Construction of SNP-Based High-Density Genetic Map Using Genotyping by Sequencing (GBS) and QTL Analysis of Growth Traits in Eucommia ulmoides Oliver

Round 1

Reviewer 1 Report (Previous Reviewer 2)

The manuscript was improved, comparing to previous version. Table N2 is too long, may it be transferred to supplements? 

Author Response

Dear Editors,

Thanks for your decision and for the reviewers’ comments concerning our manuscript (ID: forests-1898167). These comments and suggestions are quite valuable and helpful for improving our paper. Now we’ve prepared a revised version according to your suggestions and reviewers’ comments. Each answer has been given to each question raised by the reviewers in the following text. Additionally, the revised version with tracked changes has also been submitted as a supplementary file. We hope that you and reviewers can recognize our efforts and are satisfied with this revised version.

 

Reviewer1

Comments and Suggestions for Authors

The manuscript was improved, comparing to previous version. Table N2 is too long, may it be transferred to supplements?

Response: Thanks for your professional comments. The part of table2(QTL of node spacing) have been leaved in manuscripts and part of (tree height and basal diameter) have moved in supplement file linked as tableS7.  

Best wishes!

Jun Qing

Reviewer 2 Report (New Reviewer)

Title: Construction of SNP-Based High-Density Genetic Map Using Genotyping by Sequencing (GBS) and QTL Analysis of growth traits in Eucommia ulmoides

Comments to the author:

The author touched on the genetic map construction and QTL analysis of growth traits in Eucommia ulmoides, which is interesting. This research is very important for laying a solid foundation for promoting the investigation of forestry breeding efforts in E. ulmoides. However, there are some small mistakes that need to be corrected. They are listed as follows:

1.     The references’ part looks very weird, which includes several big mistakes. The most unacceptable one is that reference 16 showed in the blank. Please correct all these small mistakes and make sure the paper looks good in the format before submitting to the journal.  The bibliography didn’t match with the current journal. Please correct them and avoid these unnecessary mistakes.

2.     NO line numbers are added in the whole peer review paper, which is difficult for the reviewer to give specific reviews. Please add line numbers.

3.     P2; ‘Huazhong No.8’ and ‘Huazhong No.12’ should be the varieties; The format used in this paper should be corrected.

4.     The figures and tables are professional. Spelling should be double-checked. In Figure 5, ‘Tree Hight’ should be ‘Tree height’; Figure1 should be Figure 1. A lot of detailed information should be corrected.

 

In conclusion, this research is very impressive. However, a lot of mistakes in it needs to be corrected. I suggest the author amends it and resubmit it to the Forests.

 

 

Author Response

Dear Editors,

Thanks for your decision and for the reviewers’ comments concerning our manuscript (ID: forests-1898167). These comments and suggestions are quite valuable and helpful for improving our paper. Now we’ve prepared a revised version according to your suggestions and reviewers’ comments. Each answer has been given to each question raised by the reviewers in the following text. Additionally, the revised version with tracked changes has also been submitted as a supplementary file. We hope that you and reviewers can recognize our efforts and are satisfied with this revised version.

Reviewer 2

Comments and Suggestions for Authors

Title: Construction of SNP-Based High-Density Genetic Map Using Genotyping by Sequencing (GBS) and QTL Analysis of growth traits in Eucommia ulmoides

 

Comments to the author:

 

The author touched on the genetic map construction and QTL analysis of growth traits in Eucommia ulmoides, which is interesting. This research is very important for laying a solid foundation for promoting the investigation of forestry breeding efforts in E. ulmoides. However, there are some small mistakes that need to be corrected. They are listed as follows:

 

1. The references’ part looks very weird, which includes several big mistakes. The most unacceptable one is that reference 16 showed in the blank. Please correct all these small mistakes and make sure the paper looks good in the format before submitting to the journal. The bibliography didn’t match with the current journal. Please correct them and avoid these unnecessary mistakes.

Response：Thank for your professional comments. For the reference problems you mentioned, we have checked all the references and have revised them, including the reference format.

 

2. NO line numbers are added in the whole peer review paper, which is difficult for the reviewer to give specific reviews. Please add line numbers. （行号）

Response: Line numbers have been added to the entire article.

 

3. P2; ‘Huazhong No.8’ and ‘Huazhong No.12’ should be the varieties; The format used in this paper should be corrected.

Response: 'Huazhong No. 8' and 'Huazhong No. 12' have been rewritten to “Huazhong No. 8” and “Huazhong No. 12” [1].

4. The figures and tables are professional. Spelling should be double-checked. In Figure 5, ‘Tree Hight’ should be ‘Tree height’; Figure1 should be Figure 1. A lot of detailed information should be corrected.

Response: Than for your professional comments. The language translation of the full text has been checked again and again with the help of English professional colleagues, and the contents of the charts are included.

 

Submission Date

19 August 2022

Date of this review

25 Aug 2022 19:01:27

 

 

[1].  Wang, Z., et al., High-Density Genetic Map Construction and QTL Mapping of Leaf and Needling Traits in Ziziphus jujuba Mill. Frontiers in Plant Science, 2019. 10(1424): p. 1-11.

Best wishes!

Jun Qing

Round 2

Reviewer 2 Report (New Reviewer)

The paper is ready for publication. I don't have further suggestions. 

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

Major Comments:

1. In the abstract, please clarify what is meant by “A total of 33 candidate genes were identified by scanning”
2. In the introduction and abstract, a more concise way of saying “a single family and single genus of Eucommiaceae” could be “a monotypic family and genus”
3. The third paragraph discussing MAS breeding should provide more detail of what has been done in E. ulmoides or related species and exactly how much time could be saved using MAS over traditional breeding.
4. Could you further explain semi-full family? Are you referring to a half-sib family?
5. Correct full name of SRAP Sequence-related amplified polymorphism (SRAP) markers and inter simple sequence repeat markers (ISSR)
6. Be consistent when using either population, family, or group. These are used interchangeable throughout the text. Pick one and use it consistently.
7. It would make sense to move the Materials and Methods section 2.2 Growth traits and statistical analysis below section 2.4 SNP calling and Genotyping.
8. Fix font color in Growth traits and statistical analysis section
9. Please be more specific about phenotypic measurement of node spacing. Why was the range of nodes between 15-25 and where on the plant were these measured; from the first node above the ground to 10, 20, 30 cm high? Or was it the first bud from the top to 10, 20, 30 cm down the plant? As written it is confusing and unclear.
10. The in-house C scripts, are they publicly available in a repository?
11. Please provide the minor allele frequency cutoff (MAF) for SNP calls?
12. In section 3.3, you mention, The SNP marker detection…performed by GATK and other software. What other software and for what purpose?
13. You mention the sequence coverage was reliable, but it’s apparent from figures 4, S1 and S2 that the density of markers on LG3 is remarkably lower than the other LGs for both parents and progeny. Can you explain why this might be in the discussion.
14. You use and briefly talk about use of previous RNA-seq data to infer expression of genes based on traits you measured, but I’m not sure this information can be used in this way. Typically, this type of research would need to have occurred at the same time of your measurements to correlate and draw accurate conclusions about expression patterns from specific tissue types. Including this information is misleading and confusing.

Minor comments:

Please revise for correct grammar and spelling throughout the text. There were far too many instances to make a point by point list of what needs to be corrected.

Reviewer 2 Report

Dear Authors,

There you present the results of an interesting and relevant study in order to construct the first high-quality genetic map of E. ulmoides via Genotyping-by-Sequencing (GBS) with single nucleotide polymorphism (SNP) markers. In my opinion, you coped with the tasks and consistently described the results. However, some ambiguities and inaccuracies have been noted in the text:

Table 1 maximum instead maximum

Table 1 meaning of the last column?

Figure N4 it would be better to move to the supplements and increase resolution

Page 11 line 5: in what development stages? this is not described in the methods or elsewhere.

Page 11 line 11 Instead of „To verify whether these candidate genes were differently expressed different tissue in the development stages, the expressed patterns using previously reported RNA-seq data“

Better to write: „To verify whether these candidate genes were differently expressed in different tissue at different development stages, the expressed patterns using previously reported RNA-seq data.“?

Fig 6: how is the date expressed here? EuB520 its mean at May 20?

Page 13, paragraph 4.1.  line 4 from the bottom and in the last sentence instead of „Vivitis “ it need to write ”Vitis“

Page 13, paragraph 4.1. line 5 from the bottom instead „hawthorn (Crataeus spp )“ it is need to write „hawthorn (Crataegus spp )“

Page 13, paragraph 4.1. Last sentence :“Although our individual number is less than hawthorn and Vivitis, it is more than Ziziphus jujuba and Fraxinus pennsylvanica“ better to write: :“Although our individual number is less than Crataegus and Vitis, it is more than Ziziphus jujuba and Fraxinus pennsylvanica“

Page 14, paragraph 4.2. line 6-7 from the bottom instead of :“In this study, we obtained 456630 and 373429 SNPs d in male and female parent by GBS approach that were much higher than traditional markers number.” Could be:  “In this study, we obtained 456630 and 373429 SNPs  in male and female parent respectively by GBS approach that were much higher than traditional markers number”.

Page 14, paragraph 4.2. line 4 from the bottom: What does it mean: ” 35699,65800,68022,” ?

Page 14, paragraph 4.4 line 6-7 from top: “This method also used in QTL analyses for fiber quality, yield and morphological traits QTL analyses for fiber quality, yield and morphological traits in Gossypium hirsutum[49], Poncirus trifoliata[38] and Elymus sibiricus[50].” Sentence should be modified to eliminate recurrence

Page 14, paragraph 4.4. line 8 what is “more traits”

Page 14, paragraph 4.4. line 10 „previous“