Identification and Functional Analysis of Key Genes Regulating Organic Acid Metabolism in Jujube Fruit
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsAn interesting short paper identifying potentially critical genes in acid metabolism.
However, the authors do not list the genes they identify by abbreviation and where they might be functional.
They have selected potential genes based on correlation but not examined other candidates that may be involved.
Results. Why did the authors not measure ascorbic acid? I believe jujube is high in vitamin C
Line 163. Correlation of gene expression with a metabolite does not imply causality or control in the pathway. Gene expression can change with time of day and development stage as well as the stability of the protein product. Also with only five points correlation analysis is dubious due to lack of time points.
Fig 1 (labelled fig 20), Quinic is misspelt
Fig 3, the genes involved should be identified
Fig 4 good to see both over expression and gene silencing approaches taken
Author Response
Dear Ms. Slađana Milovac and reviewers,
Thank you very much for your invitation to revise the manuscript and the reviewers' helpful comments on our manuscript entitled “Identification and functional analysis of key genes regulating organic acid metabolism in jujube fruit” (ID: agronomy-3229720). The comments are very valuable for improving our manuscript. We have substantially revised accordingly, with major changes and the response to the reviewers' comments listed below:
Responds to the reviewers' comments:
Comments#1: An interesting short paper identifying potentially critical genes in acid metabolism. However, the authors do not list the genes they identify by abbreviation and where they might be functional.
Response: Thank you very much for your comments, we have added the specific names of the full text gene abbreviations and described and supplemented the functions of the key genes identified in the third paragraph of the discussion section.
Comments#2: They have selected potential genes based on correlation but not examined other candidates that may be involved.
Response: Thank you very much for your suggestion, in our research process, we mainly select potential genes based on correlation for in-depth analysis. For other candidate genes, after extensive literature review and rigorous evaluation and screening, we believe that these selected potential genes have the most direct and close relationship with the research content, and can provide the most valuable answers to our research questions. In subsequent studies, we will continue to pay attention to the dynamics of other candidate genes, and we will conduct in-depth research analysis in time once new evidence shows their importance to the research topic.
Comments#3: Line 32: Results. Why did the authors not measure ascorbic acid? I believe jujube is high in vitamin C.
Response: Thank you very much for your reminder, our main focus in this study was to discover the genes that regulate the organic acid content in jujube fruit. The starting point and design of this study are centered on the specific substance category of organic acids, aiming to deeply explore the main types of organic acids in jujube fruit and key candidate genes. Although jujube fruit is rich in vitamin C, it is not directly related to the determination of organic acid content, which is the core content of this study. With the limited research resources and space, to ensure that the research on organic acids can be in-depth, I have to make a reasonable selection of the research scope. I fully understand your views on the comprehensive consideration of different nutritional components in jujube. In future studies, if there is an opportunity and need, I will consider including the determination of ascorbic acid and other important nutritional components in the research scope, to provide a more comprehensive analysis of the nutritional components of jujube.
Comments#4: Line 163. Correlation of gene expression with a metabolite does not imply causality or control in the pathway. Gene expression can change with time of day and development stage as well as the stability of the protein product. Also with only five points correlation analysis is dubious due to lack of time points.
Response: Thank you very much for your comments, we fully agree that correlations between gene expression and metabolites do not imply causation or pathway control. In the paper, we do show correlations between gene expression and metabolites, but do not assert causality or absolute control of pathways. We also know that scientific research requires more in-depth experimental design and analysis to determine causal links, and this is an important direction for our future research. Changes in gene expression over time and stages of development, as well as the stability of protein products, were also taken into account during the study. However, due to limited research resources and space, a more comprehensive analysis of different time points and developmental stages has not been possible. We will pay more attention to the time dimension in future studies to better understand the dynamic changes in gene expression. We understand your concern that the relevant analysis at only five points in time has been questioned. These five time points are the key period points of jujube fruit development. Although the number of time points is limited, we have tried our best to ensure the accuracy and reliability of the data. In future studies, we will strive to increase the time point of the sample for a more comprehensive and convincing correlation analysis.
Comments#5: Fig 1 (labelled fig 20), Quinic is misspelt.
Response: Thank you very much for your reminder, We have changed 'Figure 20' to 'Figure 1' and corrected the diagram for 'Quinic acid' in Figure 1.
Comments#6: Fig 3, the genes involved should be identified.
Response: Thank you very much for your reminder, FIG. 3 shows that 12 genes were randomly selected from the candidate genes for qRT-PCR analysis, mainly to verify the accuracy and reliability of the transcriptome analysis results. The names and gene IDs of these identified candidate genes are labeled in the upper left corner of each graph. Through the gene IDs, specific gene information can be queried in NCBI so that readers can identify the genes involved.
Thanks again for your comments.
Best wishes,
Jiangbo Wang
***************************************
Jiangbo Wang (PhD/Associate Professor)
College of Horticulture and Forestry, Tarim University, Alar, Xinjiang 843300, PR China
- wjbok@126.com
Author Response File: 
Author Response.docx
Reviewer 2 Report
Comments and Suggestions for AuthorsThis manuscript is fine now.
Author Response
Dear Ms. Slađana Milovac and reviewers,
Thank you very much for your invitation to revise the manuscript and the reviewers' helpful comments on our manuscript entitled “Identification and functional analysis of key genes regulating organic acid metabolism in jujube fruit” (ID: agronomy-3229720). The comments are very valuable for improving our manuscript. We have substantially revised accordingly, with major changes and the response to the reviewers' comments listed below:
Thank you very much for your positive assessment. We are delighted to hear that the manuscript is now considered fine. Your valuable comments and suggestions have been extremely helpful in improving our work. We look forward to seeing our research contribute to the field.
Thanks again for your comments.
Best wishes,
Jiangbo Wang
***************************************
Jiangbo Wang (PhD/Associate Professor)
College of Horticulture and Forestry, Tarim University, Alar, Xinjiang 843300, PR China
- wjbok@126.com
Reviewer 3 Report
Comments and Suggestions for AuthorsIntroduction:
- The introduction provides a solid background on the importance of organic acids in jujube fruit, but it could benefit from including more recent references. Incorporating additional studies on the genetic regulation of organic acids in other fruit species would strengthen the scientific context of the work.
Methods:
- The methods section is generally well-described, but it would be helpful to add more details about the selection of developmental stages for jujube fruit sampling. Additionally, providing more explanation on the statistical analyses performed, particularly the reasoning behind the chosen methods, would enhance the clarity of this section.
Results Presentation:
- The results are presented clearly, with appropriate figures and tables. However, some figures could benefit from more detailed captions, specifically explaining key results in the context of the broader findings. This would help readers interpret the results more easily.
Discussion and Conclusions:
- The discussion does a good job of linking the findings to the broader field of organic acid metabolism. However, the authors could elaborate further on the implications of the identified genes in jujube fruit for practical applications, such as breeding programs. Additionally, discussing potential limitations of the study and future research directions would provide a more rounded conclusion.
The English in the manuscript is generally clear, but there are several areas where the language could be improved for better readability. Some sentences are complex and could be simplified, and there are minor grammatical errors throughout the text. A moderate revision focusing on simplifying sentence structures and improving flow will significantly enhance the clarity and professionalism of the manuscript.
Author Response
Dear Ms. Slađana Milovac and reviewers,
Thank you very much for your invitation to revise the manuscript and the reviewers' helpful comments on our manuscript entitled “Identification and functional analysis of key genes regulating organic acid metabolism in jujube fruit” (ID: agronomy-3229720). The comments are very valuable for improving our manuscript. We have substantially revised accordingly, with major changes and the response to the reviewers' comments listed below:
Responds to the reviewers' comments:
Comments#1: Introduction: The introduction provides a solid background on the importance of organic acids in jujube fruit, but it could benefit from including more recent references. Incorporating additional studies on the genetic regulation of organic acids in other fruit species would strengthen the scientific context of the work.
Response: Thank you very much for your comments, we have included more recent references in the introduction. Additionally, we have incorporated studies on the genetic regulation of organic acids in other fruit species.
Comments#2: Methods: The methods section is generally well-described, but it would be helpful to add more details about the selection of developmental stages for jujube fruit sampling. Additionally, providing more explanation on the statistical analyses performed, particularly the reasoning behind the chosen methods, would enhance the clarity of this section.
Response: Thank you very much for your suggestion, we have supplemented the details of the jujube fruit sampling developmental stages in the methods and provided additional explanations for the statistical analyses.
Comments#3: Results Presentation: The results are presented clearly, with appropriate figures and tables. However, some figures could benefit from more detailed captions, specifically explaining key results in the context of the broader findings. This would help readers interpret the results more easily.
Response: Thank you very much for your suggestion, we have provided detailed explanations and supplements for the key results in the result analysis.
Comments#4: Discussion and Conclusions: The discussion does a good job of linking the findings to the broader field of organic acid metabolism. However, the authors could elaborate further on the implications of the identified genes in jujube fruit for practical applications, such as breeding programs. Additionally, discussing potential limitations of the study and future research directions would provide a more rounded conclusion.
Response: Thank you very much for your comments, we have added the following content in the last part of the discussion: “The key gene functions verified in this study can be employed in breeding programs to cultivate jujube varieties with high or low organic acid contents, thereby enriching the nutritional value and taste of jujube fruits. These genes can also play a significant role in the field of food processing. For example, by regulating key genes, jujube processed products with specific acidity and flavor can be produced to meet the needs of differ-ent consumers and provide product innovation directions for food processing enter-prises. In terms of agricultural sustainable development, molecular marker-assisted selection technology can be developed for precision agricultural management to im-prove planting efficiency. Finally, the regulatory mechanisms of these genes are com-plex and may involve interactions with other genes or environmental factors. Future research directions may include investigating the interactions between these candidate genes and other genes involved in organic acid metabolism and combining them with environmental factors to cultivate jujube varieties with stronger stress resistance. Ex-ploring the epigenetic regulation of these genes could provide additional insights into the control of organic acid accumulation in jujube fruits.”
Comments#5: The English in the manuscript is generally clear, but there are several areas where the language could be improved for better readability. Some sentences are complex and could be simplified, and there are minor grammatical errors throughout the text. A moderate revision focusing on simplifying sentence structures and improving flow will significantly enhance the clarity and professionalism of the manuscript.
Response: Thank you very much for your comments, we have carried out a moderate revision of this manuscript, focusing on simplifying sentence structures and improving the fluency of the text to significantly enhance the clarity and professionalism of the manuscript. We will adopt a more rigorous attitude towards language expression to ensure that the final manuscript meets professional language quality requirements.
Thanks again for your comments.
Best wishes,
Jiangbo Wang
***************************************
Jiangbo Wang (PhD/Associate Professor)
College of Horticulture and Forestry, Tarim University, Alar, Xinjiang 843300, PR China
- wjbok@126.com
Author Response File: Author Response.docx
Reviewer 4 Report
Comments and Suggestions for AuthorsDear Authors,
Thank you very much for your interesting manuscipt. It is original and novelty. I reviewed it and recommended some suggestion/corrections as follows:
1. The sentence in lines 58-60 should be deleted in the Introduction part. Because it is similar with sentence at the end of the abstract.
2. The soil properties, climatic data and applications as fertilizer, weed control or others in the study should be given in the subsection "2.1. Materials and growth conditions".
3. Which was the experimental design used? it should be statistical subsection.
4. The subsection "3.1. Changes of organic acid components in jujube fruit during fruit development" should be explained as clearly and the results on the malic and other acids should be given details in the Results part.
5. Why was the Identification of key genes regulating Quininic acid by transcriptome analysis not carried out?
6. The Figure 2 should be given as clearly.
7. The subsections "3.3. Real-time fluorescence quantitative (qRT-PCR) analysis" and "3.4. Transient overexpression and silencing analysis" should be explained details.
8. The general results shoudl be given in the Conclusion part.
9. The manuscript has some writing errors and the English language should be revised.
Best regards,
Comments on the Quality of English LanguageThe quality of English should br revised.
Author Response
Dear Ms. Slađana Milovac and reviewers,
Thank you very much for your invitation to revise the manuscript and the reviewers' helpful comments on our manuscript entitled “Identification and functional analysis of key genes regulating organic acid metabolism in jujube fruit” (ID: agronomy-3229720). The comments are very valuable for improving our manuscript. We have substantially revised accordingly, with major changes and the response to the reviewers' comments listed below:
Responds to the reviewers' comments:
Comments#1: The sentence in lines 58-60 should be deleted in the Introduction part. Because it is similar with sentence at the end of the abstract.
Response: Thank you very much for your comments, we have deleted the sentence in lines 58-60 of the introduction part.
Comments#2: The soil properties, climatic data and applications as fertilizer, weed control or others in the study should be given in the subsection "2.1. Materials and growth conditions".
Response: Thank you very much for your suggestion, we have revised the sentences in "2.1. Materials and growth conditions" to: 'Nine individual plants of the ‘Heigeda’ cultivar were cultivated at the Tarim University Jujube Germplasm Resource Repository located at 40°54′N, 81.30′E. The soil at the test site was of sandy type. The site is distinguished by a long duration of sunlight exposure, a significant temperature difference between day and night, and scarce precipitation. Moreover, weeds at the site are cleared every month. The orchard was flat, and the conditions of soil, fertilizer, and water management were maintained consistently throughout the study.'
Comments#3: Which was the experimental design used? it should be statistical subsection.
Response: Thank you very much for your suggestion, we have added “The experiments were performed using a one-way completely randomized design” in “2.1. Materials and growth conditions”.
Comments#4: The subsection "3.1. Changes of organic acid components in jujube fruit during fruit development" should be explained as clearly and the results on the malic and other acids should be given details in the Results part.
Response: Thank you very much for your comments, we have conducted a detailed analysis and supplementation to the result analysis of “3.1. Changes of organic acid components in jujube fruit during fruit development”.
Comments#5: Why was the Identification of key genes regulating Quininic acid by transcriptome analysis not carried out?
Response: Thank you very much for your comments, because the content of quinic acid is not only low throughout the developmental period, but also significantly lower than that of malic acid and citric acid. Moreover, its proportion in the entire acid components is relatively low. Therefore, in this study, we mainly identified the key genes of malic acid and citric acid, the two main acid components, through transcriptome analysis.
Comments#6: The Figure 2 should be given as clearly.
Response: Thank you very much for your comments, we have adjusted the clarity of Figure 2 to 600 DPI. In the attachment, we also separately attach all high-definition pictures.
Comments#7: The subsections "3.3. Real-time fluorescence quantitative (qRT-PCR) analysis" and "3.4. Transient overexpression and silencing analysis" should be explained details.
Response: Thank you very much for your comments, we have conducted detailed analysis and supplementation to the result analysis of “3.3. Real-time fluorescence quantitative (qRT-PCR) analysis” and “3.4. Transient overexpression and silencing analysis”.
Comments#8: The general results should be given in the Conclusion part.
Response: Thank you very much for your comments, we have supplemented the overall results in "5. Conclusion": ‘In general, this study has identified the main organic acid components and their key metabolic genes during the development of jujube fruits, providing an important basis for an in-depth understanding of the organic acid metabolism mechanism of jujube fruits and improving the quality of jujube fruits through gene regulation’.
Comments#9: The manuscript has some writing errors and the English language should be revised.
Response: Thank you very much for your comments, we have carried out a moderate revision of this manuscript, focusing on simplifying sentence structures and improving the fluency of the text to significantly enhance the clarity and professionalism of the manuscript. We will adopt a more rigorous attitude towards language expression to ensure that the final manuscript meets professional language quality requirements.
Thanks again for your comments.
Best wishes,
Jiangbo Wang
***************************************
Jiangbo Wang (PhD/Associate Professor)
College of Horticulture and Forestry, Tarim University, Alar, Xinjiang 843300, PR China
- wjbok@126.com
Author Response File: Author Response.docx
Round 2
Reviewer 4 Report
Comments and Suggestions for AuthorsDear Authors,
Thank you very much for your revised manuscript. I think that it is better than old previous.
Best regards,
Author Response
Dear Ms. Slađana Milovac and reviewers,
Thank you very much for your positive assessment. We are delighted to hear that the manuscript is now considered fine. Your valuable comments and suggestions have been extremely helpful in improving our work. We look forward to seeing our research contribute to the field.
Thanks again for your comments.
Best wishes,
Jiangbo Wang
***************************************
Jiangbo Wang (PhD/Associate Professor)
College of Horticulture and Forestry, Tarim University, Alar, Xinjiang 843300, PR China
wjbok@126.com
