Development of SNP Markers and Core Collection Construction of Berberis L. Based on SLAF-Seq in Xinjiang, China

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The work is well written and relevant to the field of study. In this study, SLAF-seq was used to analyze the genetic diversity and population genetic structure of 150 Berberis germplasm from Xinjiang, and to construct the core germplasm resources, to provide a solid theoretical foundation and scientific basis for the effective conservation of the genetic diversity of the Berberis germplasm and the rational exploitation of the wild resources as well as for the introgression and domestication of the Berberis. Below are some observations to improve the work:

- avoid keywords in the title

- line 29: Xinjiang, which is located in the center of the European continente. Is this statement correct?

-line 41: detail other factors

-line 75: Would you have the source of these previous studies?

-line 77: Where was this material deposited (herbarium)? Who was the collector or collectors?

- figure 1b: Shouldn't the caption be in English?

- figure 2: I found the identification of the groups and the colors confusing

Discussion:

- The text mentions that other researchers obtained different numbers of SNPs, but does not discuss whether this difference is due to sample size, method used...

- values ​​of He (expected heterozygosity) and PIC (Polymorphism Information Content): explain the importance of these indices in practice.

- The phrase the impact of environmental changes and human interference as external driving forces is particularly complex and profound is vague. The text does not provide concrete examples of how these factors are affecting Berberis in Xinjiang.

-The text states that the phylogram revealed that Berberis species did not group strictly by geographic distribution, but does not discuss what this means biologically.

- that species expansion generally follows a path of least cost, such as rivers and valleys, but then points out that Xinjiang topography is complex and that natural migration of Berberis is limited. If natural dispersal is limited, how did it occur along these routes?

Author Response

Point-by-point response to Comments and Suggestions for Authors

Comments 1: line 29: Xinjiang, which is located in the center of the European continente. Is this statement correct?

Response 1: We apologise for our incorrect spelling. It is correct that Xinjiang is in the centre of Eurasia.

 

Comments 2: line 41: detail other factors

Response 2: We have rewritten this section as suggested by the reviewers. The factors causing the degradation of wild berberis in Xinjiang have been described in detail in the paper as suggested by the reviewers. In recent years, the destruction of the habitat of wild berberis germplasm due to natural factors such as climate change, species invasion and changes in soil properties, as well as anthropogenic factors such as land reclamation, over-excavation, pests and diseases and habitat destruction, has resulted in the obvious phenomenon of patchiness, a decline in the diversity of germplasm resources and restrictions on population renewal.

 

Comments 3: line 75: Would you have the source of these previous studies?

Response 3: We are very sorry, but the previous study was taken from the Xinjiang Forest Tree Germplasm Resources Survey, which is internal government information and not readily available to the public.

 

Comments 4: line 77: Where was this material deposited (herbarium)? Who was the collector or collectors?

Response 4: These materials are stored at the Xinjiang Branch of the National Forest and Grass Germplasm Resources Facility Conservation Repository.

 

Comments 5: figure 1b: Shouldn't the caption be in English?

Response 5: We are sorry for our careless behaviour. We have made changes to the paper.

 

Comments 6: figure 2: I found the identification of the groups and the colors confusing

Response 6: Thank you for your comments, Figure 2 has been revised.

 

Comments 7: values of He (expected heterozygosity) and PIC (Polymorphism Information Content): explain the importance of these indices in practice.

Response 7: We have rewritten this section in line with the reviewers' suggestions. The genetic diversity index (GDI) is an important indicator to quantify the amount of genetic variation within a population or species, and a high value of the GDI implies that there is a large amount of genetic variation within the population. This is explained at the appropriate place in the article.

 

Comments 8: The phrase the impact of environmental changes and human interference as external driving forces is particularly complex and profound is vague. The text does not provide concrete examples of how these factors are affecting Berberis in Xinjiang.

Response 8: We are deeply sorry for our negligent behaviour. The study on the migration of Berberis xinjiangensis due to external factors such as environmental changes and anthropogenic disturbances has not been reported.

 

Comments 9: The text states that the phylogram revealed that Berberis species did not group strictly by geographic distribution, but does not discuss what this means biologically.

Response 9: Berberis spp. in Xinjiang, China, are not strictly grouped according to geographical distribution, suggesting that there may be an exchange of Berberis germplasm resources between northern and southern Xinjiang. Changes have been made to the article.

 

Comments 10: that species expansion generally follows a path of least cost, such as rivers and valleys, but then points out that Xinjiang topography is complex and that natural migration of Berberis is limited. If natural dispersal is limited, how did it occur along these routes?

Response 10: Thanks to the reviewers' questions, we suggested in our paper that trade and history were the main reasons for the exchange of wild berberis genes between the northern and southern borders.

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript is interesting and in general well writen. However, several aspects should be improved. In the introduction section, the state of the art for berberis should be inlcuded in a detailed way.

MandM must mentioned more specific information, i.e a table of the samples taken should be included, showing the collection data, the code, the species, etc.

Regarding result section, there are several analysis that seems to be unrelated, maybe a deeply evaluation should be performed, considering results of tree, structure and PCoA. Besides, it is not clear enough why authors selected the core collection of 45 genotypes. Data aabout those individuals must be presented.

Discussion should be improved to better compared results with those of previous articles in related species or in the same one.

Several aditional comments were included in the main file.

Comments for author File: Comments.pdf

Author Response

Point-by-point response to Comments and Suggestions for Authors

Comments 1: The manuscript is interesting and in general well writen. However, several aspects should be improved. In the introduction section, the state of the art for berberis should be inlcuded in a detailed way.

Response 1: As suggested by the reviewers, we have included the latest research on berberis molecular techniques in the Introduction.

 

Comments 2: MandM must mentioned more specific information, i.e a table of the samples taken should be included, showing the collection data, the code, the species, etc.

Response 2: Following the reviewers' suggestions, we have added the information sheet on the Xinjiang Berberis collection to the appendix.

 

Comments 3: Regarding result section, there are several analysis that seems to be unrelated, maybe a deeply evaluation should be performed, considering results of tree, structure and PCoA. Besides, it is not clear enough why authors selected the core collection of 45 genotypes. Data aabout those individuals must be presented.

Response 3: We thank the reviewers for their comments, and a table for assessing the gene coverage of berberis in Xinjiang is provided in the Appendix.

 

Comments 4: Discussion should be improved to better compared results with those of previous articles in related species or in the same one.

Response 4: In view of the reviewer's suggestion, we have searched the major databases, and there are fewer relevant studies on berberis plants, and we have cited the ones that do exist.

 

Comments 5: Several aditional comments were included in the main file.

Response 5: We have made changes in response to the reviewers' comments and revised the full text as requested in the document.

Reviewer 3 Report

Comments and Suggestions for Authors

Dear authors, thank you for the opportunity to read your study. Here, the authors presented a study that identify SNPs and constructed a core germplasm in Berberis sp.; in general, this manuscript is well-elaborated and I have only some considerations.

 

Recommendation: major corrections are recommended.

 

Some other comments:

1. Title: provide the scientific name of berberis; provide a complement to Xinjiang, can be (China);
2. Abstract: provide and adopt the scientific name of berberis and include its genus and family; provide a complement to Xinjiang, can be (China); consider to use of short phrases; excessive use of indication “Xinjiang,”; English idiom should be improved;
3. Introduction: several scientific names should be in italics; several typing errors with text edition to be corrected; provide a complement to Xinjiang, can be (China); again consider to use of short phrases; several citations or citation format, such as “Z. D. Akishev et al[18]”, should be corrected; in addition to city/state, also provide between parentheses the country name; adopt the use of the scientific name of berberis;
4. Materials and methods: provide the geographic coordinates from Berberis germplasm in Xinjiang; several scientific names should be in italics; figure 1, legend, is very confusing the description of letters A to F. Please, provide a more detailed legend for this figure 1 and Fig. 1a should be more clear; In addition, the Figure 1 should be in English; write correctly the name of these “RsaI+HinCII” enzymes; subsection 2.3 also provide the softwares used and appropriate references. In addition, provide also the number of replicates and libraries per treatment; what is “bwa (0.7.10-r789)”? Here, “Reads to the reference sequence”, what reference sequence and provide a citation for this; in addition to software names, provide also the major parameters used in each one; provide appropriate reference to MEGAX, Kimura 2, Pophelper (and delete the link), smart PCA, EIGENSOFT, and Core Hunter II software, and others (such as qrencode software and 2D codes); question: how was validated the DNA sequencing data and SNPs?
5. Results: adopt the scientific name of berberis; table S1 to S3, provide a legend with detailed information about the abbreviations used within the table; several typing errors with text edition to be corrected; several scientific names should be in italics; Figure 2, 3A to 3C and 4, improve the resolution and consider to use for example, arial 12, black, non-bold letters; please, again, consider to use short phrases; such as here, what is these codes: “WSX6 and WSX8”?; Figure 5 should more detailed (can it be supported by any statistical?);
6. Discussion: several typing errors with text edition to be corrected; several scientific names should be in italics; citations to be corrected; again, very repetitive the use of “Xinjiang”; adopt the use of the scientific name for plant species;
7. Conclusion: some of these identified SNPs are linked, associated, or clustered to some agronomic traits? Can these SNPs be made available on some SNP database, such as VegSNPDB, dbSNP, and PlantGDB?

Comments on the Quality of English Language

No comments.

Author Response

Point-by-point response to Comments and Suggestions for Authors

Comments 1: Title: provide the scientific name of berberis; provide a complement to Xinjiang, can be (China);

Response 1: Taking the reviewers' suggestions into account, we have revised the title.

 

Comments 2: Abstract: provide and adopt the scientific name of berberis and include its genus and family; provide a complement to Xinjiang, can be (China); consider to use of short phrases; excessive use of indication “Xinjiang,”; English idiom should be improved;

Response 2: We have rewritten this section as suggested by the reviewers.

 

Comments 3: Introduction: several scientific names should be in italics; several typing errors with text edition to be corrected; provide a complement to Xinjiang, can be (China); again consider to use of short phrases; several citations or citation format, such as “Z. D. Akishev et al[18]”, should be corrected; in addition to city/state, also provide between parentheses the country name; adopt the use of the scientific name of berberis;

Response 3: We have rewritten this section as suggested by the reviewers.

 

Comments 4: Materials and methods: provide the geographic coordinates from Berberis germplasm in Xinjiang; several scientific names should be in italics; figure 1, legend, is very confusing the description of letters A to F. Please, provide a more detailed legend for this figure 1 and Fig. 1a should be more clear; In addition, the Figure 1 should be in English; write correctly the name of these “RsaI+HinCII” enzymes; subsection 2.3 also provide the softwares used and appropriate references. In addition, provide also the number of replicates and libraries per treatment; what is “bwa (0.7.10-r789)”? Here, “Reads to the reference sequence”, what reference sequence and provide a citation for this; in addition to software names, provide also the major parameters used in each one; provide appropriate reference to MEGAX, Kimura 2, Pophelper (and delete the link), smart PCA, EIGENSOFT, and Core Hunter II software, and others (such as qrencode software and 2D codes); question: how was validated the DNA sequencing data and SNPs?

Response 4: We have rewritten this section as suggested by the reviewers.

 

Comments 5: Results: adopt the scientific name of berberis; table S1 to S3, provide a legend with detailed information about the abbreviations used within the table; several typing errors with text edition to be corrected; several scientific names should be in italics; Figure 2, 3A to 3C and 4, improve the resolution and consider to use for example, arial 12, black, non-bold letters; please, again, consider to use short phrases; such as here, what is these codes: “WSX6 and WSX8”?; Figure 5 should more detailed (can it be supported by any statistical?);

Response 5: We have rewritten this section as suggested by the reviewers. We have also added a table of collection information (see Table S1).

 

Comments 6: Discussion: several typing errors with text edition to be corrected; several scientific names should be in italics; citations to be corrected; again, very repetitive the use of “Xinjiang”; adopt the use of the scientific name for plant species;

Response 6: As the reviewer suggests, this is indeed true. We have made changes in the paper.

 

Comments 7: Conclusion: some of these identified SNPs are linked, associated, or clustered to some agronomic traits? Can these SNPs be made available on some SNP database, such as VegSNPDB, dbSNP, and PlantGDB?

Response 7: The data have been submitted to the China National Center for Bioinformation and further studies are needed on the identified SNPs that are related, associated or clustered with specific agronomic traits.

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

Please be sure that all comments were addressed before submitting it again. For example: -
-references, a space before the number in [] should be added, in all the opportunities.
-Table S1 did not explain the origin of the samples, please prepare it again.
-Figure 1, please it should be rewrite. Besides, Fig. 1 B is not explained in the caption.
-Figure 2, colors should be mentioned in the caption.
-The correlation among results of tree, structure, PCoA must be commented.
-Fig 4: Where are the five subpopulations?
And so on, most of the suggestions were not solved in the present version of the manuscript. 

Author Response

Comments 1: references, a space before the number in [] should be added, in all the opportunities.
Response 1: I'm sorry, this was an oversight on our part and we've made changes in the paper.

Comments 2: Table S1 did not explain the origin of the samples, please prepare it again.
Response 2: We are sorry that we did not understand what you meant. Table S1 shows the collection coordinates of the samples.

Comments 3: Figure 1, please it should be rewrite. Besides, Fig. 1 B is not explained in the caption.
Response 3: We apologise for our oversight and have made changes to the paper.

Comments 4: Figure 2, colors should be mentioned in the caption.
Response 4: We apologise for our oversight and have amended the paper.

Comments 5: The correlation among results of tree, structure, PCoA must be commented.
Response 5: Thank you for your suggestions, which we have incorporated into the paper.

Comments 6: The correlation among results of tree, structure, PCoA must be commented.
Response 6: Thanks for the warning. The five subpopulations mentioned in this paper come from genetic structure analyses and have been added to the paper.

Reviewer 3 Report

Comments and Suggestions for Authors

Dear authors, thank you so much for the improvements performed in the actual version of this manuscript. Therefore, in my opinion, this improved version of the manuscript can be appropriated for publication at Horticulture. However, considerations of the other reviewers should also be considered for careful analysis and for the security of a well-presented document. Thanks, best regards.

Author Response

Comments 1: Dear authors, thank you so much for the improvements performed in the actual version of this manuscript. Therefore, in my opinion, this improved version of the manuscript can be appropriated for publication at Horticulture. However, considerations of the other reviewers should also be considered for careful analysis and for the security of a well-presented document. Thanks, best regards.

Response 1: We thank the reviewers for their review and recognition. We will continue to improve the paper.