Genetic Diversity and Population Structure Analysis of Hollyhock (Alcea rosea Cavan) Using High-Throughput Sequencing

Round 1

Reviewer 1 Report

The study is aimed at studying both the phenotypic and genetic diversity of mallow and carries valuable information for the selection of this crop.
Early studies were devoted to the study of the medicinal properties of mallow and its resistance to abiotic factors.
These studies are undoubtedly relevant, since mallow occupies an important place in human life. It is widely used in the landscaping of settlements, in medicine, in the food industry and in agriculture. The authors observed a wide range of phenotypic diversity in 11 morphological traits of the mallow population, including 162 samples, and found a significant positive correlation between some quantitative traits. They randomly selected a subset of 32 samples for genetic diversity analysis using high-coverage re-sequencing data and obtained more than 10 million core SNPs distributed throughout the mallow genome.
The conclusions are adequate and consistent with the research results.
The references used in the text of the article correspond to the research topic and reveal the importance of this research.
Tables and figures complement the research results well.
Overall, study provided the first estimation of genetic diversity of hollyhock
germplasm resources at the molecular and population levels.
Reviewer's recommendations:
It is necessary to continue research on the genetic diversity of mallow using molecular markers for further breeding. 

Author Response

Response: Thank you for positive comments on this work. We will continue to work on hollyhock breeding using molecular markers developed by high-throughput sequencing data. Assisted by these genome-wide markers, we hope that the level of hollyhock breeding could be improved to a large extent in near future. 

Reviewer 2 Report

The manuscript entitled “Phenotypic variability, genetic diversity and population structure analysis of hollyhock (Alcea rosea Cavan)” studies phenotypic variation for 11 traits in a hollyhock population and analyzed the genetic structure of this population, using high-coverage whole-genome re-sequencing data. However, a low number of phenotypic traits has been evaluated but great analysis and results have been represented. Manuscript needs minor revision providing addressing the following questions:

1- The title can be revised as both variability and diversity have same meaning.

2- However the manuscript is well-written, a moderate English structural and grammatical polishing is required.

3- Please add a map showing distribution of collected accessions or populations. It would to help understanding the range of regions covering the study.  

4- If possible, please do an association analysis to find the SNP candidates responsible for studied quantitative and especially qualitative traits.

5. Why accessions were selected randomly not based on the highest phenotypic represented diversities? Moreover, a clustering dendrogram of 162 accessions can be drawn and show as supplementary material.

6- Please also bring a comparative figure of some studied accessions with distinct flower morphology showing close view of flower and on whole plant scale.

7- It has been stated that population structure analysis has been done. You can bring a table showing the information of all studied accessions (origin, collection site coordination, belonging populations, code, …..)

8- Discussion section could be improved by

10- Please calculate and statistics of genetic variation like A, number of different alleles; a, mean number of alleles per locus; AE, effective number of alleles; HE, unbiased expected heterozygosity; HO, observed heterozygosity; F, fixation index (inbreeding coefficient); MAF, minor allele frequency.

 

The English language is fine however moderate polishing is required

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 3 Report

Title - Phenotypic variability, genetic diversity and population structure analysis of hollyhock (Alcea rosea Cavan)

                                      COMMENTS ON PAPER

Yue Wang et al. provided a Research article on “Phenotypic variability, genetic diversity and population structure analysis of hollyhock (Alcea rosea Cavan)” Though the topic is of current interest, the manuscript needs a substantial revision to be published. I have mentioned a few comments on the manuscript that can be considered by the authors.

 

·      There is no image regarding phenotypic variations has been given in this paper.

·      Wet lab experiments could also be performed to explain genetic diversity via molecular markers.

·      Percentages of similarity index have not been provided for 32 hollyhock accessions.

·      Recheck all the references.

Ø  Elaborate the captions of Fig. 2 (line no.182,183,184) and Fig. 3 (line no. 204,205,206) and provide a high-resolution image of Figure 2.

Ø  The sample size is very small, to improve your data accuracy you should have taken almost 25 to 30% sample size and an equal number of species from a particular place (as you mention in Table S1).

Ø  During the analysis of phenotypic variation of traits (result in 3.1 and 3.2) you should take more qualitative traits because in table number 3.1 maximum number of traits that you have taken shows the least variation.

Ø  Recheck and rearrange all the references in uniform (lines no.319 to 326 and 330) according to the journal’s format.

Ø  It is suggested to use molecular markers, such as random amplified polymorphic DNA (RFLP), amplified fragment length polymorphisms (AFLP), and even insertions/deletions also determine to reveal the genetic diversity among a population of individuals that will improve the quality of research.

Ø  It would be better if the geographical distribution of the seven provinces of China would have been presented by map.

Ø  In the method, line 114, there is a mention of an unrooted neighbour joining the phylogenetic tree, but the authors have not mentioned what bootstrap was taken to make the phylogenetic tree.

English Usage must be improved.

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Round 2

Reviewer 3 Report

Can be accepted in the Present Form