New Molecular Tool for a Quick and Easy Detection of Apple Scab in the Field
Round 1
Reviewer 1 Report
What was the difference between the primers used in LAMP assay and qPCR? Were they designed to target same sequences or different genomic regions?
Line# 14: You should mention the full name of “LAMP” first and then abbreviate.
Line# 47: ….. models based on weather alerts. that permit…..
Lines 160-162: Thirty min after inoculation, the plugs were used crude extraction (two plugs) and a commercial DNA extraction (two plugs). ?????
Author Response
Reviewer #1
We would like to thank the reviewer for the prompt and positive feedback regarding the manuscript, as well as. Please find below a description of the changes made in the manuscript. In addition, changes are tracked in the text.
What was the difference between the primers used in LAMP assay and qPCR? Were they designed to target same sequences or different genomic regions?
Both LAMP and qPCR primers were designed on the same gene, the EF1-α. However, the design of 5 LAMP primers requires a bigger region than the qPCR primers.
We added this information in lines 293-295: “EF-1α region was previously chosen by Prencipe et al. [33] to design the qPCR primers used in this study to validate the LAMP assay and consequently this gene, due to its ability to resolve the phylogenetic relationships of closed related species, was also selected for the LAMP primers design [52].
Line 14: You should mention the full name of “LAMP” first and then abbreviate.
LAMP was change to “Loop-mediated isothermal amplification (LAMP)” (Lines 14-15).
Line 47: ….. models based on weather alerts that permit…..
We modified as suggested in Line 47
Lines 160-162: Thirty min after inoculation, the plugs were used crude extraction (two plugs) and a commercial DNA extraction (two plugs). ?????
We modified the sentence to make the concept clearer. “Thirty min after inoculation, the plugs were used to perform a crude extraction (two plugs) and a commercial DNA extraction (two plugs)” (line 163).
Author Response File: 
Author Response.docx
Reviewer 2 Report
- The study aims in providing a new tool for early detection of the most serious fungal disease in apple trees - which could be of significant value for the control of the disease. The methodology followed is appropriate and of high quality. The work merits publication, while only few matters regarding presentation and use English should be imroved.
- Please check if Ref 7 and 8 are correctly placed in the text.
- line 44: Please correct: “As a result” and “Fungicide applications become”.
- line111 The whole link is not needed, NCBI GenBank more is enough.
- line 112-116: This information interrupts the text flow, maybe give it in a separate table.
- line 118: Give citation and not e-site for OligoCalc and other programms (This is a general comment that applies to the whole manuscript)
- line 334: ‘…and which make it a 335 suitable variety to test the sensitivity’. Please rephrase, the meaning of the sentence is not clear.
- lines 336-337. If I understood correctly the following is meant (Please rephrase): ‘because differences in leaf susceptibility depending on the leaf age are confirmed’
- line 355: Do you mean post-inoculation?
- Introduction is very lengthy; irrelevant information is given about disease measuring and prevention tools and on modelling, which are not the subject of the study.
Author Response
Reviewer #2
We would like to thank the reviewer for the prompt and constructive feedback regarding the manuscript. Please find below a description of the changes made in the manuscript. In addition, changes are tracked in the text.
Please check if Ref 7 and 8 are correctly placed in the text.
Ref 7 and Ref 8 have been correctly placed in the text. Ref 7 is now Ref 5.
The text has been modified too in lines 27-33 to: “Venturia inaequalis Cook (Wint.) is the causal agent of apple scab disease, the most important disease on apple orchards in temperate countries with cool and wet weather during early spring [1]. It is a worldwide-distributed species affecting all the apple growing countries and causing important economic and yield losses [1-5]. Most commercial apple varieties are susceptible to V. inaequalis [6,7] and the use of resistant apple varieties is highly recommended, though, unfortunately, some scab-resistant cultivars are not appreciated by the consumers [8].”
Line 44: Please correct: “As a result” and “Fungicide applications become”.
We modified the text as suggested (Line 44).
Line 111 The whole link is not needed, NCBI GenBank more is enough.
The link has been eliminated as suggested (Line 111).
Line 112-116: This information interrupts the text flow, maybe give it in a separate table.
As suggested by the reviewer 2, the information has been summarized in a supplementary table (Table S1) and cited in line 112.
Line 118: Give citation and not e-site for OligoCalc and other programms (This is a general comment that applies to the whole manuscript)
OligoCalc citation has been included as Ref 53 (Line 119). No citation has been found for the other programs. Reference numbers (54 to 65) were modified accordingly.
Line 334: ‘…and which make it a 335 suitable variety to test the sensitivity’. Please rephrase, the meaning of the sentence is not clear.
We modified the sentence to make the concept clearer (Lines 338-339).
Lines 336-337. If I understood correctly the following is meant (Please rephrase): ‘because differences in leaf susceptibility depending on the leaf age are confirmed’
We modified the text to make the concept clearer (Lines 340-344).
Line 355: Do you mean post-inoculation?
Yes, we changed to post-inoculation (Line 362).
Introduction is very lengthy; irrelevant information is given about disease measuring and prevention tools and on modelling, which are not the subject of the study.
As suggested by the reviewer, the information regarding modelling from the introduction has been deleted (Lines 50-59).
Author Response File: Author Response.docx
