Analysis of Genetic Diversity and Development of A Core Collection in Walnut (Juglans regia L.) Germplasm Native to China via Genotyping-by-Sequencing
Round 1
Reviewer 1 Report
This work is important in walnut breeding. The authors used sequence-based genotyping to simplify complex genomes. Nine walnut genotypes were generated. A genetic structure analysis was carried out.
The methodology and results are well described. I would just like to see the introduction and discussion supplemented with the most recent literature (studies conducted between 2019 and 2022). It would be useful to include in the methodology a map of where the material for the studies was collected. Also, in the results, figures and tables should be uploaded immediately after their first mention to make it easier for the reader to analyze the material.
Author Response
We are highly appreciative of the constructive criticisms and comments made by the #reviewer 1 on our manuscript entitled “Analysis of genetic diversity and development of a core collection in walnut (Juglans regia L.) germplasm native to China via genotyping-by-sequencing” (agronomy-2428069). We have done an extensive revision by addressing the comments suggested by #reviewer 1. The major changes are highlighted in color in the manuscript. The detailed point-by-point responses to the comments are given in the following.
Firstly, we have totally accepted your comments and have added six recent literatures conducted between 2019 and 2022, and replaced an ancient piece of literature (seen at part of References in the revised manuscript). The citation numbers were also changed according to the revision of the references. Secondly, we have added a sampling site plot to show sampling site information (Figure 1 in the revised manuscript). Finally, we have re-uploaded the figures and tables immediately after them be first mentioned in the results.
Thank you sincerely for positive comments again. We hope that the revised manuscript is satisfactory and has now become acceptable for publication.
Look forward to receiving your decision on our manuscript.
Reviewer 2 Report
The use of italic font is not correct: scientific name should be in italics (lines 3, 13, 32, 33, 37, 39 and so on, even in 277, 279, 323...) and the family name, should not (line 31)
Line 287: Wheat (42) is an annual species. I suggest, If convenient, to add (as an example) this reference about a fruit tree.
Here it was discussed that some supposed traditional Reinetas were in fact commercial ones; and that the commercial cultivar 'Verde doncella' was the same as the spanish landrace 'Verde doncella'.
Author Response
We are highly appreciative of the constructive criticisms and comments made by the #reviewer 2 on our manuscript entitled “Analysis of genetic diversity and development of a core collection in walnut (Juglans regia L.) germplasm native to China via genotyping-by-sequencing” (agronomy-2428069). We have done an extensive revision by addressing the comments suggested by #reviewer 2. The major changes are highlighted in color in the manuscript. The detailed point-by-point responses to the comments are given in the following.
We have totally accepted your comments and have re-wrote the scientific name and family name in entire manuscript. Also, we have added one literature about Chinese Chestnut to replace the literature about Wheat in the revised manuscript.
Thank you sincerely for positive comments again. We hope that the revised manuscript is satisfactory, and has now become acceptable for publication.
Look forward to receiving your decision on our manuscript.
Reviewer 3 Report
In this study, a core collection of walnut (Juglans regia) germplasm using the genotyping-by-sequencing (GBS) approach. A diversity panel of 87 walnut initial genotypes including 25 landraces, 12 cultivars, and 50 seedling-populations, mostly native to the Gansu Province of China, 110,497 quality SNPs were identified, and a core collection was designed using a set of 6,540 SNPs. Did You used 50 entire seedling populations (with many seedling lines) for this experiment? If yes, please indicate the real number of used lines. The SNPs in 5'-3'UTRs and in splice site regions are considered in the phylogenetic tree? How do You explain that large part of the chromosome 9. which is not covered by SNPs? Can the core collection date be valid for other Juglans species?
The graphs are sufficiently detailed and easy to expound. The text contains occasional typos, but it is nevertheless easy to read. Please use proper scientific expressions. The English of the manuscript needs to be excessively improved. The literature used is fairly extensive. Latin names should be in Italics. The producer of the materials is enough to be mentioned at first appearance. Minimalize the use of “>” in running text, and be consequent with the spacing before and after. Https links should be in the “Literature cited”, and referred like that. An original citation is left in line 206. Figure 3. is not informative enough, consider to remove it. Figure 2 and 6 contains redundant data. Please keep only one of them. The marking letters of Table 1. are in deceptive places (and should be in Italics).
The English of the manuscript needs to be excessively improved.
Author Response
We are highly appreciative of the constructive criticisms and comments made by the #reviewer 3 on our manuscript entitled “Analysis of genetic diversity and development of a core collection in walnut (Juglans regia L.) germplasm native to China via genotyping-by-sequencing” (agronomy-2428069). We have done an extensive revision by addressing the comments suggested by #reviewer 3. The major changes are highlighted in color in the manuscript. The detailed point-by-point responses to the comments are given in the following.
Firstly, we have totally accepted your comments. Yes, Phylogenetic trees were constructed at the DNA-level using all observed DNA-level loci including 5'-3'UTRs and splice-site regions, and the chromosome 9 showed an interesting phenomenon but we could not explain it for the time being. Of course, we will try our best to explore it in the next study in the future. Secondly, we have checked the manuscript thoroughly including the Latin names of species and others. Thirdly, https links were also added in the end of literatures. Finally, we have abandoned the Figure 6 which contains similar data with the Figure 2 in the manuscript (original version) and re-wrote the marking letters of Table 1 in Italics.
We will use a language service for the manuscript before publication.
Thank you sincerely for positive comments again. We hope that the revised manuscript is satisfactory and has now become acceptable for publication.
Look forward to receiving your decision on our manuscript.
Round 2
Reviewer 3 Report
The manuscript improved a lot, therefore I support to accept it for publication.
Its language is acceptable.
