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Dear Authors,
I am pleased to inform you that the manuscript has improved after the last revision and can be accepted for publication.
Congratulations on accepting your manuscript, and thank you for your interest in submitting your work to PeerJ.
With Thanks
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
The authors referred to the proposed remarks. Their changes are satisfactory, and therefore, the manuscript is suitable for publication.
The experimental design is well-presented.
The manuscript meets the journal's standards.
Accept in present form
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Accurate
Dear Authors
The manuscript cannot be accepted for publication in its current form. It needs a minor revision before publication. The authors are invited to revise the paper considering all the suggestions made by the reviewers. Please note that the requested changes are required for publication.
With Thanks
I have completed my evaluation of your manuscript. The manuscript deals Multi-Environment QTL Mapping Identifies Major Genetic Loci Influencing Soybean Main Stem Node Architecture. The authors generated an ample amount of information in their research work, using in field, silico techniques and some lab experiments and offers some new information.
the manuscript is clear, well-structured, and written in fluent English.
the research question is well defined and the introduction provides sufficient background.
The experimental design answers the research question effectively.
The results are well-supported by the data.
analytical methods used, are valid and appropriate.
the conclusions are sound and justified by the evidence presented.
Minor Comments:
1.Typographical Error:
oIn the sentence “but the genetic underpinnings of key architectural traits remain elusive,” consider revising “remain” to “remains” for subject-verb agreement.
2.Punctuation and Grammar:
oIn the phrase "were the environment plays a major role," change “were” to “where” for clarity.
oIn "showed that MSN traits are highly influenced by genetic factors, were the environment plays a major role," consider replacing the comma with a semicolon to better separate the two independent clauses.
3.Clarity in Results:
oThe phrase “using ICIM analysis revealed a total of 23QTLs were identified” should be revised for grammatical clarity. Consider rephrasing to "Using ICIM analysis, we identified a total of 23 QTLs."
4.Spacing Issue:
oThere is a spacing issue with “23QTLs” where a space should be added: it should read “23 QTLs.”
5.Abbreviation Consistency:
oWhen first introducing “QTLs,” please ensure you define it as "Quantitative Trait Loci" for clarity, particularly for readers who may be unfamiliar with the term.
6.Detail in Methodology:
oIn “a high-density genetic map composed of 8,078 SLAF markers,” it would be helpful to briefly explain what SLAF.
7.Clarification of Results:
oThe phrase “Notably, we identified a stable major QTL, qMSN-6-4, explaining up to 24.81% of phenotypic variation” could specify the trait being measured. For example, “explaining up to 24.81% of the phenotypic variation in main stem node number.”
8.Missing Articles:
oIn “energy metabolism, and transcriptional factors,” consider removing the comma before "and" for better flow, as it is part of a simple list.
9.Clarification of Candidate Genes:
oIn the sentence “7 potential candidate genes were identified that likely involved the growth and development of soybean MSN,” consider clarifying what "MSN" stands for in this context if it hasn’t been previously defined in the abstract.
10.Concluding Sentence:
oThe last sentence “These findings will help elucidate the genetic basis of pod number traits” may benefit from a slight rephrase to specify that the findings contribute to understanding the genetic basis of main stem node architecture, thereby connecting back to the main focus of the study.
The publication is written in clear, professional English and uses appropriate academic language. It provides sufficient QTL mapping and soybean genetics background, citing relevant literature. The structure is methodical, with well-organized sections and precise figures and tables that complement the data presented.
The discussion focuses on crucial quantitative trait loci (QTLs) influencing soybean main stem node (MSN) traits. It links these findings to hypotheses about plant architecture and productivity, making the results valuable for future soybean breeding.
The article is self-contained, well-structured, and offers meaningful insights into soybean genetics.
The publication fits within the scope of plant genetics research, addressing a well-defined research question on soybean main stem node (MSN) traits. It fills a significant knowledge gap by identifying QTLs and candidate genes, which are valuable for improving breeding programs.
The study was conducted rigorously, adhering to high technical standards. The methods, including SLAF-seq and QTL mapping, are described in sufficient detail to allow for replication.
The publication's findings are valid and supported by robust data.
The methodology section provides a comprehensive overview of the genetic mapping process. However, it would benefit from more detailed explanations regarding the selection criteria for the RIL population and the specific statistical methods used in the QTL analysis.se all typewriting error in the whole manuscript.
The research provides detailed QTL mapping and candidate gene identification for soybean MSN traits, making the results reliable. The data are well-controlled, and all underlying information has been provided, enabling meaningful replication.
The conclusions are clearly stated and directly linked to the research question, emphasizing the importance of these genetic discoveries for future breeding programs. While the impact and novelty are not deeply assessed, the study’s contributions are valuable for advancing soybean genetics.
Rewrite this sentence: “The statical analysis of the phenotype for a three year (2013, 2014, and 2015) showed that MSN traits are highly influenced by genetic factors, were the environment plays a major role”.
Line 7 add the city of study
Line 9 change Cm to cM
Add some results in the abstract
Add more recent references related to the plant architecture, especially MSN
Recheck the capital and small letters in the citation.
Ensure that all references to previous studies are up-to-date and relevant. Some citations may need to be included to support claims about the genetic mechanisms of MSN.
This research uncovers the genetic basis of soybean architecture, providing valuable insights for crop improvement and breeding strategies. How might these findings inform future breeding programs to enhance yield and resilience in diverse environments?
As a peer reviewer, I have several comments and suggestions
Abstract:
## The abstract is quite detailed but could benefit from further clarity, especially in distinguishing between statistical analysis and genetic mapping results. For instance, "The statistical analysis of the phenotype for a three-year period..." could be clearer by explaining which factors were analyzed.
## The identification of "23 QTLs across 20 chromosomes" is informative, but it would be more impactful to highlight how many of these QTLs are of major significance. You mention 5 QTLs detected in multiple years but should further emphasize the significance of these findings.
## While it’s good that candidate genes are highlighted, the mention of gene ontology appears somewhat rushed.
##The final sentence states that these findings will elucidate the genetic basis of pod number traits, yet the focus of the paper seems to be on MSN. Please ensure consistency by focusing on MSN or clearly explaining the connection between MSN and pod number traits.
Introduction:
1. The introduction provides a strong overview of the importance of MSN, but it can be further strengthened by addressing more recent studies. For instance, there is a mention of Fahim et al. (2021) and Fu et al. (2020) repeatedly, but more integration of additional relevant work (e.g., GWAS studies or other QTL mapping efforts) could add depth.
3. Some technical terms (such as "SLAF markers," "ICIM analysis," and "QTL IciMapping") are introduced without sufficient explanation. A brief definition or explanation of these methods would help readers unfamiliar with them.
Good
Conclusion:
- The sentence "The variability in the expression of these genes among parental lines" could be rephrased for clarity. For example, "The differential expression of these genes between the parental lines" would make the statement clearer and more concise.
- In the last sentence, "useful targets for marker-assisted selection and molecular breeding approaches," you could add "for improving soybean architecture and yield stability" to reinforce the practical applications of your findings.
Minor Grammar Adjustments:
- Change "logarithm of odds (LOD) scores" to "logarithm of odds (LOD) score" for consistency.
- In "a persistent rise in the average values of MSN," consider rewording to "a consistent increase in the mean MSN values."
- In "points to the presence of potentially novel regulatory pathways influencing this trait," "points to" could be replaced with "suggests" for smoother phrasing.
Formatting Issues:
• "The font size in the tables is inconsistent with the rest of the manuscript. Please ensure uniform font size throughout."
Typographical Errors:
• "There are several typographical errors on page 5 that should be corrected for clarity, such as 'molecular' spelled as 'moleculer'."
• Reference Updates:
• "Consider updating reference
These minor revisions will improve the readability, precision, and overall clarity of your manuscript.
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