Development of SSR Markers for and Fingerprinting of Walnut Genetic Resources

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The research is original and it showed relevant results for walnut germplasm. Revisions are included in the text PDF.

Comments for author File: Comments.pdf

Comments on the Quality of English Language

no special comments for english language

Author Response

Dear Reviewer 1,

Thank you for your recognition of our research. We have fully considered your suggestions and made revisions to the manuscript. All modifications are highlighted. We also made modifications to the tense and grammar errors in the text, and rewrote some long sentences. Hopefully, we have addressed all of your concerns. The revision has been resubmitted to the journal. We look forward to your positive response. The specific modifications are as follows：

1.We have revised the title of the manuscript based on your suggestion.

2.We have modified all the details you suggested for adjustment and removed any content that is not suitable in the results section.

3.We have added references on using softwarein the “Materials and methods” section.

4.We provided an explanation at the end of section 3.2 regarding the reason for selecting 14 out of 18 SSR markers.

5.We have rearranged all tables in the order they appear in the text.In addition, we have included the table you suggested for inclusion in the supplementary materials, as well as data on walnut phenotypes, in the supplementary materials.

Hopefully, we have addressed all questions in the revision, and it can be accepted for publication in the journal.

Best Regards,

Director, Jianxun Qi and Zhixia Hou

Reviewer 2 Report

Comments and Suggestions for Authors

Zhang et al. aimed to analyze the genetic diversity of Chinese walnut resources and improve the utilization of improved varieties by developing molecular markers and fingerprint construction. The researchers used eight walnut varieties and developed 14 high-quality SSR molecular markers based on genome re-sequencing. They conducted site detection and fingerprint construction on 47 walnut resources using capillary electrophoresis and the selected SSR markers.

Overall assessment: This study developed molecular markers and fingerprints for Chinese walnut resources, revealing insights into their genetic diversity and population structure. The identified core SSR markers are valuable tools for future research, breeding, and conservation efforts. The study highlights the potential for enhancing the utilization and protection of walnut varieties in China.

Comments:

1- For the introduction, I would suggest clearly and precisely articulating the study's objectives. For instance, this study seeks to achieve several goals, including molecularly identifying walnut germplasm resources, examining genetic diversity and population structure, creating a fingerprint map, and conducting association analysis between SSR markers and walnut traits.

2- For the methods, it is necessary to expand on the software employed for data analysis, providing additional details on the specific analyses conducted and the parameters used.

3- For the discussion, I would suggest explicitly comparing the study with existing literature, justifying methodological choices, and addressing limitations while offering future research directions. Thoroughly interpret results, emphasizing their biological implications in walnut breeding. Discuss the significance of SSR marker types, address differences in analyses, and propose hypotheses.

Author Response

Dear Reviewer 2,

Thank you for your recognition of our research. We have fully considered your suggestions and made revisions to the manuscript. All modifications are highlighted. We also made modifications to the tense and grammar errors in the text, and rewrote some long sentences. Hopefully, we have addressed all of your concerns. The revision has been resubmitted to the journal. We look forward to your positive response.

1-For the introduction, I would suggest clearly and precisely articulating the study's objectives. For instance, this study seeks to achieve several goals, including molecularly identifying walnut germplasm resources, examining genetic diversity and population structure, creating a fingerprint map, and conducting association analysis between SSR markers and walnut traits.

Response: Thank you for your suggestion. We have revised the description of the research objectives in the fourth paragraph of the introduction. The revised sentence was shown in lines 86-90: “This study seeks to achieve several goals, including molecularly identifying walnut germplasm resources, examining genetic diversity and population structure, creating a fingerprint map, and conducting association analysis between SSR markers and walnut traits. Overall, this study will provide a reference for future breeding of walnut germplasm with excellent traits and lay a theoretical foundation for screening walnut resources with excellent traits”.

2- For the methods, it is necessary to expand on the software employed for data analysis, providing additional details on the specific analyses conducted and the parameters used.

Response: Thank you for your suggestions. We have added references to the main software used and partially annotated the website. At the same time, we also supplemented the specific parameters of the software. The specific modifications were shown in lines 127-128, 150, 153-154, 160-162, and 167.

3- For the discussion, I would suggest explicitly comparing the study with existing literature, justifying methodological choices, and addressing limitations while offering future research directions. Thoroughly interpret results, emphasizing their biological implications in walnut breeding. Discuss the significance of SSR marker types, address differences in analyses, and propose hypotheses.

Response: Thank you for your suggestions. We have discussed the three parts you suggested and proposed hypotheses and future prospects. In lines 389-391, we have confirmed the rationality of the method used in this study through previous research and provided prospects. In lines 395-399, we discussed the differences between different types of SSRs and provided suggestions for the selection of methods for future research. In lines 525-531, we have summarized the significance of this study and emphasized its significance for walnut breeding. At the same time, prospects for future research were presented.

Hopefully, we have addressed all questions in the revision, and it can be accepted for publication in the journal.

Best Regards,

Director, Jianxun Qi and Zhixia Hou

Reviewer 3 Report

Comments and Suggestions for Authors

I reviewed the article Development of walnut SSR molecular markers and construction of 47 walnut resource fingerprints. In general it is very complete and very well structured; However, I have some observations:

Abstract: Very good, no comments.

 

Keywords: Line 28, the word SSR is already in the title, replace it with another word.

Introduction: Clearly specify the objectives. It is necessary to establish the research hypotheses.

Materials and Methods: Lines 123 to 128, cite a document that supports that part.

Discussion: this chapter is not numbered (4. Discussion); lines 423 to 425 cite one or two articles that support the idea; lines 431 to 434, corresponds to results, not discussion; lines 443 to 44 (The He value of 14,443 pairs of SSR markers was higher than the Ho value in 47 walnut resources,) expand the discussion on the implications of the fact that He was greater than Ho. Finally, in this section it would be interesting to add a subchapter on “implications for conservation.”

Conclusion: Lines 557 to 572, Review and substantially improve. The conclusions should not be another version of the summary of results.

Comments on the Quality of English Language

Only requires a minor revision.

Author Response

Dear Reviewer 3,

Thank you for your recognition of our research. We have fully considered your suggestions and made revisions to the manuscript. All modifications are highlighted. We also made modifications to the tense and grammar errors in the text, and rewrote some long sentences. Hopefully, we have addressed all of your concerns. The revision has been resubmitted to the journal. We look forward to your positive response.

Keywords: Line 28, the word SSR is already in the title, replace it with another word.

Response: Thank you for your suggestion. We replaced SSR with “Simple sequence repeats”.

Introduction: Clearly specify the objectives. It is necessary to establish the research hypotheses.

Response: Thank you for your suggestion. In lines 86-91, we proposed the hypothesis of this study.

Materials and Methods: Lines 123 to 128, cite a document that supports that part.

Response: Thank you for your suggestion. In lines 105-107 and 110, we referred to GB/T 26909-2011 "Guidelines for testing the specificity, consistency, and stability of new plant varieties: walnut genus" and the research of Zhang et al.

Discussion: this chapter is not numbered (4. Discussion); lines 423 to 425 cite one or two articles that support the idea; lines 431 to 434, corresponds to results, not discussion; lines 443 to 44 (The He value of 14,443 pairs of SSR markers was higher than the Ho value in 47 walnut resources,) expand the discussion on the implications of the fact that He was greater than Ho. Finally, in this section it would be interesting to add a subchapter on “implications for conservation.”

Response: Thank you for your suggestions. We have added the numbering for this chapter in line 384. We cited two references in line 402. In order to better introduce the content of this paragraph, we have simplified the description of this result in lines 410-411. We discussed the possible reasons why He values are greater than Ho values in line 421. In lines 525-531, we have elaborated on the positive significance of this study for the protection of walnut germplasm and proposed prospects.

Conclusion: Lines 557 to 572, Review and substantially improve. The conclusions should not be another version of the summary of results.

Response: Thank you for your suggestion. In lines 533-543, we have rewritten the results section.

 

Hopefully, we have addressed all questions in the revision, and it can be accepted for publication in the journal.

Best Regards,

Director, Jianxun Qi and Zhixia Hou