Comparative Transcriptome Analysis Reveals Key Insights into Fertility Conversion in the Thermo-Sensitive Cytoplasmic Male Sterile Wheat
Round 1
Reviewer 1 Report
Comments for author File: 
Comments.docx
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comment
I think the paper is well written, rigorous, and statistically robust.
Minor comment:
1. Section 2.4. The authors introduced two variables for the differential expression (genotype and environment): two genotypes (FA* and J*) under two different fert environments (B* and D*) and implemented mostly pairwise model framework.
It would be interesting if the authors could implement more complex model:
complex models examples:
1.genotypic DE: (B-FA*, D-FA*) vs (B-J*, D-J*)
2. residual DE: B-FA* vs B-J* vs D-FA* vs D-J*
3. 3-way DE - to determine G x E interactions
This is a suggestion and the authors are free to ignore if not part of the paper's aim.
Minor suggestion:
1. I suggest that the authors use the v2 of IWGSC. This is just a suggestion and the authors are free to ignore/consider it as I know how tedious it would be to shift to another reference genome. #line 465
2. p-value < 0.05; FDR<0.05 p values have lots of noises. why not use FDR for multiple testing Ho #line 470
3. line 477 "softwares" should be "software"
4. labels of the figures are pixilated/blurry in the manuscript (but they are clearer in the attached figures). please improve them
5. line 65-67 improve statement
6. In section 2.1, indicate statistical test used.
7. Some statements need improvement of the grammar.
Please see attached pdf file for minor edits.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
