyond ROS scavenging. The reason of studying pistils are missing. References concerning this subject and from other works in apricot are missing.

-          The number of samples and biological replicates used is missing. As such, I cannot access if the bioinformatics packages used are adequate for the analysis. The authors mention in the results that “RNA-seq data were generated for eight different cold-treated and untreated pistils to explore the molecular mechanism of the freezing resistance between CsL and CtW pistils during freezing stress.” But then they refer to 24 libraries. Without further explanation this is not comprehensive. The number of samples is apparently stated in Table 1 but it is not easy to follow the treatments.

-          Methods concerning mapping statistics, cleaning, quality control of reads or even how it was done are missing.

-          I have the same doubts for the analysis of DEGs. Authors mention “ overlapping DEGs were found in three groups.” Which 3 groups? By definition, DEGs cannot overlap anything – however, they can be shared between conditions but that needs to be explained.

 

-          “In CtW, 367 genes were up-regulated, and 142 genes were downregulated” – up and down in relation to what? 

Author Response

 

 

Reviewer 2 Report

 

Forests-1896547

 

Liu et al., submitted the manuscript entitled “Transcriptome analysis of kernel apricot pistils reveals the mechanisms underlying ROS-mediated freezing resistance

“for publication consideration in Forests. 

This study aimed to provide molecular genetics, genomic and biochemical information regarding kernel apricot, an ecological and economic dry fruit tree in China while facing spring frost which considered as a major limiting factor for kernel apricot the production and cultivation. 

The authors reported here A total of 3223 differently expressed genes (DEGs) were between two kernel apricot cultivars under freezing stress, such as bHLHs and AP2/ERF-ERFs transcription factors. By employed KEGG analysis, they concluded that DEGs were mostly enriched in the biosynthesis of secondary metabolites, metabolic pathways, and plant hormone signal transduction. The scientific soundness of this manuscript is acceptable. It meets the aims and scope of Forests journal. 

This study is interesting. The manuscript is written in a sound format, however, some issues required attention. Main points are listed below:

1.     Manuscript English writing need improvement significantly, it would be beneficial for authors asking some colleagues who speak native English help rewrite this manuscript. 

2.     Terms of spring frost, cold tolerance, freezing stress etc. were used at different sections without consistency.  It is not consistent through the manuscript and is hard to follow what exactly the authors try to explain in different sections. 

3.     It would be beneficial if the author could describe how their finding from this study would help to breed kernel apricot with improved cold tolerance (or spring frost resistance if authors preferred) trait especially in discussion section. 

The research is important and interesting. I am looking forward to see subsequent reports from the group. 

Author Response

This study is interesting. The manuscript is written in a sound format, however, some issues required attention. Main points are listed below:

1. Manuscript English writing need improvement significantly, it would be beneficial for authors asking some colleagues who speak native English help rewrite this manuscript. 

Response: We checked and revised the whole text by a professional scientific English service (https://susy.mdpi.com/user/pre_english/back/50919).

2. Terms of spring frost, cold tolerance, freezing stress etc. were used at different sections without consistency.  It is not consistent through the manuscript and is hard to follow what exactly the authors try to explain in different sections. 

Response: Cold stress contains chilling stress (0–15°C) and freezing stress (<0°C), and spring frost belongs to freezing stress. In our study, our treatments are uniformly written in terms of freezing stress, which is a simulated spring frost treatment. When referring specifically to the resistance to spring frost, it was written as frost resistance; Others according to the specific research situation were written as cold tolerance or freezing tolerance (resistance).

And we checked and corrected the use of spring frost, cold stress, freezing stress and cold tolerance terms throughout, and ensured they are in the right place.

3. It would be beneficial if the author could describe how their finding from this study would help to breed kernel apricot with improved cold tolerance (or spring frost resistance if authors preferred) trait especially in discussion section. 

Response: We added some descriptions about how our findings help breeding in the discussion section. “these potential functional genes involved in freezing stress can provide a choice for genetic engineering-assisted breeding through gene editing technology and a direction for molecular marker-assisted breeding.” And so far this help is limited for breeding.

Round 2

Reviewer 1 Report

Thank you for considering the previous comments. The names of the genes should be italicized (some are; some aren't). However, I believe this could be done during the proofreading of the final manuscript.

Reviewer 2 Report

Revised manuscript addressed all my concerns. 

Thanks