The SSR Null Allele Problem, and Its Consequences in Pedigree Reconstruction and Population Genetic Studies in Viticulture

Round 1

Reviewer 1 Report

I think this review manuscript is well written and clearly drafted. I have only two minor concerns.

1. It will be nice to have figures or tables to summerize the major ideas of the first 3 sections instead of lengthy and wordy descriptions for readers' convenience. However, I respect the authors' choice. 

2. The pixel quality of figure 1 can be improved. Also, it can be better illustrated. 

Author Response

Responses to Reviewer 1

Thank you very much for your time and effort in reviewing our study.

I think this review manuscript is well written and clearly drafted. I have only two minor concerns.

1. It will be nice to have figures or tables to summerize the major ideas of the first 3 sections instead of lengthy and wordy descriptions for readers' convenience. However, I respect the authors' choice. 

Thank you for your suggestion. In our opinion, the insertion of figures or tables in the paragraphs indicated would create redundancy and would not significantly improve the understanding of the article, so we have decided to keep the current structure.

2. The pixel quality of figure 1 can be improved. Also, it can be better illustrated. 

Thank you for your suggestion. The quality of figures is improved, and will also be inserted to our submission as separate images.

Reviewer 2 Report

Review of horticulturae-1818403

The manuscript reviews approaches to correct SSR data for null alleles with an emphasis on studies in grape.  It should be useful to readers of an organism in which SSR data is widely used as a measure of genetic diversity. 

Now many programs use either array-based SNP analysis of DNA sequence for these issues.  It is worth noting that array-based SNPs also have null alleles and many of the same considerations apply.  WGS, on the other hand, does not have this problem unless done at low depth and then the missing data estimated through imputation. I do not suggest expanding the review to these marker types, but a comment on the similarity and differences seems appropriate to me.

Many minor corrections and suggestions are made on the manuscript using notes.

Comments for author File: Comments.pdf

Author Response

Responses to Reviewer 2

Thank you very much for your time and effort in reviewing our study.

The manuscript reviews approaches to correct SSR data for null alleles with an emphasis on studies in grape.  It should be useful to readers of an organism in which SSR data is widely used as a measure of genetic diversity.

Now many programs use either array-based SNP analysis of DNA sequence for these issues.

It is worth noting that array-based SNPs also have null alleles and many of the same considerations apply. WGS, on the other hand, does not have this problem unless done at low depth and then the missing data estimated through imputation. I do not suggest expanding the review to these marker types, but a comment on the similarity and differences seems appropriate to me.

Thank you for your suggestion. A note to this regard has been inserted in the manuscript.

Many minor corrections and suggestions are made on the manuscript using notes.

Thank you for your detailed suggestions. Based on the comments, corrections have been made to the manuscript. Changes have been marked with the editing tool of MS Word and, where necessary, comments have been added to address the issues raised.