Review Reports

Round 1

Reviewer 1 Report

The manuscript presents a comprehensive literature review and bibliometric analysis on biotic and abiotic stresses affecting common bean (Phaseolus vulgaris L.) from 1971 to 2025. It evaluates research trends, key contributors, and emerging topics, and highlights the use of genomic tools such as GWAS and chromosomal mapping in improving stress resistance.

Since the work systematically compiles and analyzes existing studies, it should be categorized as a review article, not a research article, and the article type needs to be revised accordingly. The literature review section provides a broad overview of stress responses in common bean, but it is unclear whether the studies included here were selected using the methodology described in Section 3.1. If they were, this section would fit more appropriately within the bibliometric analysis section to improve structural coherence. In addition, the writing should be substantially revised for clarity and conciseness. Summarizing the content in two tables—one for major biotic stresses and one for abiotic stresses—would make the information more concise and accessible to readers.

The discussion also lacks clear segmentation, which makes it difficult to follow the key mechanisms underlying stress resistance. Dividing this section into distinct subsections would help present existing findings more clearly and provide explanations from multiple perspectives. Likewise, the conclusion is unnecessarily lengthy. It should be shortened to a few straightforward sentences that highlight the most important findings, current prospects, and future research directions. This would ensure that readers can quickly grasp the core message of the manuscript.

Finally, there are several minor errors scattered throughout the text. A few examples are listed below.

Line 37. ‘surpasses’

Line 72. ‘Affecting’

Lines 116-119, 128. What does ‘race’ mean here? Is it the species of Colletotrichum?

Line 188. “t can cause……”?

Line 308. 2.1.12?

Line 322. Where is the title for section 2.2?

Line 327. Sentence structure.

Lines 363-381. The sequencings of the titles are replicated in these texts.

Line 551. “s the 20”?

Lines 580-581. The sentence should be written in English.

Author Response

Reviewer Comments:

Reviewer 1

Comment 1: Since the work systematically compiles and analyzes existing studies, it should be categorized as a review article, not a research article, and the article type needs to be revised accordingly.

Response 1: We agree with this comment. Accordingly, in the revised version of the manuscript, it has been reclassified as a review article.

Comment 2: The literature review section provides a broad overview of stress responses in common bean, but it is unclear whether the studies included here were selected using the methodology described in Section 3.1. If they were, this section would fit more appropriately within the bibliometric analysis section to improve structural coherence.

Response 2: We agree with the comment. The literature review section was prepared following the methodology described in Section 2.1 (formerly 3.1). In the revised version of the manuscript, a dedicated subsection (Section 3; Lines 159–177) has been created to describe the main biotic and abiotic stresses affecting common bean, while the remaining bibliographic information has been incorporated into the bibliometric analysis, as recommended.

Comment 3: In addition, the writing should be substantially revised for clarity and conciseness. Summarizing the content in two tables—one for major biotic stresses and one for abiotic stresses—would make the information more concise and accessible to readers.

Response 3: We agree with the comment. The manuscript has been thoroughly reviewed and improved in terms of clarity and writing. The content on biotic and abiotic stresses, which was previously presented in subsections, has been summarized in tables in Section 3. Table 1 (Lines 167–169) presents the biotic stresses, and Table 2 (Lines 175–177) the abiotic stresses in the revised manuscript, including concise information on the damage and impacts they cause on common bean, as recommended.

Comment 4: The discussion also lacks clear segmentation, which makes it difficult to follow the key mechanisms underlying stress resistance. Dividing this section into distinct subsections would help present existing findings more clearly and provide explanations from multiple perspectives.

Response 4: We agree with the comment. In the revised version of the manuscript, the discussion section has been integrated with the results (Section 4; Lines 178–1031) to avoid presenting them in a purely descriptive manner. This approach allows the findings to be discussed and interpreted directly within each subsection, enabling a clearer and more explanatory presentation.

Comment 5:  Likewise, the conclusion is unnecessarily lengthy. It should be shortened to a few straightforward sentences that highlight the most important findings, current prospects, and future research directions. This would ensure that readers can quickly grasp the core message of the manuscript.

Response 5: We agree with the comment. In the revised version of the manuscript, the conclusions have been reformulated in accordance with the objectives set forth in the study, incorporating the suggested points (Section 6; Lines 1056–1114).

Comment 6: Finally, there are several minor errors scattered throughout the text. A few examples are listed below: Line 37: ‘surpasses’; Line 72: ‘Affecting’; Lines 116–119, 128: What does ‘race’ mean here? Is it the species of Colletotrichum?; Line 188: “t can cause……”; Line 308: 2.1.12?; Line 322: Where is the title for Section 2.2?; Line 327: Sentence structure; Lines 363–381: The sequencing of the titles is replicated in these texts; Line 551: “s the 20”?; Lines 580–581: The sentence should be written in English.

Response 6: We appreciate the comments. The manuscript has been thoroughly reviewed, and the indicated errors have been corrected throughout the document.

Author Response File: Author Response.pdf

Reviewer 2 Report

This manuscript presents a comprehensive literature review and bibliometric analysis of research on biotic and abiotic stresses in common bean (Phaseolus vulgaris L.) over the past five decades (1971–2025). The authors aim to identify key trends, themes, productive countries/institutions, and mitigation strategies used to address these stresses.

Major Comments

• The manuscript lacks a concise statement of its research questions or hypotheses. The introduction should clearly outline what specific bibliometric patterns or knowledge gaps the study intends to uncover.
• The inclusion of data from 2025 is problematic, as 2025 is not over yet. Please clarify that data from 2025 refers to data available as of mid-2025, not a full-year forecast.
• The manuscript intends to combine bibliometric analysis with a traditional literature review, but the integration between the two is limited. The bibliometric data are presented descriptively without deep interpretation, and the narrative review does not critically engage with or build upon those trends. To enhance the manuscript’s value, the authors should more clearly connect bibliometric findings with thematic insights, using one to inform and deepen the other.
• The literature review portion is mostly descriptive and lacks critical analysis. The paper would benefit from a more analytical approach to synthesizing trends—for example, by classifying themes under abiotic vs. biotic stress, genetics vs. agronomy, or molecular vs. field-based approaches.
• Consider developing a conceptual framework or timeline figure to show how mitigation strategies evolved across decades.
• It lacks detail on how the retrieved records were screened and how duplicates were handled. For transparency and reproducibility, I recommend including a brief description of the screening workflow—such as whether titles/abstracts were reviewed manually or with software assistance, whether multiple reviewers were involved, and how duplicate records were identified and removed.
• The manuscript includes a section on thematic evolution, supported by timeline visualizations. However, the interpretation remains largely descriptive. The authors are encouraged to deepen this section by critically analyzing the factors behind thematic shifts—such as technological advances, policy changes, or environmental challenges—and linking these themes to citation trends or publication volumes. Connecting the observed thematic evolution more explicitly with the literature review would also help unify the manuscript’s two core components
• The authors should also acknowledge limitations—e.g., reliance on Web of Science only and possible language or coverage biases. Finally, referencing methodological literature on database differences and clustering approaches would enhance transparency and methodological credibility.

Figures and Tables

• Some figures (e.g., collaboration maps, keyword clusters) are difficult to interpret due to low resolution or unclear legends.
• It would be helpful to include a summary table listing the top 10 most cited papers, the top journals, and recurring keywords/themes.

Mitigation Strategies

• The section on mitigation strategies (biotic and abiotic) lacks depth. More focus on how these strategies are implemented (e.g., breeding, genetic engineering, agronomic practices) and which are most effective under different conditions would enhance the review.

Minor Comments

• Consider shortening the title for clarity.
• The manuscript requires language editing. There are many awkward constructions, tense inconsistencies, and run-on sentences that impede comprehension.

Check line number 43, 59, 93, 208, 290, 449, and 534. The authors need to check the whole manuscript thoroughly.

check the major comments 

Author Response

Reviewer Comments:

Reviewer 2

Comment 1: The manuscript lacks a concise statement of its research questions or hypotheses. The introduction should clearly outline what specific bibliometric patterns or knowledge gaps the study intends to uncover.

Response 1: We agree with the comment. Accordingly, the introduction has been revised to incorporate the research gap (Lines 85–93) and to reformulate the objectives (Lines 93–97) for greater clarity.

Comment 2: The inclusion of data from 2025 is problematic, as 2025 is not over yet. Please clarify that data from 2025 refers to data available as of mid-2025, not a full-year forecast.

Response 2: We agree with the recommendation. In the methodology, it was specified that the data were collected up to June 19, 2025 (Line 141), and elsewhere in the manuscript, reference is made to the period spanning from 1971 to mid-2025.

Comment 3: The manuscript intends to combine bibliometric analysis with a traditional literature review, but the integration between the two is limited. The bibliometric data are presented descriptively without deep interpretation, and the narrative review does not critically engage with or build upon those trends. To enhance the manuscript’s value, the authors should more clearly connect bibliometric findings with thematic insights, using one to inform and deepen the other.

Response 3: Thanks for the comment. In the revised version of the manuscript, the discussions have been integrated with the bibliometric analysis results (Section 4) to move beyond a purely descriptive presentation providing a critical analysis. This approach establishes connections between the bibliometric findings, the scientific information, and a more robust critical evaluation.

Comment 4: The literature review portion is mostly descriptive and lacks critical analysis. The paper would benefit from a more analytical approach to synthesizing trends—for example, by classifying themes under abiotic vs. biotic stress, genetics vs. agronomy, or molecular vs. field-based approaches.

Response 4. We agree with the comment. Accordingly, in the revised version of the manuscript, a more organized analysis has been conducted. For example, in the thematic map analysis (Lines 500–786), the bibliometric results are presented according to four categories (basic, motor, niche, and emerging topics), linking each type of stress to its position on the map based on its connection with other disciplines and its level of development. Within these groups, abiotic stresses such as drought and salinity, as well as diseases, are addressed in detail, specifying advances and findings in agronomic, physiological, genetic, molecular, and field evaluation contexts, with a critical approach. In this way, the bibliometric findings are directly connected to the types of stress, rather than being limited to a description or enumeration of biotic and abiotic stresses.

Comment 5: Consider developing a conceptual framework or timeline figure to show how mitigation strategies evolved across decades.

Response 5: Thank you for the recommendation. Two timeline graphs were created to show the evolution of biotic stress mitigation strategies (Figure 10; Lines 977–978) and abiotic stress mitigation strategies (Figure 11; Lines 1030–1031). Additionally, a conceptual framework describing this evolution was developed, complemented with specific citations of the strategies (Section 4.10; Lines 948–1031).

Comment 6: It lacks detail on how the retrieved records were screened and how duplicates were handled. For transparency and reproducibility, I recommend including a brief description of the screening workflow—such as whether titles/abstracts were reviewed manually or with software assistance, whether multiple reviewers were involved, and how duplicate records were identified and removed.

Response 6: We agree with the comment. In the revised version of the manuscript, the explanation of the data search and extraction strategy has been expanded in M&M (Section 2.3; Lines 141–148). Additionally, Figure 1 has been replaced with a new flow diagram based on the PRISMA methodology (Lines 148–149), providing a more detailed description of this process.

Comment 7: The manuscript includes a section on thematic evolution, supported by timeline visualizations. However, the interpretation remains largely descriptive. The authors are encouraged to deepen this section by critically analyzing the factors behind thematic shifts—such as technological advances, policy changes, or environmental challenges—and linking these themes to citation trends or publication volumes. Connecting the observed thematic evolution more explicitly with the literature review would also help unify the manuscript’s two core components

Response 7: We agree with the comment. In the revised version of the manuscript, the thematic evolution is analyzed based on the results of the bibliometric analysis and Figure 9, describing emerging topics and topic transitions (Section 4.9; Lines 812–836). Additionally, specific subsections were developed in this section to describe emerging and declining themes, supported by scientific evidence and a critical analysis that considers the existing challenges in the field. Finally, this thematic evolution is linked to the findings from the literature review, allowing the two main components of the manuscript to be unified.

Comment 8: The authors should also acknowledge limitations—e.g., reliance on Web of Science only and possible language or coverage biases. Finally, referencing methodological literature on database differences and clustering approaches would enhance transparency and methodological credibility.

Response 8: We agree with the comment. In the revised version of the manuscript, Section 5 has been added to detail the study’s limitations, including the use of a single database for the bibliometric analysis. Furthermore, Section 2.1 (Lines 99–110) describes the existing databases and justifies the selection of Scopus as the primary source.

Comment 9: Some figures (e.g., collaboration maps, keyword clusters) are difficult to interpret due to low resolution or unclear legends.

Response 9: We agree with the comment. In the revised version of the manuscript, the resolution of the figures and tables has been improved, and the legends have been revised to include clearer and more detailed descriptions of their elements.

Comment 10: It would be helpful to include a summary table listing the top 10 most cited papers, the top journals, and recurring keywords/themes.

Response 10: Thank you for the recommendation. In the revised version of the manuscript, Figure 5 (radial graph) has been replaced with a table summarizing the ten most cited documents, the main journals, and the recurring topics/keywords (Table 5; Line 366).

Comment 11: The section on mitigation strategies (biotic and abiotic) lacks depth. More focus on how these strategies are implemented (e.g., breeding, genetic engineering, agronomic practices) and which are most effective under different conditions would enhance the review.

Response 11: We agree with the comment. This point is detailed in Section 4.10 (Lines 948–975; 978–1030), where the implementation of the mitigation strategies is described, specifying whether they were applied through foliar application, inoculation, or pretreatment, and highlighting the type of stress factor targeted and the effects achieved. This provides a more comprehensive and accurate overview of the various strategies used over time.

Comment 12: Consider shortening the title for clarity.

Response 12: We agree with the comment and appreciate the recommendation. In the revised version of the manuscript, the title has been modified for greater clarity (Lines 2–3).

Comment 13: The manuscript requires language editing. There are many awkward constructions, tense inconsistencies, and run-on sentences that impede comprehension. Check line number 43, 59, 93, 208, 290, 449, and 534. The authors need to check the whole manuscript thoroughly.

Response 13: Thank you for the recommendation. The manuscript was carefully reviewed, and errors in writing, verb tense, and sentence structure have been corrected throughout the document.

Author Response File: Author Response.pdf

Reviewer 3 Report

I believe that after corrections to the manuscript this study can be published.

The study could benefit from clearer methodological descriptions and a more balanced interpretation of results.

The authors should be mindful of the tense that is used in the manuscript. They should re-check the whole document for the minor mistakes with regards to the grammar tense. The manuscript should be submitted for English editing, for grammar purposes. More comments can be accessed on the revised copy of the manuscript.

Comments for author File: Comments.pdf

Author Response

Reviewer Comments:

Reviewer 3

Comment 1: The study could benefit from clearer methodological descriptions and a more balanced interpretation of results.

Response 1: We agree with the comment. In the revised version of the manuscript, the methodology has been adjusted (Section 2; Lines 98–157) to improve clarity, and Figure 1 has been replaced with a clearer flowchart, as recommended.

Comment 2: The authors should be mindful of the tense that is used in the manuscript. They should re-check the whole document for the minor mistakes with regards to the grammar tense. The manuscript should be submitted for English editing, for grammar purposes. More comments can be accessed on the revised copy of the manuscript.

Response 2: We agree with the recommendations. The revised version of the manuscript has been thoroughly reviewed, and grammar and verb tense errors have been corrected throughout the document. 

Comment 3: More comments can be accessed on the revised copy of the manuscript.

Response 3: Thanks for the corrections. We update the manuscript and correct the errors with your suggestions. 

Comment 4:  Use keywords that differ from the title.

Response 4: We agree with the recommendation. In the revised version of the manuscript, keywords different from the title have been included.

Comment 5: Look for recent studies and remove those that are more than 5 years old unless they are important.

Response 5: We agree with the comment. In the revised version of the manuscript, references from the last five years were prioritized in the introduction to ensure up-to-date information (Lines 35–80). However, this exclusion criterion was not applied in the bibliometric analysis and discussion, as the analysis period established in the study’s first objective was followed (Line 94). This approach was necessary to examine global trends and consolidate all available knowledge on common bean. It also allowed the inclusion of relevant historical publications from different countries and in multiple languages, in accordance with the methodology described in Section 2.2 (Lines 111–122).

Comment 6: The authors are encouraged to introduce novel contributions to the existing model to enhance its value and applicability for the broader scientific community. Substantial revisions are required to strengthen the clarity, rigor, and overall scientific contribution of the study.

Response 6: We agree with the comment and appreciate the recommendation. In the revised version of the manuscript, a paragraph has been added highlighting the study’s contribution by identifying knowledge gaps and research trends in common bean (Lines 81–93). Additionally, the specific objectives have been reformulated to enhance the clarity and scientific rigor of the work (Lines 93–97).

Comment 7: Review the references again and put them in line with the journal's standards.

Response 7: We agree with the comment. A thorough review of all references was conducted to ensure compliance with the formatting standards required by the journal.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

The authors have substantially revised this manuscript, making significant improvements, particularly in the logic flow. I have no further comments. 

There are still some minor style errors in the manuscript that can be addressed during the proofing process.

Reviewer 2 Report

no further comments

no further comments