Genome Enhanced Marker Improvement for Potato Virus Y Disease Resistance in Potato
, Anthony T. Slater 1 and Noel O. I. Cogan 1,2,*Round 1
Reviewer 1 Report
In the manuscript the authors presented an important point, although the manuscript has some drawbacks.
Main remarks:
1. Literature review - after the "introduction", there should be a part of "literature review".
2. Figure - figure 1 is hardly visible.
3. Discussion - please break down the "discussion" into "discussion" and "conclusions".
4. Conclusions - in your conclusions, please also answer the following questions:
• what are the directions for the future?
• what are the research gaps?
• what is new to this manuscript?
Author Response
- Literature review- after the "introduction", there should be a part of "literature review".
I have readjusted my manuscript to follow the template provided by Agronomy here https://susy.mdpi.com/user/manuscripts/upload/6785726fa5069ac57906e8801f6eac9d?form%5Bjournal_id%5D=34, I believe that all the required sections have been covered using the format provided by the journal.
- Figure -figure 1 is hardly visible.
Line 278 - I have resized the image to make it more readable
- Discussion - please break down the "discussion" into "discussion" and "conclusions".
Line 414 – added conclusion section
- Conclusions- in your conclusions, please also answer the following questions:
• what are the directions for the future?
• what are the research gaps?
• what is new to this manuscript?
Line 414-429 – Thank you for the direction, I have updated the conclusion section to address the above questions.
Reviewer 2 Report
The authors integrated genomic information, resistant accessions, segregating populations and marker testing to produce better markers for PVY resistance. Specifically the Ryadg locus. This framework could be a useful examples to others to improve markers.
Comments
The use of the word “advanced” the title is probably over the top. The methods used here are good but not that novel. It’s more accurate to describe the paper as “Genome enhanced marker improvement for PVY disease resistance in potato”
Also, in general, use of words like “exceptionally” and “enormous” (I noted those in the abstract), are probably not necessary unless qualified. It sounds unprofessional.
Please mention the reference potato accession when first mentioning it. It may also be useful to state that it is not carrying the R allele.
In the discussion of the candidate protein, you cite a paper that discusses the role of plant TIR domains as NADases, but only mention “protein-protein interactions”.
When discussing the possibilities for the R gene itself, you should reference one of the RenSeq studies (J. Jones or B Staskawicz papers). They showed that there are many additional NLR paralogs in non-reference genomes. It’s likely that the source of Ryadg is some novel paralog not present in the reference genome.
Author Response
The use of the word “advanced” the title is probably over the top. The methods used here are good but not that novel. It’s more accurate to describe the paper as “Genome enhanced marker improvement for PVY disease resistance in potato”
Line 2 – thank you for the suggestion, I have updated the title to “Genome enhanced marker improvement for PVY disease resistance in potato”
Also, in general, use of words like “exceptionally” and “enormous” (I noted those in the abstract), are probably not necessary unless qualified. It sounds unprofessional.
Line 9 – I have removed all instances of the words “exceptionally” and “enormous” from the paper, thank you for your suggestion.
Please mention the reference potato accession when first mentioning it. It may also be useful to state that it is not carrying the R allele.
Line 149 – I have included additional details about the nature of the reference genome
Line 333 – The following sentence was included to make it clear to the reader that the reference will not contain the R allele “As the reference genome was derived from a S. tuberosum Phureja clone, it is also expected that the reference sequence does not contain the Ryadg gene.”
In the discussion of the candidate protein, you cite a paper that discusses the role of plant TIR domains as NADases, but only mention “protein-protein interactions”.
Line 397 – We have removed “protein-protein interactions” and replaced it with “cell death and disease resistance across all kingdoms” to concentrate the readers focus on the general significance rather than the specific mechanism.
When discussing the possibilities for the R gene itself, you should reference one of the RenSeq studies (J. Jones or B Staskawicz papers). They showed that there are many additional NLR paralogs in non-reference genomes. It’s likely that the source of Ryadg is some novel paralog not present in the reference genome.
Line 352 - I have included a new sentence with an appropriate recent reference
Reviewer 3 Report
This paper describes a new marker for PVY resistance that has higher accuracy than previously-described markers. A KASP assay was designed to detect the RYadg SNPs. The methods are well-described, and the marker has potential high value to potato breeders.
Minor comment:
Bottom of page 3: "Initial sequence data fastq files were processed through a custom perl script for quality trimming and adaptor removal using cutadapt v1.9"
Either a custom perl script was used for quality trimming and adaptor removal, or cutadapt was used. If a custom perl script was used for some other purpose, this needs to be clarified.
Author Response
Bottom of page 3: "Initial sequence data fastq files were processed through a custom perl script for quality trimming and adaptor removal using cutadapt v1.9"
Either a custom perl script was used for quality trimming and adaptor removal, or cutadapt was used. If a custom perl script was used for some other purpose, this needs to be clarified.
Line 146 - Thank you for the comment, I have attempted to clarify my meaning on line 146
Round 2
Reviewer 1 Report
Accept in present form.
