Revealing Genetic Variations Associated with Chip-Processing Properties in Potato (Solanum tuberosum L.)
Round 1
Reviewer 1 Report
The manuscript uses GWAS and selective sweep approaches to to reveal SNP associations with chip processing traits. The manuscript is clearly written but I will point out a few cases where changes could be made to improve the final manuscript.
Line 66 - I would not use arabidopsis as an example of breeding progress.
Lines 67-68 - I disagree that we have examples of fixing homozygous conditions in tetraploid potato with marker assisted selection.
Lines 165-168 - References for tuber glucose, chip color measurement and dry matter content should be included.
Line 241 - SRA abbreviation is not described.
General note - chip processing does not need to be capitalized.
Lines 267-270 - the two sentences have awkward wording "showed to reduce" and "reproduced".
Figure 1 - I am not familiar with the term Miami plot
Figure 5 - TPM should not be abbreviated in legend. Also, can chromosome number of the candidate genes be listed in the figure?
Figure 6 - can the organization of the figure be improved?
Line 553 - remove the word "another"
Author Response
Line 66 - I would not use arabidopsis as an example of breeding progress.
Answer- Yes, I agree with your comment. I deleted the word “Arabidopsis.”
Lines 67-68 - I disagree that we have examples of fixing homozygous conditions in tetraploid potato with marker assisted selection.
Answer- Ok, in order for the readers not to be confused, the sentence was modified as follows;
In the current potato breeding system, characterized by tetraploidy (2n = 4x = 48) and intolerance to inbreeding, superior allele combinations can be achieved via marker-assisted selection (MAS).
Lines 165-168 - References for tuber glucose, chip color measurement and dry matter content should be included.
Answer- The sentence was modified as follows;
The following traits were analyzed; the ratio of tuber length to width (LW) [42], specific gravity measured by weighing a sample in air and then reweighing the sample in water (https://www.agric.wa.gov.au/potatoes/specific-gravity-potato-tubers), tuber glucose content (grams 100 gram-1 fresh weight) as described in [43], L* as the lightness measurement of the external color of the potato chips by using a Chroma meter (Model, Minilta Corp, Japan) [42] and dry matter content (%) measured by a freeze-dry method [44]. A log10-transformation was performed for the tuber glucose content and BLUEs (best linear unbiased estimates) were calculated for all traits of study with restricted maximum likelihood (REML) using the software package META-R [45].
Line 241 - SRA abbreviation is not described.
Answer- I put the full name; the Sequence Read Archive (SRA)
General note - chip processing does not need to be capitalized.
Answer- changed into small letter
Lines 267-270 - the two sentences have awkward wording "showed to reduce" and "reproduced".
Answer- The sentence was modified as follows;
Although the K model reduced inflation significantly relative to naïve model (Supplementary Figure S2b and c), the signal on chromosome 4, when implemented QDAPC+K model, disappeared and the GWAS signal on chromosome 10 has been reproduced (Figure 1a).
Figure 1 - I am not familiar with the term Miami plot
Answer- sorry, the word is deleted and descriptions were modified a little.
Figure 1. The genome-wide association analysis for 95 chip processing cases and 298 controls. The plot represents the Q+K corrected-GWAS of chip processing for the 393-line panel (a). The x-axis shows the chromosomal position, and the y-axis shows the significance of association (−log10(p)). The dotted horizontal line shows the genome-wide significance level (−log10(p) = 4.9) calculated by Bonferroni method. In this study, we used the additive model and two simplex dominant models (1_dom_alt and 1_dom_ref). On the right is the quantile-quantile (Q-Q) plot for GWAS of additive model using 3977 SNPs for the 393-line panel (b). The area shaded in light blue indicates the 95% confidence interval under the null hypothesis.
Figure 5 - TPM should not be abbreviated in legend. Also, can chromosome number of the candidate genes be listed in the figure?
Answer- the Transcripts Per Kilobase Million (TPM)
The number is the chromosome number after Soltu.DM.
e.g. for Soltu.DM.04G010300.1, 04 indicates chromosome number 4.
Figure 6 - can the organization of the figure be improved?
Answer- There is no need to put all three markers, so a new figure was generated, in which KASP_c1_8021 was deleted and descriptions were changed.
Line 553 - remove the word "another"
Answers- it was deleted.
Reviewer 2 Report
The authors analyzed 8303 SolCAP SNP genotyping array data for 393 tetraploid potato clones bred by global potato breeding programs from Japan, North America, the Netherlands, Germany, Chile, New Zealand, and Austria. They detected strong significant GWAS signals on chromosome 10 and hundreds of regions across the genome that had been differentially selected between Chip processing market class and all of the rest market classes. To validate the results, they used the KASP to validate the genetic variants they found. The authors presented a well-designed experiment and used proper analyses to find and validate the genetic variants on chromosome 10. The tables and figures clearly showed the results of this study, and no major grammar issues were found. This manuscript can be considered to be published.
Author Response
thanks!
Reviewer 3 Report
Good manuscript, just minor revisions:
1. Can you attach the R code (or share the repository) used to run the GWAS, selective seeps analysis, and RNAseq?
2. Additionally, you can share the genotypic and phenotypic datasets used to run this analysis.
3. In general section 2.5 needs to be expanded. Software, number of lines, reads, or filters.
4. L240: explain TPM.
5. Figure 3: Remove the figure's text and change the barplot to boxplot.
Author Response
- Can you attach the R code (or share the repository) used to run the GWAS, selective seeps analysis, and RNAseq?
Answer- In Methods, how to run the programs used was described sufficiently, I think. In near future, I can upload the scripts in the Github repository..
- Additionally, you can share the genotypic and phenotypic datasets used to run this analysis.
Answer- All datasets are available in the Supplementary information.
- In general section 2.5 needs to be expanded. Software, number of lines, reads, or filters.
Answer- We use data which were downloaded from the Spud DB database (http://spuddb.uga.edu/dm_v6_1_download.shtml).
- L240: explain TPM.
Answer- the Transcripts Per Kilobase Million (TPM)
- Figure 3: Remove the figure's text and change the barplot to boxplot.
Answer- In the manuscript, we are using the z-score calculator for two population proportions (https://www.socscistatistics.com/tests/ztest/).
Sometimes, readers seem to like real data, though we can also provide the boxplots of correlation between the traits of study and genotyping groups.
