Effects of Traditional Ethnic Minority Food Culture on Genetic Diversity in Rice Landraces in Guizhou Province, China

Round 1

Reviewer 1 Report

The manuscript entitled "Effects of traditional ethnic minority food culture on genetic diversity in rice landraces in Guizhou Province, China" authored by Liu et al. is highly informative and interesting to see the genetic diversity existing in rice landraces in Guizhou province, China. Even though domestication events occurred, they still preserved the ethnic minorities' dietary cultures in these regions which are very interesting to see throughout the analysis. A few things need to be attended to before considering the manuscript further.

Minor comments

Follow a common pattern of writing. For example, indica and japonica were italicized throughout the manuscript except in a few places. Also, in situ and ex situ - Check lines 351 and 363. 

Major comments

Line 100-101 and Table 1: Six ecologically distinct rice farming zones in Guizhou Province (P1 through P6). It is not clear to me why the authors made P4-1 (Southern Guizhou) and P4-2 (Southeastern Guizhou) instead of P5, even though these are 2 distinct geographic areas. It is clear from the phylogenetic tree the landraces are clearly different. Explain.

Line 117: It is mentioned as a modified CTAB procedure. Provide a reference for the original CTAB procedure.

Line 120: How are the 36 SSRs markers used in this are selected? Is there SSRs are already published? Mention details. Why only selected 36 SSR markers for the study? It is well-known fact that as the number of markers increases, the study will be more robust. Explain.

It is better to provide the used SSR markers are generic SSR or Genomic SSR. Out of the 36 SSRs, 22 SSRs are di-nucleotides. Why selected more than 60% di-di-nucleotides? Any reasons?

Line 132: Why used Mega6.0 for NJ? The latest version of Mega is 11. Any specific reasons to use v.6? Explain

Line 133-134: What were the criteria for selecting these six nuclear genes (SKC1, SAP8, Pid3, Xa23, GS5, and Ehd1)? Explain

Line 150: He is genetic diversity index. Table 2 footnote He, genetic diversity. Table 3: He, gene diversity. ´Make it uniform.

Line 167: *N, sample size. What is * denotes? * is not mentioned anywhere in Table 3.

Line 237-238: The sequence length of each locus was 4268 bp, with a range of 482-670 bp. The same set of nuclear genes was used in another manuscript published by the same authors in Front. Plant Sci. 13:830556 in 2022. In that manuscript, the aligned sequence length for each locus ranged from 482 to 670 bp, with a total length of 3,700 bp. Can you explain why a difference in the total length of the sequence if the same set of primers were used in both cases? 

Also, can you please explain what are the major differences between the current manuscript and the published one Front. Plant Sci. 13:830556 in 2022?

Author Response

Dear reviewer, 

Thank you for your  careful and rigorous review. 

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

The authors put a lot of effort into this study by collecting a large number of rice accessions and exploring their genetic diversity, population structure, and haplotype. The manuscript is well structured, well presented, and provides a fairly robust dataset accordingly, it deserves to be published after minor revision.  

 

Specific comments

The manuscript needs major English editing.

Abstract

The summary of obtained results needs to be improved in the abstract

Introduction

 The importance of exploring genetic diversity in rice should be improved. Besides, the significance of molecular markers in exploring genetic diversity needs to be highlighted. The value of the conservation of genetic resources should be emphasized. Impact of the ethnic minority on genetic diversity should be summarized and delete repeated information.

 Materials and Methods

In table 1 please replace “Quantity” with “Number of accessions”.

A summary of the second set of accession can be added to Table 1 with the first accession.

The basis of selecting the 36 polymorphic SSRs for this study should be clarified.

The scientific name of the used crop (Oryza sativa) should be mentioned.

 Results

More explanation on the detected mono and polymorphic markers are needed.

Titles of the tables and figures need to be improved and extended.

Statistical analysis of total genetic diversity and population genetic analysis were presented for just the first set but not for the second set of accessions.

Lines 204 – 212 belong to the discussion section.

 Discussion

The detected genetic diversity among the tested a large number of accession need to be better discussed. Also, the influence of ethnic minorities on genetic diversity needs to be improved.

References

 

The journal name should be abbreviated in all references and the journal style should be revised.

Author Response

Dear reviewer, 

Thank you for your  careful and rigorous review. 

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 3 Report

 

The authors have done an interesting work that should be published in the journal Agronomy

Authors should more clearly state the purpose of their study. In the presented version of the article, the prospects for the use of the performed research are formulated.

It is advisable to indicate at least once (for example, after "42 wild rice" (line 101)) the botanical name of the crop - Oryza sativa L.

Since the authors write that "The DNA sequences of parts of six genes were obtained from the NCBI database." (line 135-136), another table with sample numbers taken from the NCBI should be provided in the Supplementary Materials. It is also necessary to upload the samples studied by the authors to the NCBI database and give a table with the numbers of the samples uploaded from NCBI in Supplementary Materials. This will allow other researchers to use the authors' materials in further work.

Author Response

Dear reviewer, 

Thank you for your  careful and rigorous review. 

Please see the attachment.

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

The manuscript entitled "Effects of traditional ethnic minority food culture on genetic diversity in rice landraces in Guizhou Province, China" authored by Liu et al. improved significantly after modification. Still, I could see a few things missing in the manuscript.  

Minor comments

Line 133: Modified CTAB reference missing

Line 136: SSR marker information of genic or genomic region is still missing. Please add that in Supplementary Table 3. 

Line 153, 248 - 249: Check comma (,) between the genes

Author Response

Please see the attachment.

Author Response File: Author Response.docx