Genome-Wide Analysis of the Rice Gibberellin Dioxygenases Family Genes
Round 1
Reviewer 1 Report
Dear authors,
The study aims to investigate GA oxidase genes in rice in terms of their phylogenetic relationship, gene structure, and gene expressions. However, the objectives need to be more specific. I have significant concerns in the method section of gene expression analysis with GA3 treatment especially experiment design. here are my comments below:
Comments for author File: 
Comments.pdf
Author Response
Reviewer 1:
- Line54-55: Which varieties belong to indica or japonica groups?
- Line 58: Which season and months is considered as rice growing season in China?
- Line 114: Range means a difference between the smallest and largest value. What does range stand for? Please clarify. What do SD and CV stand for. Mention an elaboration form of SD and CV. Have you looked at whether these coefficient of variations are significant or not between samples? You need to add a column with a significant value for coefficient of variation.
- Line 188-190. This sentence is long and confusing. Revised of this sentence is required.
- Line 267: Grain appearance is evaluated by its size and shape, length and width, length, and width percentage (L/W), translucency, and chalkiness of the endosperm. In the discussion, you have mentioned only about grain chalkiness though you have presented results for grain size. It is recommended to discuss every aspects of grain appearance in the discussion. The discussion should capture more properties of rice.
Response: We are sorry that we can not address these questions, those might be from another manuscript. We do not perform the experiments about Grain appearance and so on in this study. As a Chinese scientist, I can answer your second question. In China, the sowing and growing season depends on different place (or area). In some areas, farmers can sow and harvest the rice for twice in one year. For example, in Hubei province, we can sow the rice seeds from April to June depends on the whole growth duration of the different varieties. Some varieties were photo-sensitive and only can be sowed after May. Therefore, it is too complicated to address this question.
Reviewer 2 Report
The manuscript describes the analysis of rice gibberellin-dioxygenases in rice and provides diverse ideas about potential functions. The aim is to provide comprehensive analysis and a basis for further studies. The analyses show insights into the structure and relationships of the different GAox genes.
In a large part, the manuscript is well written and easy to read. Its main weakness is the speculative part concerning the potential role of the genes in Oryza sativa. Whereas such speculations are surely legitimate, the reader might get the impression of experimental evidence where there is only interpretation.
It would be interesting to learn more about the growing conditions and the stress treatment, including the sampling, in the greenhouse. For this part, the experimental details are poorly described.
I do not support highly speculative deductions as in lines 227-228 or 229-230. Expression patterns, especially if determined as the authors did, in my opinion are not indicative of gene functions, they may only give a hint, unless the authors support their speculations with own or published experimental evidence. I miss this line of evidence and feel that many parts of Chapter 3.4. should be transferred to the discussion part and presented by putting them into context with other research, where available. The same applies to Chapter 3.5., in particular when expression and function are described.
The discussion part should be improved significantly: I would expect that the results are discussed in the context of published studies. Some parts of the discussion could be moved to the results section, whereas part of the results could be moved to the discussion and put into context as indicated before.
The authors conclude that their results serve as reference to improve rice yield. I recommend that they should design their discussion section to support this conclusion.
Some parts of the manuscript need reconsideration and revision of the language, also to increase readability – as examples lines 76-83, 140-142, 148-149, 176-179, 221-225,256-263, 266-269, 290-299,300-302, 307-316, or 328-331.
Please check the correct use of fonts throughout the manuscript.
Please check the caption of Figure 4.
Please expand the caption of Figure 6.
221: please describe abbreviation
The presentation of the references needs revision and harmonization.
Author Response
Reviewer 2:
The manuscript describes the analysis of rice gibberellin-dioxygenases in rice and provides diverse ideas about potential functions. The aim is to provide comprehensive analysis and a basis for further studies. The analyses show insights into the structure and relationships of the different GAox genes.
In a large part, the manuscript is well written and easy to read. Its main weakness is the speculative part concerning the potential role of the genes in Oryza sativa. Whereas such speculations are surely legitimate, the reader might get the impression of experimental evidence where there is only interpretation.
It would be interesting to learn more about the growing conditions and the stress treatment, including the sampling, in the greenhouse. For this part, the experimental details are poorly described.
Response: Thank you for your advice, we added more description in this revision.
I do not support highly speculative deductions as in lines 227-228 or 229-230. Expression patterns, especially if determined as the authors did, in my opinion are not indicative of gene functions, they may only give a hint, unless the authors support their speculations with own or published experimental evidence. I miss this line of evidence and feel that many parts of Chapter 3.4. should be transferred to the discussion part and presented by putting them into context with other research, where available. The same applies to Chapter 3.5., in particular when expression and function are described.
Response: Thank you for your suggestion. We moved some parts of chapter 3.1.4 and 3.1.5 to discussion part.
The discussion part should be improved significantly: I would expect that the results are discussed in the context of published studies. Some parts of the discussion could be moved to the results section, whereas part of the results could be moved to the discussion and put into context as indicated before.
Response: Thank you for your suggestion. We moved some parts of discussion part to the result parts.
The authors conclude that their results serve as reference to improve rice yield. I recommend that they should design their discussion section to support this conclusion.
Some parts of the manuscript need reconsideration and revision of the language, also to increase readability – as examples lines 76-83, 140-142, 148-149, 176-179, 221-225,256-263, 266-269, 290-299,300-302, 307-316, or 328-331.
Response: Thank you for your suggestion. We checked it carefully again in this revision.
Please check the correct use of fonts throughout the manuscript.
Response: Thank you for your suggestion. We checked it carefully again in this revision.
Please check the caption of Figure 4.
Please expand the caption of Figure 6.
Response: Thank you for your suggestion. We checked them in this revision.
221: please describe abbreviation
Response: Thank you for your suggestion. We revised it in this revision.
The presentation of the references needs revision and harmonization.
Response: Thank you for your suggestion. We improved it in this revision.
