The Integration of Metabolomics and Transcriptomics Provides New Insights for the Identification of Genes Key to Auxin Synthesis at Different Growth Stages of Maize

Round 1

Reviewer 1 Report

The manuscript “Integration of metabolomics and transcriptomics provides new insights for identification of key genes for auxin synthesis at different growth stages of maize” by Zhenzhong Jiang et al. analyzed global gene expression and metabolites dynamics during different growth stages of Maize. The authors integrated transcriptome and metabolome analysis to find differential regulated genes and secondary metabolites. Besides, the authors focused on the auxin biosynthesis pathway to understand how auxin is regulated during maize development. Overall, the research aim is of great interest for both fundamental research and application, the manuscript might require minor revision.

 

Minor points:

1.     line418-419：Please provide basic information on the growth conditions, e.g., temperature, soil, irrigation, and fertilization.Please also specify the city location of the study site. It is also good practice to specify the latitudinal and longitudinal coordinates of the study site.

2.     Line420: (maize inbred line) You currently provide no information on the inbred lines used, their origins, and whether either have a varietal name/code. In addition, there is no information on the number of plants grown and the planting density.

3.     Line450“the reference genome”Please specify the version and source of the genome assembly used.

4.     So that the figure is understandable in isolation from the text, I suggest adding legends

Author Response

The manuscript “Integration of metabolomics and transcriptomics provides new insights for identification of key genes for auxin synthesis at different growth stages of maize” by Zhenzhong Jiang et al. analyzed global gene expression and metabolites dynamics during different growth stages of Maize. The authors integrated transcriptome and metabolome analysis to find differential regulated genes and secondary metabolites. Besides, the authors focused on the auxin biosynthesis pathway to understand how auxin is regulated during maize development. Overall, the research aim is of great interest for both fundamental research and application, the manuscript might require minor revision.

Reply: Thanks for your suggestion, I made changes in the manuscript, and the changes are marked in green

Minor points:

1. line418-419：Please provide basic information on the growth conditions, e.g., temperature, soil, irrigation, and fertilization.Please also specify the city location of the study site. It is also good practice to specify the latitudinal and longitudinal coordinates of the study site.

Reply: Thanks for your advice, I have provided sample growth conditions and site location in 4.1

2. Line420: (maize inbred line) You currently provide no information on the inbred lines used, their origins, and whether either have a varietal name/code. In addition, there is no information on the number of plants grown and the planting density.

Reply: Thanks for your advice, I have added the growing conditions and growth details of the maize inbred line in 4.1

3. Line450“the reference genome”Please specify the version and source of the genome assembly used.

Reply: Thanks for your suggestion, I added "the reference genome" details to 4.3

4.So that the figure is understandable in isolation from the text, I suggest adding legends

Reply: I checked all the annotations to make sure they described the image in detail.

Author Response File: Author Response.docx

Reviewer 2 Report

This manuscript tried to provide the understanding of the accumulation of auxin during maize growth stages using transcriptomic and metabonomic analysis. However, the overall results and data processing are superficial, the current data with a pedestrian piece of writing show few insights into the auxin synthesis.

 

In specific:

 

1.     The descriptions of data and result are too digitized, which lacks the clear conclusions and key information, such as the analysis of transcriptomics and metabolomics. Thus, it is a bit of boring to read the manuscript.

 

2.     At the first part of Result (2.1), it needs some statements/justifications to describe the details of samples, such as, CK1-3, M1-3. Otherwise, it is very confused to read, even the author put this information in Method.

 

3.     From Line 102-104, why do CK and M show different trends between trp and IAA content, any discussion or reason for this point?

 

4.     Figures 1 to 5 could be modified better, the text in current version is too small.

Author Response

This manuscript tried to provide the understanding of the accumulation of auxin during maize growth stages using transcriptomic and metabonomic analysis. However, the overall results and data processing are superficial, the current data with a pedestrian piece of writing show few insights into the auxin synthesis.

Reply: Thanks for your suggestion, I made changes in the manuscript, and the changes are marked in yellow

In specific:

1. The descriptions of data and result are too digitized, which lacks the clear conclusions and key information, such as the analysis of transcriptomics and metabolomics. Thus, it is a bit of boring to read the manuscript.

Reply: Thanks for the suggestion, I think it will make the article more understandable. I added new conclusions in 2.3, 2.4, 2.5

2. At the first part of Result (2.1), it needs some statements/justifications to describe the details of samples, such as, CK1-3, M1-3. Otherwise, it is very confused to read, even the author put this information in Method.

Reply: Thanks for your suggestion, I have written the introductory sample into the result (2.1). And increased the planting details of CK and M.

3. From Line 102-104, why do CK and M show different trends between trp and IAA content, any discussion or reason for this point?

Reply: I added to the discussion section about why CK and M show different trends between TRP and IAA content

4. Figures 1 to 5 could be modified better, the text in current version is too small.

Reply: Figures 1 to 5 have enlarged the text to make the content clearer.

Author Response File: Author Response.docx