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Article
Peer-Review Record

Molecular Mechanism of Oryza sativa L. Under Long Day Regime Based on Transcriptome Analysis

Diversity 2025, 17(9), 603; https://doi.org/10.3390/d17090603
by Wenju Luo 1,2,3,†, Yufeng Li 1,2,†, Xianbin Hou 1,2, Chun Wei 1,2, Zheng Teng 1,2, Cuifeng Yang 1,2, Hongzhu Su 1,2, Xiaoli Wang 3,* and Zhengjie Zhu 1,2,*
Reviewer 1: Anonymous
Reviewer 2:
Diversity 2025, 17(9), 603; https://doi.org/10.3390/d17090603
Submission received: 24 July 2025 / Revised: 23 August 2025 / Accepted: 24 August 2025 / Published: 28 August 2025
(This article belongs to the Section Plant Diversity)

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This study studied how photoperiod affects gene expression in rice leaves. The authors compare normal rice and rice with the FaGI gene at two growth stages: nutrient growth and flowering. They used RNA sequencing to find many different genes that change expression. These genes are mostly related to photosynthesis and flowering. The study gives initial information about how rice responds to day length changes at the gene level.

 

Major comments:

 

- The study could clearly state its main questions and goals. It would help readers understand what the authors want to find.

- More information is needed about how they defined the growth stages, like how they told when flowering started.

- The authors did not say if they used other methods like qRT-PCR to check their RNA sequencing results.

- The criteria for selecting differentially expressed genes (like cutoffs for fold-change and p-values) are not clear.

- It is not clear if they checked for batch effects or other factors that could affect results.

- The discussion links gene changes to traits like flowering time but lacks direct evidence like measurements of flowering or photosynthesis.

- Some gene functions, such as those related to MAPK signaling, are mentioned but not well explained in connection with photoperiod.

- The study mainly provides gene expression data. It would be stronger with lab tests that show how these genes affect the plant, such as gene knockouts or observing plant traits under different day lengths.

 

Minor comments:

 

- Most figures are hard to read and need clearer labels and higher quality.

- The Venn diagram should show total gene counts more clearly.

- Some sentences are awkward or have grammar mistakes. Fixing these would make the paper easier to read.

- Phrases like "better photosynthetic potential" could be clearer, like saying "improved photosynthesis."

- Update references with newer studies on rice and photoperiod if possible.

- They should clarify if raw RNA sequencing data are publicly available, according to journal rules.

- The description of software and settings used for data analysis could be more complete.

 

The quality of most figures and tables is very poor, which affects the clarity of the manuscript. Although the study was carefully prepared, these issues, along with the other comments mentioned, need serious attention. Therefore, I recommend rejection of the manuscript in its current form. However, I encourage the authors to make thorough revisions and address all the major and minor points before resubmitting for review.

Comments on the Quality of English Language

The English could be improved to more clearly express the research.

Author Response

Hello teacher, I have carefully revised the comments mentioned in the manuscript. Please review them. Thank you.
老师您好,我已经仔细修改了我的评论。请审查它们。感谢您的评分

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript addresses an important topic in plant molecular biology, focusing on the identification and characterization of photoperiod-related differentially expressed genes (DEGs) in rice under long-day conditions using RNA-seq technology. The findings could contribute to a better understanding of photoperiod-associated regulatory mechanisms, which are crucial for rice breeding programs targeting yield, flowering time, and adaptation to different environments.


Comments:
Please modify the title to include the requested phrase: “Pilot approach” at the end.
The abstract is overloaded with numeric details but lacks a concise explanation of the biological implications. Consider briefly summarizing the key pathways enriched and their relevance to photoperiod regulation in rice.


The introduction is too long and should be reorganized into approximately 5 concise paragraphs:
•    Background on photoperiod and its importance in rice.
•    Previous studies and knowledge gaps.
•    Overview of trans-FaGI rice and rationale for this study.
•    Brief mention of RNA-seq and its relevance to the research question.
•    Clear statement of objectives.

The objective is currently vague. Suggested rewrite: "This study aimed to identify photoperiod-related differentially expressed genes in trans-FaGI and wild-type rice leaves under long-day conditions, characterize their diurnal expression patterns, and determine enriched molecular functions, biological processes, and pathways using RNA-seq data."

 


Figures
o    Figure 1: Not legible; please increase resolution and adjust labels.
o    Figure 2: Add a clear legend explaining the meaning of the overlaps and colors in the Venn diagram.
o    Figure 6: The GO functional classification figure is not legible. Increase font size and improve image quality.

Results - when presenting large numerical datasets, avoid excessive repetition. Summarize key figures in the text and refer readers to tables/figures for details.

The conclusion should be rewritten to more accurately reflect the results.

The study contains valuable data, but improvements in structure, figure quality, clarity of objectives, and alignment of conclusions with results are necessary before it can be considered for publication.

Author Response

Hello teacher, I have carefully revised the comments mentioned in the manuscript. Please review them. Thank you.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Authors have diligently carried out revisions based on the reviewer's comments.

I recommend the manuscript for publication in its current form. 

Author Response

Thank you, teacher. Wishing you a happy life and smooth work.

Author Response File: Author Response.docx

Reviewer 2 Report

Comments and Suggestions for Authors

Congratulation!

Author Response

Thank you, teacher. Wishing you a happy life and smooth work

Author Response File: Author Response.docx

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