Transcriptomic Response to Drought Stress in Populus davidiana Dode

Round 1

Reviewer 1 Report

The provided manuscript deal with the transcriptomic response of Populus davidiana Dode to drought revealed by Illumina high-throughput sequencing, which gives valuable contents on Populus davidiana, Results included phenotypic and physiological changes including ROS production in guard cells using fluorescent dye. Statistical analysis was very clear and simple only figure 2 g at least if nonsignificant  in my opinion it should show (ns).

Author Response

Please see the attachment

Author Response File: Author Response.pdf

Reviewer 2 Report

In the paper “The transcriptomic response of Populus davidiana Dode to drought revealed by Illumina high-throughput sequencing”, transcriptomic, physiological, and biochemical analyses have been conducted to mine P. davidiana response to drought stress. Metabolic pathways and genes modulated by water stress have been discovered and a hypothetical model of drought tolerance mechanisms in this poplar species have been proposed. The work represents a good starting point to mine P. davidiana response to limited water, but some parts are unclear and improvements are needed. Please consider the following comments:

1)      As indicated in the abstract (lane 18) and in Conclusions (lane 579) authors aimed at revealing the basis for the development and application of drought-tolerant genetic resources. Nonetheless, only one genotype has been utilized that, even if it is tolerant to drought stress, is not sufficient for such purpose. The comparison with one or more susceptible individuals is pivotal to discriminate between genes/metabolic pathways associated to resistance and those involved in basal stress response.

2)      The experimental design for RNA-Seq has not been described. In particular, how many biological replicates have been utilized? From Table 1 it looks that only one replicate has been considered even if it is not sufficient to support RNA-Seq statistical requirements. One biological replicate should be extensively validated by qPCRs on additional replicates. In this case, even for qPCRs the number of biological replicates is not indicated. In addition, the genes for validation have been chosen randomly. This is a good option for technical validation, but qPCRs should be conducted also for candidate genes in order to support their involvement in the considered metabolic process.

3)      A summary of the most interesting genes, including function, should be provided. A table might be useful.

4)      ANOVA test has been conducted on biochemical data. Did authors check for normality in data distribution?

5)      Transcriptomic data should be statistically integrated with physiological, morphological, and biochemical data. This analysis supports the discovery of candidate genes/pathways that has been indicated in lanes 422-423.

6)      A hypothetical model of drought tolerance mechanisms in this species has been delivered. A model showing gene interactions should be more useful. Authors can use WGCNA.

7)      A complete list of the identified DEGs is missing.

8)      Raw reads should be uploaded in a public database.

9)      Please avoid the description of NGS in introduction. On the other hand, the introduction on poplar drought response should be implemented with recent studies.

Sincerely.

English must be improved.

Author Response

Please see the attachment

Author Response File: Author Response.docx

Round 2

Reviewer 2 Report

The paper has been improved and some parts have been clarified.

It will be worth to add WGCNA interactions. The authors can ask more time for revisions to the editor.

The integration of transcriptomic, physiological, morphological, and biochemical data can be performed by means of PLS.

Sincerely

Minor revision

Author Response

Please see the attachment.

Author Response File: Author Response.docx