Genome-Wide Association Mapping Revealed SNP Alleles Associated with Spike Traits in Wheat

Round 1

Reviewer 1 Report

While the subject of the manuscript has merit and the science behind the manuscript seems sounds, I am struggling to understand a large proportion of the manuscript due to the English. In some cases there are minor faults such as spelling errors and excessive use of parentheses which do not affect the meaning. In other cases, confused sentences hinder the reader from understanding the meaning.

I suggest a native English speaker or proofreading service be used to bring this manuscript to a suitable format. I have highlighted some of the errors, but please note that I did not highlight everything so the manuscript must be checked.

Comments for author File: Comments.pdf

Author Response

Dear Dr. Reviewer 1

 

Thank you so much for your comments in our manuscript which is undoubtedly improved our text

I have addressed all comments raised by you. Genereally, we had made many changes in the manuscript text according to your recommendations. Below is our detailed answer on your questions

• Confused sentence, do you mean on different chromosomes?

Thank you for your comment, I mean on the different environments there is no correlation or it’s very weak correlation. But inside each location, we have a strong positive correlation between the traits, and I have wrote this sentence to be more clear look at the line (41-43) in the abstract section

• This is too vague about “using the Ensemble Plants database to better understand the GWAS findings.”

I have rephrased this sentence to be more clear line number (213-218)

• Depending on the trait or the environment? No or low correlation was observed between yield related traits in both environments

I have rephrased this sentence to be more clear line number (268-269

• Is this the only highly positive correlation?

Thank you for this comment, first I would like you to ask the editor to send the PowerPoint file for the figures to you because the MDPI merge our figures inside the text in bad resolution

Second, my answer is we have many values of high positive correlation between all the traits

But for your comment, we indicate to the correlation between the grain yield which scored in (Eltaher et al 2021a) and the yield related traits in the present study

GY-LN with TKNS-LN = 0.85

GY-LN with TSNS-LN= 0.68

GY-LN with SW-LN= 0.65

GY-LN with SL-LN= 0.57

• Do you mean 'with the exception of'?

Yes I meant that , we have high positive correlation between the GY in Lincoln and the yield related traits with exception of TKW

I will use your word (with the exception of instead of except)

• A?

I have changed in the text

• Do you mean 'with the exception of'?

I have changed in the text

• Please use numeral 0 for statistics

Done thanks for your valuable comment

• This figure is too low quality. I cannot read the text.

Thank you for this comment, I recommend to  you to ask the assistant editor ( Ferry Wang E-Mail: [email protected]) to send the PowerPoint file for the figures to you because the MDPI merge our figures inside the text in bad resolution

 

• I don't feel that 3a or 3c are very informative. You could remove them and focus more on figure 3b

It is useful as it shows there no shared markers between the two locations.

• The English is particularly confusing in this paragraph?

I have rephrased the paragraph

• If you refer to the number in text, you don't need parentheses.

The value ranged from 5 to 7

The R2 ranged from 5.69% to 9.01%. I omitted all the parentheses

• Range

I have edited it in the Table

• I am assuming that the chromosome order is 1A, 1B, 1D, 2A... but I think it would be beneficial to either include this in the figure, or mention the order in the legend.

I add the order of chromosome as legend as a key in the figure

• are shown?

Done

• Range

I have edited it in the Table

• The ?

Done

• Consider horizontal lines on this table. It appears that S5A46628103 has the trait 'SW' twice?

I was providing the horizontal lines in all the table format in the separate table file So, you can ask the editor to send the table file to you

• Should there be two markers here? You only mention one.?

Thanks for this notice it’s only one marker and I have edited the sentence

• Is this correct? S6D_469537865 was not the last marker mentioned.

I just mean it’s last one in the fourth common markers in Lincoln but I have omitted the words las one to avoid the misunderstanding

• Using 'this marker' implies the marker in the sentence S3B_60737182 but I don't think that is what you mean. Unless it is a typing error?

It’s typing error and I have edited the sentence

• Ensembl

Also, this isn't quite clear.  Have you submitted your variant to Ensembl plants? When I search with your SNP name I cannot find a hit. There are no listed variants in some of these regions so I don't think it has an alternative name. I don't think that you have to submit your variant to Ensembl plants, but make it clear in your results and method.

Thank you for your comment; the correct approach to search the Ensemble plant database is to use the physical position of each significant SNP marker, instead of the SNP ID.

This section has been rewritten in the materials and methods part line number (213-218)

• I cannot read this figure due to the low quality. Also, it was generated using the Wheat eFP browser without credit. Please cite it in the legend.

https://www.science.org/doi/10.1126/science.aar6089

and  https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000718

 

Regarding the low-quality figures, we have provided very high quality figures in power point but the system of journal for somehow it positioned all figures within the test. We will upload the figures and tables as supplementary tables folder. Please see them.

Regarding the citation I have add it in the material and methods part line number (220-221)

 

 

Author Response File: Author Response.pdf

Reviewer 2 Report

The present study has run GWAS using a quite big number of markers on 270 advanced breeding lines for five yield related traits. Many MTAs have been identified from this analysis. Basically the analysis is sound and conclusions are clear, but technically the experimental design was lack of replication. It is an important issue particularly when the two environments the study used were completely different from each. 

1) The broad-sense heritability estimates were 0.73, 0.73, 0.71, 0.72 and 0.56 for SW, SL, TSNS, TKNS and TKW, respectively. In the two very different environments and very weak correlations, how to get the broad-sense heritability at such high values?

2) The authors probably need repeat the experimental trials in both locations, and remove any environment where the data is weird.

3) How to apply your result in breeding when the very different QTL or candidate genes were identified in two separate environments?

There are typos or format issues across the manuscript which need significantly improved.

 

Author Response

Thank you so much for your comments on our manuscript which is undoubtedly improved our text

I have addressed all comments raised by you. Generally, we had made many changes in the manuscript text according to your recommendations. Below is our detailed answer on your questions

• The broad-sense heritability estimates were 0.73, 0.73, 0.71, 0.72 and 0.56 for SW, SL, TSNS, TKNS and TKW, respectively. In the two very different environments and very weak correlations, how to get the broad-sense heritability at such high values?

In each location, we have sown one replication due to the huge number of experiments (with different populations) we planted in Lincoln and North Platte we analyzed six samples from each block. Therefore, we could not make replications. Instead, we harvested six samples from each location and dealt with them as replications. We could not analyze the data as one replication in the R package we used. The software was run with 6 replications (6 samples) in each location. Therefore, in the ANOVA, each genotype was replicated six times in each location. Any better recommendation from your side?.  

• The authors probably need repeat the experimental trials in both locations, and remove any environment where the data is weird.

Thank you for your comment, our study was conducted in the Unreplicated Augmented incomplete block design with repeated checks cultivar. Repeated checks are used to estimate the error mean square and the block effect. This design was used because at this generation there are limited seed supplies of the experimental lines and the number of genotypes per replicate was large hence there was likely to be spatial heterogeneity within the same environment

• How to apply your result in breeding when the very different QTL or candidate genes were identified in two separate environments?

This kind of results gives us an advantage and ability to use each environment as a separate breeding program because each genotype had a different response in each environment and it gives different QTLs and different candidate genes

• There are typos or format issues across the manuscript that need significantly improved.

Thank you again for your notices we will do our best to improve the English language in this manuscript

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Thank you for your response.  The manuscript has been greatly improved but there are still some more minor comments that I would like to make.

1) I have attached the manuscript with comments covering small typing errors and some sentences that I feel need clarification. In the reference section I have highlighted issues with character formats and missing information, but I have not checked extensively so please double check that the references are useable.

2) The conclusion is clear and in line with the results, but the discussion contains a lot of excessive information that does not seem relevant to your conclusion.  I would suggest that in the section 'Gene Annotation for Yield Related Traits' that you reduce the length of description for each gene and focus only on that which is relevant to the traits studied.

Comments for author File: Comments.pdf

Author Response

Dear Dr. Reviewer 

Thank you again a lot for your comments. in the attached pdf, we found your old comments. When we compared the old one with the new one, We found only a new comment regarding the quality of the picture. I would like to inform you that we have submitted high-quality figures as PowerPoint but unfroutanly, I do not know how the journal inserts the figures into text with this low quality. 

I will leave a remark to the editorial office to send you the files we submitted

Reagrds 

Ahmed Sallam