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Review
Peer-Review Record

A Comprehensive Review of BBX Protein-Mediated Regulation of Anthocyanin Biosynthesis in Horticultural Plants

Horticulturae 2025, 11(8), 894; https://doi.org/10.3390/horticulturae11080894
by Hongwei Li 1, Kuanping Deng 2, Yingying Zhao 2,* and Delin Xu 1,*
Reviewer 1: Anonymous
Reviewer 2: Anonymous
Horticulturae 2025, 11(8), 894; https://doi.org/10.3390/horticulturae11080894
Submission received: 27 June 2025 / Revised: 20 July 2025 / Accepted: 22 July 2025 / Published: 2 August 2025

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This review aims to provide an integrative overview of the structural features and functional roles of BBX transcription factors in regulating anthocyanin biosynthesis, with a focus on their implications for ornamental traits, molecular breeding, and the genetic improvement of horticultural crops.

The manuscript presents potentially valuable insights; however, several key aspects require improvement to meet the standards of scientific rigor and clarity expected in this field.

1- In the paragraph discussing the gaps in previous research, I recommend a more in-depth and critical exploration. Currently, the discussion remains somewhat general and lacks specificity regarding the methodological, conceptual, or contextual limitations of past studies.

2- For the section 2.1.1 seed germination, this section would benefit from a brief and integrative reference to key hormonal regulators of germination. Specifically, the antagonism between abscisic acid and gibberellins. 

3- The section on flowering 2.1.3 lacks sufficient integration with existing literature. I suggest the authors expand the reference to previous studies, particularly those elucidating the genetic and hormonal regulation of flowering (e.g., roles of FT, FLC, gibberellins, and photoperiod pathways). A more synthetic and critical analysis of how internal signals and environmental cues converge to control floral transition would enhance both clarity and scientific depth.

4- The manuscript would benefit from a more thorough engagement with the relevant and up-to-date scientific literature. At present, references to key foundational and recent studies are limited across several sections, which weakens the contextual and conceptual framework of the work. I recommend that the authors systematically incorporate pertinent references, particularly in areas concerning hormonal regulation, developmental biology, and environmental interactions. A more critical and synthetic integration of existing knowledge would significantly enhance the scholarly rigor and interpretative depth of the manuscript.

5- The authors should more clearly articulate the added value of their study. It is important to highlight how the findings advance current understanding in the field and to indicate potential applications—whether in breeding programs, physiological modeling, or agronomic practices. Additionally, I encourage the authors to outline specific and realistic directions for future research that build upon their findings, thereby offering a pathway for subsequent investigations.

6-Please ensure that all abbreviations used throughout the manuscript are included in the list of abbreviations and that each abbreviation is clearly defined upon its first appearance in the text.

 

Author Response

Response to Reviewer 1 Comments

Dear Reviewer,

We sincerely thank you for taking the time to review our manuscript and for providing numerous constructive and insightful comments. Your valuable suggestions have significantly improved the quality of our paper and have also offered important guidance and inspiration for our future research.

In response to the reviewers’ comments, we have carefully addressed each point in detail below and have thoroughly revised the manuscript accordingly. We have made every effort to enhance the academic value and clarity of our work.

Once again, we deeply appreciate your hard work and kind support. Below is the Point-by-point response to Comments and Suggestions for Authors.

 

Reviewer 1:

Comments 1: In the paragraph discussing the gaps in previous research, I recommend a more in-depth and critical exploration. Currently, the discussion remains somewhat general and lacks specificity regarding the methodological, conceptual, or contextual limitations of past studies.

Response 1: Thank you for your valuable suggestions. We fully agree that a more in-depth and specific analysis of the limitations of existing studies—in terms of methodology, theoretical framework, and research subjects—should be included in the introduction. According to your recommendation, we have added a new paragraph after “Although previous studies have preliminarily revealed the important role of BBX proteins…” in the introduction. This paragraph systematically summarizes the main limitations of current research on BBX proteins, including: (1) an over-reliance on studies in model plants and a lack of functional validation in horticultural crops; (2) neglect of potential synergistic or antagonistic interactions among BBX family members; (3) predominant focus on light signaling regulation, with insufficient exploration of the influence of other environmental factors; and (4) the use of relatively traditional research methods, with a lack of high-throughput techniques and detailed spatiotemporal expression analyses. These revisions aim to more thoroughly highlight current research gaps and clarify the specific issues this review intends to address. The relevant changes have been marked in the manuscript for your reference. Please refer to lines 63 to 79 of the Revised manuscript with tracked changes.

 

Comments 2: For the section 2.1.1 seed germination, this section would benefit from a brief and integrative reference to key hormonal regulators of germination. Specifically, the antagonism between abscisic acid and gibberellins.

Response 2: Thank you for your constructive feedback on Section 2.1.1. We agree that highlighting the hormonal regulation of seed germination would provide important biological context. In the Revised manuscript with tracked changes, we have added a concise but integrative discussion of the well-established antagonistic relationship between abscisic acid (ABA) and gibberellins (GA), which plays a central role in regulating the dormancy-to-germination transition. This addition aims to give readers a clearer understanding of how hormonal balance influences seed behavior and how BBX proteins may potentially intersect with these pathways. We appreciate your suggestion, which has helped improve the completeness and relevance of this section. Please refer to lines 133 to 164 of the Revised manuscript with tracked changes.

 

Comments 3: The section on flowering 2.1.3 lacks sufficient integration with existing literature. I suggest the authors expand the reference to previous studies, particularly those elucidating the genetic and hormonal regulation of flowering (e.g., roles of FT, FLC, gibberellins, and photoperiod pathways). A more synthetic and critical analysis of how internal signals and environmental cues converge to control floral transition would enhance both clarity and scientific depth.

Response 3: Thank you for pointing out the need for a deeper integration of relevant literature in Section 2.1.3. We fully acknowledge that the discussion on flowering regulation would benefit from a more comprehensive overview of established genetic and hormonal pathways. In the revised version, we have expanded this section to include key studies on FT, FLC, gibberellins, and photoperiod-regulated networks, emphasizing how these internal and environmental factors coordinate to govern the floral transition. In addition, we incorporated a more critical synthesis of how these pathways intersect, aiming to provide a clearer conceptual framework for understanding BBX proteins within the broader flowering regulatory network. We greatly appreciate your recommendation, which has significantly improved the depth and contextual grounding of this section. Please refer to lines 184 to 231 of the Revised manuscript with tracked changes.

 

Comments 4: The manuscript would benefit from a more thorough engagement with the relevant and up-to-date scientific literature. At present, references to key foundational and recent studies are limited across several sections, which weakens the contextual and conceptual framework of the work. I recommend that the authors systematically incorporate pertinent references, particularly in areas concerning hormonal regulation, developmental biology, and environmental interactions. A more critical and synthetic integration of existing knowledge would significantly enhance the scholarly rigor and interpretative depth of the manuscript.

Response 4: We sincerely appreciate your valuable comments regarding the need to reference relevant and up-to-date scientific literature more comprehensively. We fully understand that certain sections of the manuscript, particularly those related to hormonal regulation, developmental biology, and environmental interactions, require further background and depth. Accordingly, we have systematically revised sections such as “Seed Development, Flowering Regulation, and Secondary Metabolism” to incorporate key foundational studies as well as the most recent research advances. These efforts are intended to strengthen the conceptual framework of our work and to provide a more critical and integrated discussion of current understanding in the field. Once again, we thank you for your constructive and insightful suggestions.

 

 

Comments 5: The authors should more clearly articulate the added value of their study. It is important to highlight how the findings advance current understanding in the field and to indicate potential applications—whether in breeding programs, physiological modeling, or agronomic practices. Additionally, I encourage the authors to outline specific and realistic directions for future research that build upon their findings, thereby offering a pathway for subsequent investigations.

Response 5: Thank you very much for your valuable recommendation. In response, we have revised the manuscript to more clearly articulate the added value of our study. Specifically, we now emphasize the central role of BBX transcription factors as multifunctional and integrative regulators of anthocyanin biosynthesis, particularly in their capacity to coordinate light and hormone signaling pathways. This highlights their potential as regulatory “hubs” in plant secondary metabolism and development. We also discuss how our findings contribute to current understanding by identifying BBX genes as promising molecular targets for improving coloration and quality traits in horticultural crops.

Furthermore, we have expanded the future perspectives section to propose realistic and impactful directions for subsequent research. These include functional investigations of BBX genes in a broader range of crop species (beyond model and fruit plants), the application of CRISPR/Cas9 and transient expression systems, and the elucidation of BBX interaction networks with key transcription factors such as HY5, COP1, and the MYB-bHLH complex using approaches like ChIP-seq and yeast two-hybrid assays. We also highlight the potential of marker-assisted selection for superior BBX alleles in breeding programs aimed at enhancing pigment accumulation and stress resistance.

We hope these revisions effectively address your suggestion and strengthen the overall contribution and forward-looking impact of the study. Please refer to lines 803 to 830 of the Revised manuscript with tracked changes.

 

Comments 6: Please ensure that all abbreviations used throughout the manuscript are included in the list of abbreviations and that each abbreviation is clearly defined upon its first appearance in the text.

Response 6: Thank you for your valuable suggestion. We have carefully reviewed the manuscript and ensured that all abbreviations are clearly defined at their first occurrence in the text. Additionally, we have included a comprehensive list of abbreviations to enhance clarity and consistency throughout the manuscript. Please refer to lines 863 to 865 of the Revised manuscript with tracked changes.

 

Besides, as to the Editor’s Comments on the Quality of English Language

Response: Thank you for highlighting the importance of language quality in our manuscript. We recognize that effective scientific writing relies on clarity and precision. Accordingly, we have thoroughly edited the manuscript, focusing on sentence structure, word choice, and overall tone. We believe these enhancements will help make our paper clearer and more engaging for readers.

 

We believe that the revisions made in response to the reviewers' insightful comments have significantly strengthened our manuscript. The enhanced depth of molecular mechanisms, inclusion of the latest research data, and improved clarity on species-specific analyses align our work more closely with the standards of your esteemed journal. We are grateful for the reviewers' careful consideration and are confident that the revised manuscript now meets the criteria for publication.

Thank you for your time and consideration.

 

Sincerely yours,

Prof. Dr. Delin Xu

July 18, 2025                                                                  

Department of Medical Instrumental Analysis, Zunyi Medical University

No.6 Xuefuxi Road, Xinpu District, Zunyi Guizhou 563003, China

 

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

I have read this manuscript, which proposes a comprehensive review on B-box (BBX) proteins as emerging transcription factors regulating anthocyanin biosynthesis in horticultural plants. Among different related aspects, the review aims to offer theoretical and research perspectives to improve ornamental traits and the intrinsic quality of horticultural plants. I also provide the following comments:
Regarding the title, since this is a review, it might be beneficial to explicitly incorporate "Review" or "Comprehensive Review" in the title to better align with the nature of the work and enhance the reader’s understanding of the format.
In any case, the final decision is up to the authors.
Regarding the abstract, when the authors state that comprehensive reviews on BBX TFs remain limited, and their precise roles in regulating anthocyanin biosynthesis are yet to be fully elucidated (lines 13–15), the statement could be stronger by emphasizing the urgent need for such a review, rather than just noting the limitation.
In addition, a more concise mention of the types of mechanisms (direct, indirect, co-regulation) addressed and presented in the manuscript sections would be appropriate. It is also relevant to increase the length of the abstract by providing more details about mechanisms and upstream/downstream targets of BBX proteins, as well as their significance for horticultural research.
Introduction
The transition between the mention of MYB/bHLH/WD40 and the introduction of BBX could be improved to give more emphasis to the emergence of BBX as the main focus.
It could also be considered to briefly mention the economic relevance of anthocyanins early in the section to reinforce their “pivotal role.”
Figures
The figures throughout the manuscript could be significantly improved to be more informative and to cover mechanisms across a broader range of plant species.

Tables
It is essential to include tables summarizing the research progress on BBX. In such tables, quantitative information in the related columns is relevant. If the authors intend to resubmit the manuscript, I find it highly important that such tables are included.

It is also relevant to discuss the multifaceted and integrative nature of BBX transcription factors in horticultural plants, while highlighting that insights exist in crops with other purposes—this would emphasize the need to resolve or fill research gaps in horticultural crops.
It may also be worth noting their role as regulatory "hubs."
Regarding the section on "Secondary metabolism," the focus on artemisinin and flavonoids is appropriate. However, considering the title of the review, it would be valuable to make a more explicit connection here on how this secondary metabolism section serves as a bridge to the main focus on anthocyanins, even if the detailed discussion comes later.

In the subsection on bioactivities, a brief discussion on the relevance of these bioactivities for the horticultural plants themselves, in greater depth—beyond the already well-addressed benefits to human health—could enrich the section, especially considering that the review focuses on “horticultural plants.” Although the abstract mentions “enhancing stress tolerance” and “pollinator attraction,” the bioactivity section needs more depth for the journal’s scope.

A table summarizing specific examples of BBX TFs, species, type of regulation (direct/indirect/co-regulation), target genes, and the final effect on anthocyanin biosynthesis would be relevant.
It may also be worth considering a brief discussion paragraph that synthesizes trends or patterns observed in the mechanisms—for example, the prevalence of interaction with HY5 or the importance of feedback pathways.

In the discussion on optimizing light conditions, it would be interesting to explicitly connect how light optimization interacts with BBX TFs to promote anthocyanin biosynthesis. For example, mentioning that certain light conditions induce the expression or activity of positive BBX regulators or repress negative ones could provide a more direct optimization mechanism.
It would be appropriate to add a point about the need for large-scale functional studies (e.g., high-throughput screening) or the application of multi-omics techniques (e.g. genomics, transcriptomics, proteomics, metabolomics) to more comprehensively unravel complex regulatory networks

Author Response

Response to Reviewer 2 Comments

Dear Reviewer,

We would like to express our heartfelt gratitude for your careful review of our manuscript and the many constructive and insightful comments you provided. Your valuable feedback has not only enhanced the quality of our paper but has also given us important direction and inspiration for future research.

In response to your suggestions, we have systematically addressed each comment in detail and revised the manuscript thoroughly. We have endeavored to improve both the academic rigor and the clarity of our work.

Thank you once again for your dedicated effort and kind support. Below is the Point-by-point response for your former Comments and Suggestions.

 

Reviewer 2:

Comments 1: Regarding the title, since this is a review, it might be beneficial to explicitly incorporate "Review" or "Comprehensive Review" in the title to better align with the nature of the work and enhance the reader’s understanding of the format. In any case, the final decision is up to the authors.

Response 1: Thank you for your thoughtful suggestion regarding the title. We appreciate your advice and agree that including "Review" in the title could help clarify the nature of the manuscript. We have revised the title accordingly to better reflect the content and format of the work. We hope this adjustment improves the readability and accessibility of our review. Please refer to lines 2 to 3 of the revised manuscript.

 

Comments 2: Regarding the abstract, when the authors state that comprehensive reviews on BBX TFs remain limited, and their precise roles in regulating anthocyanin biosynthesis are yet to be fully elucidated (lines 13–15), the statement could be stronger by emphasizing the urgent need for such a review, rather than just noting the limitation. In addition, a more concise mention of the types of mechanisms (direct, indirect, co-regulation) addressed and presented in the manuscript sections would be appropriate. It is also relevant to increase the length of the abstract by providing more details about mechanisms and upstream/downstream targets of BBX proteins, as well as their significance for horticultural research.

Response 2: Thank you very much for your insightful and constructive feedback regarding the abstract. We fully agree with your suggestion that the statement on the limited number of comprehensive reviews could be strengthened. In the revised version, we have emphasized the pressing need for an in-depth synthesis of current findings on BBX transcription factors and their roles in anthocyanin biosynthesis. Additionally, we have revised the abstract to include a more concise overview of the direct, indirect, and co-regulatory mechanisms by which BBX proteins influence anthocyanin biosynthesis, as well as highlighting representative upstream regulators and downstream target genes. We also elaborated on the broader significance of these regulatory pathways in the context of horticultural plant research. We sincerely appreciate your valuable comments, which have helped us improve the clarity and completeness of the abstract. Please refer to lines 13 to 26 of the revised manuscript.

 

Comments 3: Introduction. (a)The transition between the mention of MYB/bHLH/WD40 and the introduction of BBX could be improved to give more emphasis to the emergence of BBX as the main focus. (b) It could also be considered to briefly mention the economic relevance of anthocyanins early in the section to reinforce their “pivotal role.”

Response 3: (a)Thank you for your thoughtful comment regarding the transition between the discussion of MYB/bHLH/WD40 complexes and the introduction of BBX proteins. We appreciate your suggestion to enhance the clarity and emphasis on BBX as the main focus of the review. In the revised manuscript, we have refined the transition to more clearly highlight the emergence of BBX proteins as a distinct and increasingly important class of transcription factors in the regulation of anthocyanin biosynthesis, thereby strengthening the narrative flow and thematic focus of the review. Please refer to lines 55 to 62 of the revised manuscript.

(b) Thank you for your valuable suggestion. We agree that briefly highlighting the economic relevance of anthocyanins at the beginning of the section would help reinforce their pivotal role in plant physiology and their broader significance. Accordingly, we have added a sentence early in the section to emphasize that anthocyanins are not only important pigments contributing to plant stress tolerance and reproductive success but also possess high commercial value due to their applications in the food, cosmetic, and pharmaceutical industries. This addition helps frame the biological discussion within a more applied and economically relevant context. Please refer to lines 31 to 44 of the revised manuscript.

 

Comments 4: Figures. The figures throughout the manuscript could be significantly improved to be more informative and to cover mechanisms across a broader range of plant species.

Response 4: Thank you very much for your valuable suggestion regarding improving the figures to enhance their informativeness and to cover regulatory mechanisms across a broader range of plant species. At present, the figures in the manuscript have been compiled based on results that have been experimentally validated in different plant species and published in peer-reviewed literature, with the aim of accurately reflecting the latest findings in the field. To ensure the scientific rigor and reliability of the information presented, mechanisms that have not been sufficiently confirmed across multiple species have not been included in the figures. We have also carefully reviewed all figures to ensure the accuracy of the content displayed.

 

Comments 5: Tables. It is essential to include tables summarizing the research progress on BBX. In such tables, quantitative information in the related columns is relevant. If the authors intend to resubmit the manuscript, I find it highly important that such tables are included.

Response 5: Thank you very much for your valuable and constructive feedback. We appreciate your suggestion to include tables summarizing the research progress on BBX, as well as your emphasis on providing quantitative information in the relevant columns. We agree that such tables will enhance the clarity and comprehensiveness of our manuscript. In our revised version, we will carefully prepare and incorporate these tables to better summarize the key findings and developments in BBX research. Thank you again for your helpful recommendation. Please refer to Table 1 of the revised manuscript.

 

Comments 6: It is also relevant to discuss the multifaceted and integrative nature of BBX transcription factors in horticultural plants, while highlighting that insights exist in crops with other purposes—this would emphasize the need to resolve or fill research gaps in horticultural crops. It may also be worth noting their role as regulatory "hubs."

Response 6: Thank you for your valuable suggestion. We appreciate the recommendation to emphasize the multifaceted and integrative roles of BBX transcription factors in horticultural plants. In the revised version of the manuscript, we have expanded our discussion to underscore the regulatory versatility of BBX proteins, particularly their ability to integrate light and hormonal signaling pathways. Additionally, we now highlight that while functional insights into BBX genes have been gained from studies in staple crops and model plants, similar comprehensive analyses remain limited in many horticultural species. This reinforces the importance of addressing current research gaps. We have also incorporated a brief note on the emerging view of BBX proteins as central regulatory “hubs” in the transcriptional networks governing secondary metabolism and developmental processes. Please refer to lines 803 to 830 of the revised manuscript.

 

Comments 7: Regarding the section on "Secondary metabolism," the focus on artemisinin and flavonoids is appropriate. However, considering the title of the review, it would be valuable to make a more explicit connection here on how this secondary metabolism section serves as a bridge to the main focus on anthocyanins, even if the detailed discussion comes later.

Response 7: Thank you very much for your insightful comment. We fully agree that a clearer linkage between the general discussion on secondary metabolism and the main focus on anthocyanins would enhance the coherence of the review. In response, we have revised the relevant section to briefly highlight how the regulatory principles discussed for other secondary metabolites—such as artemisinin and flavonoids—also apply to anthocyanin biosynthesis. Specifically, we have introduced a short example involving BBX transcription factors, which not only participate in general secondary metabolic pathways but have also been shown to directly regulate anthocyanin accumulation. For instance, recent studies in sweet cherry fruit have demonstrated that several BBX genes (e.g., PavBBX6, PavBBX9) exhibit expression patterns highly correlated with anthocyanin biosynthesis genes like CHS, F3H, and DFR during fruit ripening. This example helps illustrate the regulatory continuity from general secondary metabolism to the specific focus on anthocyanins that follows in the subsequent sections. Please refer to lines 248 to 258 of the revised manuscript.

 

Comments 8: In the subsection on bioactivities, a brief discussion on the relevance of these bioactivities for the horticultural plants themselves, in greater depth—beyond the already well-addressed benefits to human health—could enrich the section, especially considering that the review focuses on “horticultural plants.” Although the abstract mentions “enhancing stress tolerance” and “pollinator attraction,” the bioactivity section needs more depth for the journal’s scope.

Response 8: Thank you for your valuable suggestion. We fully agree that, given the focus of this review on horticultural plants, it is important to elaborate more deeply on the biological significance of anthocyanin bioactivities for the plants themselves, beyond their well-known benefits to human health. In the revised manuscript, we have expanded the subsection on bioactivities to include a more detailed discussion of how anthocyanins contribute to stress tolerance (e.g., UV protection, oxidative stress mitigation, and pathogen defense) and ecological functions such as pollinator and seed disperser attraction. This addition aims to align more closely with the journal’s scope and to highlight the evolutionary and physiological relevance of these compounds in horticultural plant systems. Please refer to lines 443 to 467 of the revised manuscript.

Comments 9: A table summarizing specific examples of BBX TFs, species, type of regulation (direct/indirect/co-regulation), target genes, and the final effect on anthocyanin biosynthesis would be relevant.

Response 9: Thank you very much for your insightful suggestion. We agree that a summary table outlining specific BBX transcription factors, their associated species, regulatory modes (direct, indirect, or co-regulation), target genes, and their effects on anthocyanin biosynthesis would greatly enhance the clarity and comprehensiveness of the review. In response, we have now included a new table (Table X) that compiles representative examples from recent studies, aiming to provide readers with a more intuitive overview of the diverse roles of BBX proteins in anthocyanin regulation across different plant species. Please refer to Table 2 of the revised manuscript.

 

Comments 10: It may also be worth considering a brief discussion paragraph that synthesizes trends or patterns observed in the mechanisms—for example, the prevalence of interaction with HY5 or the importance of feedback pathways.

Response 10: Thank you very much for this excellent suggestion. We agree that a brief synthesis of the key mechanistic trends such as the frequent interaction of BBX proteins with HY5 and the involvement of feedback regulatory loops would enhance the depth and integrative value of the review. In response, we have added a dedicated discussion paragraph summarizing the common regulatory patterns observed across different BBX mediated pathways. This addition aims to provide readers with a clearer understanding of the overarching mechanisms and their biological relevance, especially in the context of light signaling and anthocyanin accumulation. We truly appreciate your insightful recommendation which has contributed to a more comprehensive and cohesive analysis. Please refer to lines 663 to 676 of the revised manuscript.

 

Comments 11: In the discussion on optimizing light conditions, it would be interesting to explicitly connect how light optimization interacts with BBX TFs to promote anthocyanin biosynthesis. For example, mentioning that certain light conditions induce the expression or activity of positive BBX regulators or repress negative ones could provide a more direct optimization mechanism.

Response 11: Thank you very much for your insightful suggestion regarding the need to more explicitly connect light optimization with the regulation of BBX transcription factors in the context of anthocyanin biosynthesis. In response, we have revised the discussion section to incorporate specific examples that illustrate how light conditions modulate the expression or activity of both positive and negative BBX regulators. As highlighted in the revised text, we now discuss how MiBBX24 and MiBBX27 are upregulated under blue light and positively regulate MiMYB1 to promote anthocyanin accumulation in mango peel, while MdBBX37 acts as a negative regulator whose expression is suppressed by light exposure. These cases exemplify how manipulating light parameters—such as wavelength and intensity—can effectively induce or repress BBX transcription factors to fine-tune anthocyanin biosynthesis. We believe this addition helps clarify the mechanistic basis by which light optimization can be harnessed as a practical strategy to enhance pigment accumulation. We sincerely appreciate your valuable feedback, which has helped improve the depth and clarity of our discussion. Please refer to lines 778 to 793 of the revised manuscript.

 

Comments 12: It would be appropriate to add a point about the need for large-scale functional studies (e.g., high-throughput screening) or the application of multi-omics techniques (e.g. genomics, transcriptomics, proteomics, metabolomics) to more comprehensively unravel complex regulatory networks.

Response 12: Thank you for your valuable suggestion. We fully agree with your perspective that conducting large-scale functional studies such as high throughput screening and applying multi-omics approaches including genomics, transcriptomics, proteomics and metabolomics will greatly facilitate a more comprehensive understanding of the complex regulatory networks underlying anthocyanin biosynthesis in horticultural plants. Accordingly, we have added a relevant discussion in the revised manuscript to emphasize the importance and potential of these advanced technologies in future research. Please refer to lines 836 to 840 of the revised manuscript.

 

Besides, as to the Editor’s Comments on the Quality of English Language

Response: We appreciate your attention to the linguistic aspects of our manuscript. We understand that clear and concise communication is essential for scientific writing. In response, we have carefully revised the language, paying attention to sentence structure, vocabulary choices, and tone. We believe that these improvements will make our paper more accessible and engaging for readers.

 

We believe that the revisions made in response to the reviewers' insightful comments have significantly strengthened our manuscript. The enhanced depth of molecular mechanisms, inclusion of the latest research data, and improved clarity on species-specific analyses align our work more closely with the standards of your esteemed journal. We are grateful for the reviewers' careful consideration and are confident that the revised manuscript now meets the criteria for publication.

Thank you for your time and consideration.

 

Sincerely yours,

Prof. Dr. Delin Xu

July 18, 2025                                                                  

Department of Medical Instrumental Analysis, Zunyi Medical University

No.6 Xuefuxi Road, Xinpu District, Zunyi Guizhou 563003, China

 

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

I would like to commend the authors for the substantial improvements made to the manuscript.  The revised version reflects a significant enhancement in terms of scientific quality, clarity, and structure. The authors have thoroughly addressed the previously raised concerns, and the manuscript is now much more robust and coherent.

Only minor points remain:

-Introduction: While the background is generally well-written, it would benefit from the inclusion of additional recent and relevant references to further support key claims and better frame the study within the broader research landscape.

-The expression "vivid hues" and the phrase "from an aesthetic perspective Line 443" introduce a subjective tone that may be less appropriate for the scientific rigor. I recommend rephrasing this sentence using more objective and discipline-appropriate terminology—e.g., "intense pigmentation", "distinct coloration". This will ensure consistency with the formal style of the manuscript and improve clarity for a scientific audience.

-Line 779-793 This section would benefit from the inclusion of relevant and up-to-date references to support the claims presented. I recommend citing recent peer-reviewed publications that provide empirical evidence or theoretical grounding for these statements. This will enhance the scientific rigor and credibility of the manuscript

-Line184-339 the scientific names should be italicized

Once these points are addressed, I believe the manuscript will be ready for publication.

Author Response

Response to Reviewer 1 Comments

Dear Reviewer,

We sincerely appreciate you taking the time once again to review our manuscript and providing us with more detailed and valuable suggestions. Your invaluable feedback has greatly enhanced the quality of our paper and has offered important guidance and inspiration for our future research.

In response to the reviewers’ comments, we have carefully addressed each point in detail below and have thoroughly revised the manuscript accordingly. We have made every effort to enhance the academic value and clarity of our work.

Once again, we deeply appreciate your hard work and kind support. Below is the Point-by-point response to Comments and Suggestions for Authors.

 

Reviewer 1:

Comments 1: Introduction: While the background is generally well-written, it would benefit from the inclusion of additional recent and relevant references to further support key claims and better frame the study within the broader research landscape.

Response 1: Thank you very much for your valuable feedback on the background section. We fully agree with your observation that the references cited in the previous introduction were indeed somewhat limited. In the revised manuscript, we have supplemented it with more recent and relevant literature to further support key statements and to better integrate this study into a broader research context. We greatly appreciate your constructive suggestions once again. Please refer to lines 33 to 63 of the Revised manuscript with tracked changes.

 

Comments 2: The expression "vivid hues" and the phrase "from an aesthetic perspective Line 443" introduce a subjective tone that may be less appropriate for the scientific rigor. I recommend rephrasing this sentence using more objective and discipline-appropriate terminologye.g., "intense pigmentation", "distinct coloration". This will ensure consistency with the formal style of the manuscript and improve clarity for a scientific audience.

Response 2: We sincerely appreciate your insightful feedback. Thank you for highlighting the need for more objective and discipline-appropriate terminology. In the revised manuscript, we have replaced the phrases "vivid hues" and "from an aesthetic perspective" with more precise scientific terms such as "intense pigmentation" and "distinct coloration." We believe these changes improve both the clarity and the scientific rigor of the manuscript. Thank you again for your valuable suggestion. Please refer to lines 445 to 447 of the Revised manuscript with tracked changes.

 

Comments 3: Line 779-793 This section would benefit from the inclusion of relevant and up-to-date references to support the claims presented. I recommend citing recent peer-reviewed publications that provide empirical evidence or theoretical grounding for these statements. This will enhance the scientific rigor and credibility of the manuscript.

Response 3: Thank you very much for your constructive suggestion. We apologize for the oversight in not including relevant and up-to-date references in Lines 779–793. In the revised manuscript, we have carefully added recent peer-reviewed publications to support the claims presented in this section. We believe these additions will enhance the scientific rigor and credibility of our work. We appreciate your helpful recommendation and attention to detail. Please refer to lines 786 to 790 of the Revised manuscript with tracked changes.

 

Comments 4: Line184-339 the scientific names should be italicized.

Response 4: Thank you very much for pointing out the formatting issue regarding the scientific names in Lines 184–339. We apologize for this oversight. In the revised manuscript, we have italicized the scientific names as required and have also carefully reviewed the entire manuscript to ensure that all scientific names are correctly formatted throughout. We appreciate your attentive review and helpful feedback. Please refer to lines 185 and 341 of the Revised manuscript with tracked changes.

 

 

We believe that the revisions made in response to the reviewers' insightful comments have significantly strengthened our manuscript. The enhanced depth of molecular mechanisms, inclusion of the latest research data, and improved clarity on species-specific analyses align our work more closely with the standards of your esteemed journal. We are grateful for the reviewers' careful consideration and are confident that the revised manuscript now meets the criteria for publication.

Thank you for your time and consideration.

 

Sincerely yours,

Prof. Dr. Delin Xu

July 20, 2025                                                                   

Department of Medical Instrumental Analysis, Zunyi Medical University

No.6 Xuefuxi Road, Xinpu District, Zunyi Guizhou 563003, China

 

Reviewer 2 Report

Comments and Suggestions for Authors

Improvements have been incorporated as per provided recommendations. I have no further comments.

Author Response

Response to Reviewer 2 Comments

Dear Reviewer,

We sincerely appreciate you taking the time once again to review our manuscript and providing us with more detailed and valuable suggestions. Your invaluable feedback has greatly enhanced the quality of our paper and has offered important guidance and inspiration for our future research.

We believe that with your kind helps,  the former revisions responsed to your insightful comments would have significantly strengthened our manuscript. 

Thank you again for your time and consideration.

 

Sincerely yours,

Prof. Dr. Delin Xu

July 20, 2025                                                                   

Department of Medical Instrumental Analysis, Zunyi Medical University

No.6 Xuefuxi Road, Xinpu District, Zunyi Guizhou 563003, China

 

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