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I am pleased to inform you that your revised manuscript, having been thoroughly reviewed by the initial reviewers, has met their satisfaction. Two reviewers have expressed their approval of the revisions made. Based on their positive feedback and the quality of the revisions, I am happy to accept your manuscript for publication.
Congratulations, and thank you for your contribution
[# PeerJ Staff Note - this decision was reviewed and approved by Vladimir Uversky, a PeerJ Section Editor covering this Section #]
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The authors have made the changes I suggested in the last review. I recommend its publication in this journal.
I have reviewed the revised version of your manuscript titled "[Metabolomic Analysis of Rice Cultivars from Diverse Production Areas]". I can confirm that the submitted revisions have addressed the requested changes and it is now suitable to be published at PeerJ Journal
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The study used a comprehensive metabolomics approach to investigate the metabolic profiles of different rice genotypes grown in various regions of Yunnan Province, China. It aimed to provide insights into rice quality, origin tracing, and variety differentiation. Three experts in the field have reviewed the manuscript. All reviewers have recognized the study scientific quality and have recommended revisions to enhance the manuscript clarity, depth, and overall quality. Please revise the manuscript according to the reviewers' comments. Focus on improving clarity, expanding the discussion, and enhancing the visual presentation of data. Addressing these points will significantly enhance the manuscript's quality and its suitability for publication.
Please submit the revised manuscript along with a detailed response to the reviewers' comments, outlining the changes made and explaining how the manuscript has been improved.
Thank you for your submission, and we look forward to receiving the revised version.
Best regards,
Elsayed Mansour
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The study demonstrates a fair experimental design.
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This research used 15 rice samples (divided into 5 groups) as research materials, and the metabolites of rice were detected using an extensively employed method in the field of metabolomics, known as ultra-high performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS), and their differences were compared and analyzed. This study successfully identified and compared metabolite profiles of rice samples, revealing distinct metabolic signatures for the five identified groups. The data suggests potential differences in biological processes among the rice varieties.
-Comments and Suggestions for Authors
- Abstract
-In abstract, consider adding a sentence at the beginning that briefly introduces the importance of metabolite composition in rice. For example, “Rice grown in Yunnan Province is known for its excellent taste and consumer preference. However, the metabolite composition of this unique rice remains unclear.”
- Introduction
The introduction provides a good foundation for your research on using metabolomics for rice quality and adulteration identification in Yunnan Province.
While the introduction mentions adulteration as a national issue, you could add a sentence or two specifically highlighting concerns about adulteration of Yunnan's unique rice varieties.
- Materials & Methods
- This section is well-written and provides a good level of detail for researchers to understand and potentially replicate your experiment.
- If the sample preparation or UPLC-MS/MS procedures are based on established protocols, you could mention the relevant references to provide context and credibility.
- It would be helpful to specify which packages of R software were used for PCA, CA, OPLS-DA, etc.
- Results
- The result section presents a well-conducted metabolic profiling study on rice samples. The analysis effectively identified a wide range of metabolites and demonstrated significant differences in metabolic profiles between sample
- Discussion
- Remove the subtitles in discussion section
- The discussion section needs to be restructured and revised. Please find my suggestions in the annotated pdf file to help you revise your discussion.
- Conclusion
Consider replacing "functional compounds" with more specific examples identified in the study (e.g., flavonoids, phenolic acids). This provides a clearer picture of the functional value.
References
Please use the suitable reference style for Peerj
Review of: Metabolomics reveals the effects of producing region and varieties on substance variation in characteristic rice in Yunnan
This manuscript describes a study on the metabolite composition of rice varieties grown in different regions of Yunnan Province, China. Here's an evaluation of the experimental design and the validity of the findings:
Strengths:
• Clear research question: The study aims to identify differences in metabolite profiles of rice varieties from various regions to potentially differentiate origin and identify adulteration.
• Appropriate analytical technique: UPLC-MS/MS is a well-established technique for metabolomic analysis and can detect a wide range of metabolites.
• Multivariate statistical analysis: The use of PCA and OPLS-DA is appropriate to analyze the large dataset of metabolites and identify potential differences between groups.
• Pathway enrichment analysis: This helps understand the biological processes potentially affected by the observed metabolite variations.
Weaknesses:
• Limited sample size: With only 15 samples (3 replicates each for 5 groups), the study might not be statistically robust for generalizability.
• Missing information on growth conditions: Factors like soil composition, fertilizer use, and irrigation practices can influence metabolite profiles. Without this information, it's difficult to isolate the effect of region on the observed differences.
• Limited discussion on biological significance: The manuscript focuses on identifying differential metabolites but doesn't discuss the potential biological implications of these variations in the context of rice quality or taste.
Overall, the study provides a good starting point for understanding the metabolic diversity of rice from different regions of Yunnan Province. However, further research with a larger sample size, controlled growth conditions, and a more in-depth analysis of the biological significance of the findings is needed to strengthen the validity of the results. I have a few comments/ suggestions for the authors to improve the article, that are embedded into the annotated copy.
Relatively well designed
Here are some additional points to consider:
• Validation of identified metabolites: Techniques like metabolite standards or comparison with public databases could strengthen the confidence in metabolite identification.
• Replication of the findings: Repeating the experiment with independent samples could improve the generalizability of the results.
The manuscript entitled " Metabolomics reveals the effects of producing region and varieties on substance variation in characteristic rice in Yunnan” addresses an interesting topic. However, it is necessary to include many changes to improve its structure and presentation.
Title
The title could be enhanced to be “Metabolomic Analysis of Rice Cultivars from Diverse Production Areas”
Abstract
1- The abstract section requires further clarification and revision
2- The presentation of the problem, methods, conclusions, and implications in the article should be concise and requires improvement.
3- Some scored data should be stated.
Introduction
1- The introduction needs improvement regarding the study gap, hypothesis, and clear objectives.
2- The introduction is relatively brief and requires expansion for a more comprehensive overview.
3- Line 56: Add paragraph about the metabolomics analysis and its important in rice.
4- Line 68: The aim of the study needs to re-write
Material and methods
Line 74: “Study materials” should be changed to Genetic materials.
Line 76: Clarify the nature of the rice material. Fifteen rice samples or Fifteen rice varieties.
Line 77: Clearly state the basis for grouping into 5 groups.
Results
1- Improve the reporting language and avoid jargon. Directly state the results. Authors must quantitatively report their results. Make the results section concise and specific.
2- Line 153: The authors does not address the variability within the 15 rice samples analyzed. Were the results consistent across all samples, or was there significant variability? Additionally, there’s no mention of any statistical analysis to determine if the difference in metabolite counts across classes are significant.
3- Line 168: The explained variance (27.32% by PC1 and 18.08% by PC2) is not sufficient to draw meaningful conclusions
4- The quality of Figure 1A and 1 B need improvement
Discussion
1- Line 297: The authors mentions that 1,005 metabolites were identified, compared to 732 in colored rice and 672 in millet. However, they did not delve into why this difference in numbers is important. Are the additional metabolites found in this study novel or of particular interest?
2- The authors stated that most of the differential metabolites were flavonoids, lipids, and phenolic acids, but they did not provide specific examples or insights into the functional differences between the rice groups
Conclusion
1- The conclusion makes broad statements about the usefulness of the study for understanding metabolite composition and functional compounds, but it lacks specificity.
2- The authors should provide recommendations for future research directions that could build upon or address limitations of the current work.
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