Transcriptome and Metabolome Profiling Unveil Pigment Formation Variations in Brown Cotton Lines (Gossypium hirsutum L.)

Round 1

Reviewer 1 Report

Colored cotton has been a major interest to cotton breeders and a lucrative proposition for cotton industry. Although several colors and the variants of shades have been developed but the major constraint in industrialization of colored cotton has been due to medium fiber length, low strength and color fading. The manuscript ijms-2233301 describes the transcriptomics and metabolomics analysis of WCF, LCF and DCF. It is the first in depth study on the subject. The differentially expressed genes in the three cotton lines have been very well studied along with their relevant pathways. The upregulated and down regulated genes and metabolites have been identified for the color variants and the findings will no doubt pave way to utilize the reported information to engineer color pigmentation pathways in cotton lines haven best fiber traits. The manuscript provides extensive amount of data for further explorations. I believe the authors will further try to identify the photo reactive metabolites responsible for color leaching to consider the alternative approach to the proposed one.

Author Response

Dear reviewer,

    Thank you very much for your valuable comments. According to the results of the research in the manuscript, we have selected some DEGs relative to signification metabolites to further study their functions responsible for pigment formation in natural colored cotton, and achieved some satisfactory results. The findings will provide new insights for cotton breeders.

Reviewer 2 Report

In the current study, the authors have compared the deep brown cotton, white cotton and light brown cotton using transcriptomics and metabolomics tools. They provide new insights related to regulatory mechanism controlling different brown pigmentation in cotton fibers. In my opinion, this manuscript has good potential for publishing in IJMS.

My comments:

-          Line 72-73: Scientific name should be provided in italic.  Please check the entire text.

-          I suggest to transfer Table 1 to Supplementary data.

-          Line 254-265: gene name be provided in italic. Please check the entire text.

-          Main conclusion should be added to manuscript.

Author Response

Dear reviewer,

    Thank you for your attentive suggestions. We have modified the details and provided a point-by-point response to the reviewer’s comments as follows:

1. We have changed the names of species into italics through the entire text in the revised manuscript.
2. We put Table 1 in the text as a supplemental data.
3. We have modified all gene name in italic through the whole article in the revision of manuscript.
4. Some main conclusion have been added to the appropriate paragraph in the revised manuscript.