Generation of a High-Density Genetic Map of Pepper (Capsicum annuum L.) by SLAF-seq and QTL Analysis of Phytophthora capsici Resistance
Round 1
Reviewer 1 Report
General comments
- This is an important study for the journal horticultuae.
Major comments
- The short reads are directory mapping to the reference, Zunla-1 v2.0. The QTL-GWAS procedure, your paper will be highly evaluated. Then figure 3, it will be unnecessary.
Author Response
I am very grateful to your comments for the manuscript.
Reviewer 2 Report
The manuscript, entitled “Generation of a High-Density Genetic Map of Pepper (Capsicum annuum L.) by SLAF-Seq and QTL Analysis of Phytophthora capsici Resistance” describes and announces the genome resource of pepper generated by SLAF-Seq and QTL analysis of P. capsici resistance. In general, the genome resource is well presented and the assembly reported. The manuscript is well-written in English, but with few typing errors, and uses unclear legends/captions of figures/tables. The results and the genome resources in this manuscript are worth to be published in Horticulturae (ISSN 2311-7524). I think this manuscript is acceptable for publication after minor revision (see suggestions below).
Point 1. Please add the references in relation to every software used in this manuscript, to make the writing more persuasive.
Point 2. I would suggest using full name or adding some appropriate notes for the abbreviations (such as LOD, DOM, PVE, COG, KEGG…) in figures/tables of the whole manuscript.
Point 3. In introduction, please add some descriptions in detail for races of P. capsici.
Point 4. In conclusion, please add the discussion for future works after this study.
Point 5. Please improve picture quality of the Figures 3 & 5, and re-typeset the Table 5.
Point 6. Other minor comments are:
Line 35, Change “anthracnose” to “Colletotrichum spp.”.
Line 36, Change “induced” to “caused”.
Line 121, Change “remove” to “extract”.
Lines 177-178, Revise as “Quantitative PCR was conducted on a 7500 Real Time PCR System (Thermo Fisher Scientific, USA)”
Delete Lines 188-190.
Line 197, Change “Oryza sativa” to “Oryza sativa”.
Line 201, Change “F2” to “F2”.
Line 233-236, Revise as “The largest Chr was Chr03, which consisted of 444 markers, showed a length of 169.18 cM, and an average marker-to-marker distance of 0.19 cM, while the smallest Chr was Chr05 that consisted of 460 markers, showed a length of 99.98 cM, and an average marker-to-marker distance of 0.36 cM (Table 3)”
Table 3, the values of the “Average distance between markers (cM)” typed in the “Total” and “Average” should be switched.
Line 323, Change “Figure.3” to “Figure 3.”.
Line 425, Change “Figure. 5” to “Figure 5.”.
Change “hypothetical protein” to “Hypothetical protein” in the whole Table 7.
Table 8, Change “Table8” to “Table 8”; add the PCR product size of Actin in the Table.
Line 434, Revise as “Phytophthora blight caused by P. capsici is one of the most serious diseases in pepper, …”
Author Response
I am very grateful to your comments for the manuscript. According with your advice, we amended the relevant part in manuscript. Some of your questions were Response below.
Point 1. Please add the references in relation to every software used in this manuscript, to make the writing more persuasive.
Response 1: 1. The version number and country have been added to the "DPS" software. The version number and country have been added to the DPS software. The software "highmap" has been added with references.
Point 2. I would suggest using full name or adding some appropriate notes for the abbreviations (such as LOD, DOM, PVE, COG, KEGG…) in figures/tables of the whole manuscript.
Response 2: The full name of the abbreviations has been added to the tables as a note, in cluding LOD, DOM, PVE, COG and KEGG.
Point 3. In introduction, please add some descriptions in detail for races of P. capsici.
Response 3. In introduction, the race of P. capsici has been added. added “The three physiological races of P. capsici, named races 1-3, have been determined by their virulence on four pepper varieties: early Calwonder (sensitive), PI201234 (resistant), PBC137 (partially resistant) and PBC602 (partial resistance).”
Point 4. In conclusion, please add the discussion for future works after this study.
Response 4. In conclusion, future works has been added in the discussion. added “The result of this study would provide information for the next stage of research such as gene functional analysis, pyramiding breeding and marker-assisted selection (MAS) as well.”
Point 5. Please improve picture quality of the Figures 3 & 5, and re-typeset the Table 5.
Response 5. Figures 3 & 5 have replaced the original image with a clear one, and Table 5 has been adjusted.
Point 6. Other minor comments.
Response 6. Each small problem has been modified.
Reviewer 3 Report
The paper on the generation of a high density genetic map of pepper for P. capsici resistance shows the use of SLAF seq and QTL analysis applied to a F2 population of pepper. The work is well designed and conducted and I do not have any practical suggestion to increase the value of the text. In my opinion it is a fine piece of paper worth publishing in this form.
Author Response
Thank you very much for your recognition of this manuscript.
Round 2
Reviewer 1 Report
Minor comments
- L120. The sentence “S is the representative score of the highest disease level” is confusing. Could you try explaining it in a different way.
- L167. The sentence “Therefore, the maximum LOD value of 6.972 was used as the threshold to determine the existence of QTL.” should replace to the part of results.
- Table 5. The digits (Max, Range …) maybe different.
- Table 6. The LOD Threshold should replace to the footnote.
- Table 6. The unit of your additive and dominance effect values is uncommon.
Author Response
Dear Reviewer:
I am very grateful to your comments for the manuscript. According with your advice, we amended the relevant part in manuscript. Some of your questions were Response below.
Point 1. L120. The sentence “S is the representative score of the highest disease level” is confusing. Could you try explaining it in a different way.
Response 1: Revise as “and S is the representative value of the highest disease level which is 5”.
Point 2. L167. The sentence “Therefore, the maximum LOD value of 6.972 was used as the threshold to determine the existence of QTL.” should replace to the part of results.
Response 2: Delete Lines 167-168. Lines 331 added “In present study, the maximum LOD value of 6.972 was used as the threshold to determine the existence of QTL.”
Point 3. Table 5. The digits (Max, Range …) maybe different.
Response 3. Table 5. The digits range revise as “0-1”.
Point 4. Table 6. The LOD Threshold should replace to the footnote.
Response 4. Table 6. In footnote added “Maximum LOD score (QTL peak).”
Point 5. Table 6. The unit of your additive and dominance effect values is uncommon.
Response 5. Table 6. In Table 6, “additive effects” revise as “ADD”. In footnote, added “ADD, additive effects.”
We tried our best to improve the manuscript and made some changes in the manuscript.
We appreciate for Reviewers’ warm work earnestly, and hope that the correction will meet with approval.
Once again, thank you very much for your comments and suggestion.
Yi-fei Li
Author Response File: 
Author Response.docx
