QTL Mapping for Resistance to Early Blight in a Tetraploid Potato Population

Round 1

Reviewer 1 Report

The paper reports and discuss results from experiments concerning early blight (EB) (caused by Alternaria solani) in a tetraploid potato population segregating for EB resistance. QTL for defoliation and EB resistance on both foliage and tubers were mapped based on field and laboratory evaluations and a 10K SNP array. Some clones showed high EB resistance in both foliage and tubers and a number of interesting QTL were mapped for all three traits. Both QTL and resistant clones are useful for breeding purposes and further investigations.

Line 47 to 50: Please, rephrase this part.

Line 60-62: Roman numbers are used to designate chromosomes (also line 216 and 251), but in other passages the decimal number system is used for this purpose (line 71, 239, 242, Table 2 etc.). Please, be consistent.

Line 90: Please, add the number of weeks/months the plants were growing before the tubers were harvested.

Line 94: How was the presence of EB determined? Did you test this?

Line 107: How often or on which dates did you collect leaf samples to verify presence of A. solani in the field?

Line 183-184: Is there a specific reason why you don’t mention the four clones with the highest and lowest foliage resistance according to Supplementary Figure 1? Such as you do for the tuber resistance.

Line 195-196: Can you mention some clones showing both high foliage and high tuber resistance? These clones would be interesting for breeding purposes or further studies.

Line 227-228: This is unclear: “the traits the predicted are of the QTL can be linked to”. Please rephrase.

Line 232: This text “Bold text identifies the foliar resistance and defoliation QTL which were found to be independent from one another” is a repetition from line 228, so either one of these should be deleted.

Line 302: New results are introduced here. They should be moved to the Results section.

Line 303: There could also be other reasons apart from physiological age for the apparent decrease in resistance. Maybe the tubers are stressed by storage, or they are affected by other pathogens, which develops during storage. Is there any literature about this that could be included and discussed?

Line 317-318: Are the values in the Supplementary Figure 1 a mean of the results in 2014 and 2016 for the rAUDPC in the foliage and for the two experiments in 2014 concerning the VIA in the tubers? Please indicate.

Author Response

Dear reviewer,

Thank you for your valuable comments and suggestions. We have considered all your comments and suggestions and made changes accordingly.

Please see the attached file which contains all the responses to your comments.

 

Best regards,

Firuz Odilbekov

Author Response File: Author Response.docx

Reviewer 2 Report

The manuscript ‘QTL mapping for resistance to early blight in a tetraploid potato population’ from Odilbekov et al. comprises interesting results regarding EB in tetraploid potato. The authors used F₁ cross between the cultivars ‘Matilda’ (susceptible) × ‘Magnum 74 Bonum’ (resistance) to identify novel QTL in the challenging genetic background of autotetraploid potatoes. Three criteria were used for phenotyping EB resistance: Foliar EB symptoms, defoliation and tuber resistance assay. The study identified a number of QTL for the individual and for combinations of these traits, which resembles promising germplasm for EB breeding in potato.

 

The experimental setup and QTL analysis seem solid, however the manuscript in its current form lacks clarity and a detailed interpretation of the results of the QTL mapping, resulting in the following comments/questions:

 

1. How many tubers from each clone (replicates per clone) were used for the field experiments and the tuber resistance test?
2. What is the phenotypic distribution of defoliation (rAUC)? (data should be added to Figure 1)
3. What is the correlation between foliar EB symptoms and defoliation? (data should be added to Figure 2)
4. How did the phenotypical data vary between the years? Apparently no EB symptoms were identified in 2015, but how did defoliation and EB symptoms in 2014 and 2016 vary?
5. The authors should comment on the absence of EB symptoms in 2015?
6. QTL analysis should also be performed for individual years and differences reported if applicable.
7. Why were the tuber tests only conducted in 2014?
8. Linkage maps with marker positions should be provided. Graphical overviews of the confidence interval of the different QTL and marker positions either combined with the linkage map or as separate figure would improve clarity of the results.
9. The authors should point out the physical size of the QTL confidence intervals and comment on potential candidate genes for EB resistance in the QTL regions?
10. The authors should compare the physical position of the de-novo identified QTL in the tetraploid potato F₁ population (this study) and published QTL for resistance to EB (e.g. in diploid potato by Zhang et al., 2003 or by genome synteny of QTLs for EB resistance in tomato).
11. Line 263-266: ‘It has been shown that EB resistance is associated with late maturity [10,20,48], therefore, introgression of the resistant genes for EB to the new commercial cultivars without the compromise in earliness is complicated.’ The authors should comment on late or early maturity in ‘Matilda’ and ‘Magnum Bonum’?
12. Line 193: The cultivar ‘Matilda’ as a susceptible parent of this crossing population had better resistance to EB in the tuber than the EB resistant parent ‘Magnum Bonum’. The authors should discuss how the QTL analysis reflects this result?
13. Line 295: Some of the progeny clones had good resistance in both leaves and tubers (Supplementary Figure 1) and they could be potential candidates for EB resistance breeding programs.

The authors should comment on the genotype of these clones for the main QTL for tuber and foliar resistance?

14. There are several QTL which seem interesting from EB resistance breeding perspective which were not discussed by the authors, e.g. QTL associated with tuber and foliage resistance traits or even all three traits (group 7 in Figure 3 and Table 2).

Also, QTL on Chr 05 of ‘Magnum Bonum’ at marker PotVar0079374 were high significant for foliar resistance and defoliation (LOD score 9.857 and 8.104) and therefore also an interesting candidate for subsequent EB resistance breeding.

On the other hand, it seems unclear, why the authors explicitly refer to QTL which were not associated with defoliation (line 276).

The authors should provide a clearer interpretation of the results in context of the output of this study in terms of potential marker/pre-breeding material for MAS for EB resistance in potato.

15. Line 254 to 259 needs rewording. Meaning is currently unclear.
16. Line 303:’ This indicates that resistance decrease with increasing physiological age of the tubers.’ The decrease in resistance over tuber storage time would need a comparison between resistant and susceptible plants. However, in context of QTL mapping, these results might not be crucial and do not add to the clarity of the manuscript. The authors might consider to leave them out or provide more detailed data.

Minor correction:

1. line 35 -36: Not sure which point the authors want to make with the following sentence:’ However, in Europe, it is not considered as an economically important disease, but losses up to 30% have been reported during storage’, since losses up to 30% are presumably economically significant.
2. Chromosome labels are inconsistent and switch between arabic and roman numerals (e.g. line 251,252)
3. line 72: Delete sentences:’ So far, the genetic background of EB resistance in tetraploid potato has remained unexplored, as well as other high-value complex traits in potato.’
4. line 145: specifics/manufacturer or reference for the used 10K SNP array

Author Response

Dear reviewer,

Thank you for your valuable comments and suggestions. We have considered all your comments and suggestions and made changes accordingly.

Please see the attached file which contains all the responses to your comments.

 

Best regards,

Firuz Odilbekov

Author Response File: Author Response.docx

Round 2

Reviewer 2 Report

The authors addressed several points sufficiently. However, the following points are not resolved entirely and would need further revision:

Point 6:

Point 6: QTL analysis should also be performed for individual years and differences reported if applicable.
Response 6: Table (Table 3) added with results from QTL analysis for individual years. Comments have been written about the highlights of the results in the results part, below the previous QTL results with data mean of both years.

Comment:

Phenotyping data seem to vary between years leading to inconsistent QTL mapping results between the individual years and to the used approach using mean values of phenotyping data of several years. Whilst some QTL are highly significant in only one year, some are in several years and some are not significant in a single year, but reach significant thresholds if mean data of several years are used. The manuscript does not discuss this discrepancy and what it means for reliable QTL identification at the moment. Also, it remains unclear why the chosen mean value approach is advantageous. It would also be helpful to refer to previous studies which have applied this method in the past.

Also, Figure 1 should include distribution of the phenotyping data for the individual years for more transparency.

The responses to point 4 and 5 by the authors already provide important background information regarding phenotypic variation between the years and should be incorporated in the discussion.

Point 7:

Point 7: Why were the tuber tests only conducted in 2014?
Response 7: The tuber test experiments were conducted in control condition two times in 2014 and therefore we decided not to repeat again.

Comment:

It seems understandable not to perform tuber tests in 2015, due to the lack of EB symptoms. However, it is not conclusive why no tuber tests were not repeated in 2016.

 

Point 8:

Point 8: Linkage maps with marker positions should be provided. Graphical overviews of the confidence interval of the different QTL and marker positions either combined with the linkage map or as separate figure would improve clarity of the results.
Response 8: The software (TetraploidMap) we are using does not provide an overview map for the whole genome. We have 67 separate linkage maps (one for each linkage group). We think that this quantity of figures is too large even for supplementary files and would make it more difficult rather than easier to understand the results.

Comment: Linkage maps with markers positions should be provided and can be summarized as supplementary table.

A graphical overview encompassing QTL confidence interval in relation to marker positions is highly recommended and would be helpful for the reader to quickly identify QTL positions and overlaps among QTL. This figure should focus on plotted chromosomes with significant QTL and rather not include all 67 linkage groups. Also pointing out the QTL detected in different years.

Also:

line 328: 'as can be noticed when considering at', should be rephrased.

line 332: 'Finding cheap, PCR primers for these QTL would be the first step for applying MAS for resistance to EB.' should be rephrased.

 

Author Response

Dear reviewer,

Thank you for your valuable comments and suggestions. We have considered all your comments and suggestions and made changes accordingly.

Please see the attached file which contains all the responses to your comments.

Best regards,

Firuz Odilbekov

Author Response File: Author Response.docx