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Dear Dr. Wang,
Thank you for revising and submitting your manuscript to PeerJ.
I am writing to inform you that your manuscript - Genetic dissection of grain iron concentration in hexaploid wheat (Triticum aestivum L.) using a genome-wide association analysis method - has been accepted for publication. Congratulations!
Sincerely,
Tika Adhikari
[# PeerJ Staff Note - this decision was reviewed and approved by Julin Maloof, a PeerJ Section Editor covering this Section #]
[# PeerJ Staff Note: Although the Academic and Section Editors are happy to accept your article as being scientifically sound, a final check of the manuscript shows that it would benefit from further English editing. Therefore, please identify necessary edits and address these while in proof stage. #]
Please see the attached file from the Academic Editor.
Dear authors:
Thank you very much for revising your manuscript entitled "Genetic dissection of grain iron concentration in hexaploid wheat (Triticum aestivum L.) using a genome-wide association analysis method".
Also, thank you for your patience and understanding of the delay in the review process of your manuscript.
I had received a few comments (below) from the Section Editor and would highly appreciate your revising the manuscript before accepting it for publication in PeerJ.
Comments:
1: p-value threshold of 0.001 is way more lenient than the standard procedure in GWAS and is not appropriate. Please note that at p < 0.001 one expects a false positive in 1 out of every 1,000 tests by random chance. 200,000 + SNPs are tested here, so at p < 0.001 we expect 2,000 false positives. Possible approaches are Bonferroni, FDR, or an FDR that tries to account for LD among SNPs. Please check this reference, https://doi.org/10.1534/genetics.116.193987.
2. GWAS methods are not adequately described. GAPIT has many models, just saying that GAPIT was used with a kinship matrix is not enough. Which model was used?
3. Statistical analysis likely should be improved. Specifically, a mixed-effect model accounting for blocks should be used.
4. Broad sense heritability needs to be calculated. \
5. Manuscript needs significant editing for proper grammar."
Thank you.
Best regards,
Tika Adhikari
[# PeerJ Staff Note: The Academic Editor has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at [email protected] for pricing (be sure to provide your manuscript number and title) #]
Dear Dr. Wang:
Thank you for your patience and understanding. Please see the attached file and revise your manuscript. Thank you.
Best regards,
Tika Adhikari
A sufficient field background was provided. The authors have changed the article however, some of the sentences need to be revised (mentioned in the article).
The research was well designed, relevant information was provided and the research was conducted in the prevailing ethical standards
The authors have changed the article however, Some of the sections could be revised (mentioned in the article).
After revision, it has improved, but still needs to be revised in tables and figures. Details are as follows:
In table1, there were no explaination for the three letters,"h,j,j" , please deleted or explaination.
In Figure2, the 21 chromosomes should be added at the Horizontal axis.
In table2, in the coloum P value, the numbers should be superscripted, please check the number.
no comment
no comment
no
Dear Dr. Wang:
Thank you for your submission to PeerJ.
Your manuscript has been reviewed by two experts in your research area. Based on their reviews and my assessment, your manuscript entitled "Genetic dissection of grain iron concentration in hexaploid wheat (Triticum aestivum L.) using a genome-wide association analysis method" requires Major Revisions. Thank you,
Best regards,
Sincerely,
Tika Adhikari
[# PeerJ Staff Note: Please ensure that all review and editorial comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. #]
A sufficient field background was provided. However, Some of the sentences need to be revised (mentioned in the article).
Figures are relevant, however, Figures 2, 3, 4 could be merged into a single one. Similarly, Figures of Manhattan plots (Figures 5, 6, 7) and QQ plots (Figures 8, 9, 10) could be merged into a single one. It would be better to have LD and population structure figures
In Tables, some of the missing information must be included (mentioned in the article)
The research was well designed, relevant information was provided and the research was conducted in the prevailing ethical standards
The results were well written, however, some of the sections could be revised (mentioned in the article).
Some of the sentences are repeated and the flow of the information is lacking in the discussion section.
The conclusion needs to be revised
NA
This article was well described, and the results will be available for improving the wheat Fe content by MAS in future. But it needs major revision. Detail revisions were as follows:
Introduction
(1) In this part, the advantages of GWAS and SNP marker were introduced too much, but there is no introduction on previous researches on mapping of minerals using linkage map and GWAS. So recommend the author to add this content.
(2) Line 85: “of” should be deleted.
Materials and methods
Line134: “ Heinongjiang” changed to "Heilongjiang"
Line140-143 and Line 145-146: the wheat grains were physiologically mature or completely mature for Fe content analysis? It seemed to be inconsistent.
Line166 and Line169: the number of SNP markers “244,508” or “1.25 million SNPs” in GWAS analysis was inconsistent.
Line187-188, this sentence is not clear.
In addition, because the Fe content of grain is affected by soil minerals, so the minerals content of soil at three experiment locations should be introduced.
Results
Line191-194: The sentences from “Grain Fe concentration” to “depicted in Figure 2, Figure 3 and Figure 4.” Should be deleted.
Line213 "." should be deleted
Line272 “Detailed descriptions of the 10 candidate genes are summarized in Table 3.” Should be deleted.
Line301 “and” should be added before “Pu”.
The references in latest three years should be added and compared analysis, for example, the reference “Identification of novel genomic regions associated with nine mineral elements in Chinese winter wheat grain” has been published on BMC Plant Biol (2021) 21:311”.
Discussion needs further revision.
Because the Fe content of grain is affected by soil minerals, so the minerals content of soil at three experiment locations should be introduced.
The results will be available for improving the wheat Fe content by MAS in future.
Major revision
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