De novo QTL-seq Identifies Loci Linked to Blanchability in Peanut (Arachis hypogaea) and Refines Previously Identified QTL with Low Coverage Sequence

Round 1

Reviewer 1 Report

• Line # 181-182: Give the details on the method of identifying the QTL on A06 and B11. Also, provide the distance between the SNP marker and the QTL.
• How many SNPs did you identify between the two bulks? How did you arrive at only two QTLs?
• What are the results of QTL mapping with the RIL population?
• Provide relevant connection between the introgression and mapping in this study
• Refining the previously identified QTL needs proper elaboration.

Author Response

1. The two bulks were applied to khufu (https://www.hudsonalpha.org/khufudata/), and khufu did run marker calling and QTL-seq analysis. A sliding window were used to narrow down the region of QTL-seq, so the top point of the peak represents multiple markers, which are more likely the causal markers. This is more precise than traditional QTL-seq or other QTL analysis method, which refer to regions of mega bases to have the QTL
2. khufu produced graph per chromosome. Two peaks were formed above the confidence interval line (vertical line in figure 1B) in chromosomes A06 & B01.
3. We did not carry out QTL-seq in the validation population, only assayed the identified markers from the original QTL-seq analysis. The RIL population was genotyped with the 48k SNP array, but as those markers are fixed, they are not as relevant to the population as sequencing based markers.  A QTL mapping was conducted and showed signal in the same locations as the QTL-seq analysis.  Because the QTL-seq is more precise, we do not show these analyses.
4. The connection between the introgression in these regions were published in different studies (referenced in the manuscript).

Reviewer 2 Report

Dear Authors,

The authors found a QTL associated to blanchability in peanut by the QTL sequencing (QTL-seq) approach and tested KASP (PCR) markers to validate the identified regions. I did not find objective errors, but some methods and results need to be better reported with much more detail or improved by in-depth analysis to give more experimental or analytical evidence to the results. Although no particular experience can be directly extrapolated, these cases can still provide useful information and use of the Knufu pipeline for further improvements of peanut associated with desirable traits.
My major comment is in below sections:
(1)    What type of planting procedures were followed, selected lines (based on how and what criteria), and phenotyping for Blanchability? 
(2)    All the supplemental Tables and Figure files are not available. I was not able to find Tables associated with the manuscript.
(3)    Line 233-235. The B11 mentioned in the text, however, on Table is written B01, is given linkage group is correct? A similar contrasting interpretation was mentioned on Line 206, the text, and Figure 1 C.
(4)    Figure 1 has low resolution, and C) Validation of markers in an independent RIL population needs improvement. 
(5)    Line 346-349, what is TSWV mean? Give full avoid abbreviation on the first mention.  

Best regards,

Asekova Sovetgul

Author Response

1. The high and low individuals were selected and provided from Wright et al., 2018 study (line 127).
2. The files were sent to the editor. I will contact the editor to ensure implementing them.
3. Line 233-235, Yes, as peanut is tetraploid of two genome sets (A & B), and every genome set is 10. Sometimes, we used continuous numbers when we reference to B subset (B 11-20), or, we start from 1 (B 1-10). The mentioned concern was corrected to keep the consensus structure across the manuscript.
4. The low resolution because that the figures were impeded into the text based on the journal instructions. But final version should have more resolution. The figure was updated for a better resolution.
5. The abbreviation was identified