Genetic Diversity and Population Structure of Prunus persica Cultivars Revealed by Genotyping-by-Sequencing (GBS)
, Artem Pronozin 2, Irina Rozanova 1, Valentina Tsiupka 1, Gennady Vasiliev 2, Yuri Plugatar 1, Sergey Dolgov 1,3 and Anatoly Smykov 1Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThis is the valuable study about genetic Diversity and Population Structure of Prunus persica Cultivars Revealed by Genotyping-by-Sequencing (GBS).
The study reveals the genetic diversity of P. persica specific collection and identified informative SNPs. The readability of the manuscript is fluent and understandable. There are some concerns which should be addressed before accepting for publication:
1. Additional English editing should be done; please check the use of prepositions (I am not a native English speaker but there might be some corrections needed for the final tuning of the manuscript).
2. Key words should not be repeated if already stated in the title. Please check and correct.
3. Since this is a nice and very well prepared population genetics study using a novel genotyping procedure (GBS) it would be prudent to somehow conclude the story with the applicative value of the results: e.g. to somehow prepare a core collection to present the max diversity of the whole collection and/or maybe associate genomic data -SNPs with some traits of interest to present the data for the breeding purposes if possible?
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThe authors conducted a study on Genetic Diversity and Population Structure of Prunus persica Cultivars Revealed by Genotyping-by-Sequencing. Overall, the research has significant value; however, the presentation, particularly the citation of ref, is poorly handled. Below are the concerns.
Line 24: “and identified differences. What kinds of differences? Readers cannot obtain effective information from this sentence.”
Line 43-44: “China [13-15], USA [16, 17], Spain [18, 19], Turkey [20], Brazil [21-23], Russia [24-26], India [27], Italy [28], France [29].” This way of citing references is inappropriate. Please clarify what kind of research was conducted.
Line 54: “‘have been used in most of the studies on peach population structure [13, 14, 17, 18, 27, 28, 35-39].’ This citation style is also inappropriate. Readers cannot obtain specific information, and there is a suspicion of excessive citation. Please clarify what kind of research was conducted.”
Line 52: “‘RFLP [33] and RAPD,’ the abbreviations should be spelled out in full when mentioned for the first time. This applies to other instances as well.”
Line 64-69: “287 accessions from two Spanish peach germplasm collections (CITA and CSIC) [19, 49, 50], 183 accessions from MAS.PES Italy collection [51], 161 accessions from the Hexi Corridor and the Tarim Basin, Northwest China [52], 195 accessions from China, the US, and Italy [53], 417 accessions from China [1, 15, 54], 220 peach genotypes from Brazilian peach breeding germplasm [55], 1,576 peach accessions from Spain, Italy, France, and China collections [46]. "Similarly, this is also an incomplete description. The authors should briefly summarize based on the objectives of their article.
In the background section, the concept of genotyping-by-sequencing (GBS) should be analyzed and explained further, as not all readers may be familiar with it.
Line 82: “‘Moreover, it is needed for the next GWAS.’ The authors should provide sufficient background on GBS and GWAS; otherwise, it will appear abrupt here.”
The introduction must be restructured. In such a short introduction, the authors have already cited 63 references, many of which I believe are unnecessary. The authors should focus on the core content of their research.
Line 108-109: “Data preprocessing included FastQC v0.12.1, FastP v0.23.4 [65], and MultiQC v1.17 [66] programs". This is unnecessary as their functions are similar.
Line 148-149: ‘high quality (Q20 ≥ 89%, Q30 ≥ 78%)’. Strictly speaking, this can no longer be considered high quality.
Line 152: ‘mapping rate of 75%’. Have the authors checked the reasons for this mapping rate? Is it due to sample differences or quality issues?
Line 152-153: ‘The average sequencing depth was 6-7.5×, and for over 25% of the samples, sequencing reads covered 5-8% of the peach reference genome.’ This might lead readers to think that the genome-wide sequencing depth is 6-7.5×. Please clarify.
The article mentions ‘SNPs were widely and equally distributed over eight chromosomes,’ but it then states that ‘the SNP density at the top of chromosome 2 is three times higher than on other chromosomes.’ These two statements are contradictory.
The number of SNPs on chromosome 1 is significantly higher than on chromosome 5. The authors should mention possible reasons for this.
Figure 3: Please revise the figure as there are large gaps between chr2-8.
Line 327-330: This is merely a possible hypothesis. The authors have not tested other restriction enzymes, so this can only be considered speculative.
Line 349-355: Please provide ref for these results. If they are unpublished experimental data, relevant data should be provided.
Line 356-357: The content transition from GBS to GWAS is missing.
Line 358-361:“‘Authors should discuss the results and how they can be interpreted from the perspective of previous studies and the working hypotheses. The findings and their implications should be discussed in the broadest context possible. Future research directions may also be highlighted.’ Please clarify what this is referring to.
The authors should conduct a comprehensive and careful revision of the entire text!
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for Authors1. Some more details are needed about the pipeline used for variant calling
2. Filtration criteria used for SNP should be elaborated more. As MAF .01 is not a high-quality criterion. Filtration criteria directly effects phylogenetic studies so different criteria will give different results (RICK ET AL. 2024‑ REFERENCE BIAS IN PHYLOGENOMICS)
3. For FST Analysis more details are required. Which 2 populations were used?
4. In Figure 3, values on the X-axis are not visible
5. In Figure 4, values on X and Y-axis are not visible
6. This statement needs more justification “No dependence was found between population grouping and the origin of the accessions”
7. In think the same names should be used for populations in admixture, phylogenetics, and PCA. If you sed pop1, pop2,….. Then same in all three or you want to name based on origins like Europe, USA….this is also fine but should be the same. Can you explain why populations having the same origins are divided into distant clusters and clades?
8. Line 358-361. Authors should discuss the results and how they can be interpreted from the perspective of previous studies and of the working hypotheses. The findings and their implications should be discussed in the broadest context possible. Future research directions may also be highlighted. Incorporate all these suggestions already written at end of your article.
9. Line 70 replace detected with detect L71 replace agricultural traits with agronomic traits
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
Comments and Suggestions for AuthorsThe author has answered my question, and I have no further comments.
Author Response
Comments 1: The author has answered my question, and I have no further comments
Response 1: We thank the Reviewer very much for the careful reading of our manuscript. This has helped to make this study better.
Reviewer 3 Report
Comments and Suggestions for AuthorsThe authors have substantially improved the article. However, this question has not been addressed. Line 358-361. The authors should discuss the results and how they can be interpreted from the perspective of previous studies and the working hypothesis. The findings and their implications should be discussed in the broadest context possible. Future research directions may also be highlighted. Incorporate all these suggestions already written at the end of your article.
Author Response
Comments 1: The authors have substantially improved the article. However, this question has not been addressed. Line 358-361. The authors should discuss the results and how they can be interpreted from the perspective of previous studies and the working hypothesis. The findings and their implications should be discussed in the broadest context possible. Future research directions may also be highlighted. Incorporate all these suggestions already written at the end of your article.
Response 1: We thank the Reviewer very much for the careful reading of our manuscript. We have rewrote the Discussion following the comment of the Reviewer. We compare our investigation with previous studies and highlighted future research directions based on our results.
