Unraveling the Genetic Architecture for Low Temperature Germinability-Related Traits in Rice Using Genome-Wide Association Study

Round 1

Reviewer 1 Report

The research paper by Li et al. performed a genome-wide association study to dissect the genomic regions and candidate genes associated with low-temperature germinability related traits in rice. However, I have some crucial criticisms/comments (detailed below):

Concerns:

1. As per the manuscript, the authors did phenotyping for only one year/environment. But to identify the stable and reliable QTLs, one should perform analysis using multi-location/year phenotypic data (at least three years or locations). So, in my opinion, this data is less to conclude any results.
2. Details of experimental design (randomized complete blocks design (RCBD), alpha lattice, etc.) used in this study were not provided.
3. How following six indices (LTGP, RGP, RPL, PLR, PLRR and RAPL) were measured? Related information was not provided.
4. The following traits/indices used for analysis do not show normal distribution, for GWAS or QTL napping traits should show a normal distribution.
5. Results section authors do not provide results of Structure analysis and LD analysis.
6. How candidate genes are identified. Detail information should be provided.
7. Section 3.2 is written like a discussion (lines 11 to 22).
8. The discussion section should improve. They have to discuss their results and compare them with some earlier QTLs associated with low-temperature germinability related traits in more depth.

Author Response

Thank you for your review of this article, and we have responded to your suggestions one by one.

Author Response File: Author Response.docx

Reviewer 2 Report

The discussion must be rewritten in a cleare way  so that it is easer fotr the reader to understand the results . Additionally the sentenses are too long, so I suggest that they should be split up  into shorter sentenses. 

Author Response

Thank you for your review of this article. We have revised the article according to your suggestions.

Author Response File: Author Response.docx

Reviewer 3 Report

Dear;
I send you my minor comments for the approval process of the article.

In the section "2.1 Plant Material and Population Structure Analysis"

How were the parameters set to run the population analysis? in structure software?

Where and how the PCA and kinship analyzes were performed?

Further detail on how the analyzes were performed is necessary.

Author Response

Thank you for your review of this article. We have revised the article according to your suggestions.

Author Response File: Author Response.docx