High-Resolution 3D Reconstruction of Individual Rice Tillers for Genetic Studies

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript presents key findings but need to be significantly improved.

Points for Improvement:

1. Validation Gap: The authors acknowledge that only tiller length was validated against manual measurements. Other phenotypic traits (angles and internode lengths) should be similarly validated to increase confidence in the trait dataset. Future work should include at least partial manual validation of the additional traits reported.

2. Field-to-Lab Transfer Effects: While the authors mention challenges with tissue wilting during transfer, more clarity is needed on how this was mitigated, especially for delicate traits like leaf angle. also, the study might benefit from testing the method in field conditions or with in situ imaging platforms, which is currently a limitation.

3. Dataset and Reproducibility: The phenotypic dataset is only described in supplementary tables. The inclusion of processed example data and intermediate outputs from ScaleCalculator in a repository would help improve reproducibility.

4. GWAS Interpretation: While the GWAS findings are interesting, the results would benefit from a more thorough discussion of potential false positives and corrections applied. Some Manhattan plots are not well-annotated in the provided figure legend, and also provide the QQ-plot to judge the Manhattan plots.

Minor Issues:

• Typos and formatting inconsistencies appear in some references and equations

• A few figures (especially Figure 7 & 8) could be better labeled to improve readability for readers less familiar with Manhattan plots.

Major Revision

The manuscript presents novel and technically sound work with real potential impact on plant phenotyping and functional genomics.

These need to be clarified

1- Extending trait validation,

2- Clarifying data robustness and transport-induced effects.

3- Improving GWAS result discussion and figure quality.

Comments on the Quality of English Language

Need to be improved

Author Response

Please see the attachment

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript contains interesting applications of the phenotyping method for rice shoots based on 3D models. I would like to ask the Authors to explain the significance of their research results. How can they be applied in practice? Can they also be applied to other plant species? If so, which ones? What problems need to be solved?

Comments

Introduction

Please present the economic importance of rice based on the most recent FAOSTAT data.

Materials and Methods

Please include a figure showing the location of the research site to make it easier for readers outside China to understand.

The description of the figure should come first, followed by the figure, not the other way around.

Please provide full details of the producers of the equipment and software used in the research.

Results

The description of the figure should come first, followed by the figure, not the other way around.

Discussion

It is far too short. Please expand it.

Conclusions

Please shorten it significantly.

References

Please remove publications older than 10 years, unless they are necessary to characterise the research methodology.

Author Response

Please see the attachment

Author Response File: Author Response.pdf