Genetic Purity of Cacao Criollo from Honduras Is Revealed by SSR Molecular Markers

Round 1

Reviewer 1 Report

line 159: how did you correlate the accuracy of reference samples dataset with you dataset? Did you run some reference data with you samples or did you repeat the run of reference data? 

 

Figure 3 - 4: it's a little bit confusing to use green color for criollo cluster in figure 3 and then blue in figure 4. I suggest to use the same ore otherwise two other colors for figure 4.

 

 

Author Response

Dear reviewer, as some comments request a cumulative reply we enclose the letter we have prepared to answer to all the three reviewers in charge for the revision of the paper.

Hoping this is not a trouble, we send our thankings for your helpful comments.

Please see the attachment

Best regards 

Author Response File: Author Response.docx

Reviewer 2 Report

The manuscript article by López et al. entitled "Genetic purity of cacao Criollo from Honduras is revealed by SSR molecular markers" is a very nice attempt to screen 89 samples collected from 4 regions of Honduras using 16 SSR markers for their genetic purity and phylogenetic analysis. Their report confirms the genetic purity of Criollo cacao in Honduras, reaffirming the theory that Mesoamerica is a cacao domestication center.

The manuscript is written very well and easy to understand language. The author pointed out the genetic diversity based on SSR genotyping. But only 16 SSRs are not enough to study the crop germplasm for their genetic diversity, genetic purity and phylogenetic analysis. It is advisable to use more SSR markers and also use the advances genotyping tools like SNPs and genome sequence based tools.

I have some specific points/questions to the authors:

Q1. Is there any geographical isolation barrier present between Olancho and other 3 places (Copán, Santa Bárbara and Intibucá)?

Figure 2: The figure numbering with A, B, C, D are not clearly visible. So change the colour anyway. Also put the scale bar.

Table 1: It can be placed in supplementary file.

Table 2: Please write the chromosomal locations of each SSRs and their expected product size. Moreover, '5’ Forward Primer' and '3’ Reverse Primer' are not the right way to write the primers. For each forward and reverse, you need to mention 5'-3' position in left and right side of the sequence.

Based on these points, I would like to suggest authors major corrections to perform more experiments for the robust experimental conclusion.

Author Response

Dear reviewer, as some comments request a cumulative reply we enclose the letter we have prepared to answer to all the three reviewers in charge for the revision of the paper.

Hoping this is not a trouble, we send our thankings for your helpful comments.

Please see the attachment

Best regards

Author Response File: Author Response.docx

Reviewer 3 Report

The paper presents a specific topic of interest only to a small group of readers who deal with characterization studies of cacao germplasm. It is a simple and descriptive work; however, it could have interesting implications in order to avoid fraud in the production of fine chocolate.

The Authors claim the genetic purity of some samples of cacao Criollo from Honduras on the basis of the results obtained from a STRUCTURE analysis. I am not sure that is adequate using only 16 SSR markers for a correct population structure analysis, in other species it is necessary to use a higher number of markers. Moreover, I would recommend adding in the supplementary materials a table showing the allelic profiles of the samples.

 

Lines 47 to 49 Please, clarify the correlation between the selection for specific genes and the maintenance of a high frequency of deleterious genes. What are the consequences of this selection process?

Line 49 “deleterious genes” or “deleterious mutations”?

Line 216 Table 3 I recommend inserting in the table the polymorphism information content (PIC) for each SSR marker.

Lines 268 to 270 I do not completely agree with what has been stated, because from the analysis of the principal coordinates (Fig 5) it is evident that numerous Honduran samples were clustered on the right side of the plot, too. Please, provide more explanations.

Lines 280 to 282 Please, provide more explanation regarding the choice of these specific eight Honduran pure Criollo cacaos samples.

Line 318 Please, change “criollo” to “Criollo”.

Lines 337 to 339 This statement is not in agreement with what is reported in "Cluster analysis" regarding the description of Fig. 3, in fact the results show that thirty samples, belonging to all four departments, can be considered "pure Criollo". Please, clarify the results.

Lines 352 to 357 and 362 to 367 I notice some repetitions and lack of clarity. Please, integrate the two small paragraphs appropriately.

Author Response

Dear reviewer, as some comments request a cumulative reply we enclose the letter we have prepared to answer to all the three reviewers in charge for the revision of the paper.

Hoping this is not a trouble, we send our thankings for your helpful comments.

Please see the attachment

Best regards

Author Response File: Author Response.docx

Round 2

Reviewer 2 Report

The authors performed a great job of corrections to improve their paper. Now it is in publishable form.

Reviewer 3 Report

In my opinion the manuscript has been significantly improved and can be accepted for the publication.