Genotypic and Phenotypic Characterization of Two Triticum aestivum L.—Dasypyrum villosum Translocations Lines in the Same Wheat Genetic Background
Round 1
Reviewer 1 Report
The Abstract must be improved with comprehensive information. The conclusion is written a little vague. So, it must be improved for reader.
Overall comments. The manuscript agronomy-1101597 provides a lot insigts on translocations lines with parent line and these findings can be useful for wheat breeders and geneticists. However, there are several comments to be addressed.
Comments-
- Line18-19 in abstract t section, the distribution of SNPs between lines were mainly dense not concentrated.
- The translocation lines A303, and 303 or 6V#4s.DL and 6V#2S.6L are not clearly explained in the text. Readers might misunderstand these lines as separate material.
- Introduction needs more background information on translocations lines and research related to them.
- Agronomic traits evaluation translocation lines with parent line is not clear.
- Did authors do any analysis using SNPs in these lines for SNP correlation as they have poor distribution of SNPs .
- Conclusion needs more concrete summary of the findings in thr5 study.
Author Response
Q: The manuscript agronomy-1101597 provides a lot insights on translocations lines with parent line and these findings can be useful for wheat breeders and geneticists. However, there are several comments to be addressed.
A: Many thanks you for your time and comments.
Q: Line18-19 in abstract section, the distribution of SNPs between lines were mainly dense not concentrated.
A: Thanks for your kind recommend. We have modified to use the "dense" you suggested
Q: The translocation lines A303, and 303 or 6V#4S. 6DL and 6V#2S.6AL are not clearly explained in the text. Readers might misunderstand these lines as separate material.
A: Many thanks for your good advice. We actually mentioned the relationship on the introduction part, now we add more details in the introduction for help the reader to memorize the connection of these translation lines and their inbred line name. It’s really a good point, many thanks for that.
Q: Agronomic traits evaluation translocation lines with parent line is not clear.
A: Thank you very much for your reminder. We modified this part. And thank you for your advice.
Q Did authors do any analysis using SNPs in these lines for SNP correlation as they have poor distribution of SNPs.
A: No, we didn’t.
Q: Conclusion needs more concrete summary of the findings in the study.
A: That’s really a good point, we actually rewrite this part for corresponding our aim. and we added more highlight point on this part. And again, Thanks for your time and patient.
Author Response File: 
Author Response.docx
Reviewer 2 Report
Review
Wang et al, “Diversity investigation of 6V#4S.6DL and 6V#2S.6AL translocations using 660K SNP array and phenotypic identification in 3 the same wheat genetic background”
Manuscript number: agronomy-1101597
General comments:
Overall is well written, easy to follow.
This manuscript details a genotypic and phenotypic characterization of three lines, and two translocation lines showed strong resistance to PM and very good agronomic trait. Which was the objective of the study and was achieved. This is very important for breeding purposes.
The experiments appear to be robust, but organization and explanation need some improvement.
Addressing the points below would more clearly communicate this research.
I wish, the authors have included the donor Dasypyrum villosum of resistance in all the analysis and assays
Introduction: I am missing information about the PM disease, severity, yield losses, etc.
In materials and methods there is information that is missing that once is describes, I think would make this paper better.
It needs a better description of the materials/populations used I this study and the experimental design. is missing a lot of details.
Is a bit confusing all the experiments and the purpose of each. A detailed information is well appreciated.
Probe could be replaced by “SNP” throughout.
Statistical analysis for agronomic traits is seem to be robust, but I am missing this for the resistance assays.
Comments for line numbers according to PDF file “agronomy-1101597-peer-review-v1.pdf”.
Lines 2-4: tittle is confusing and the names 6V#4S.6DL and 6V#2S.6AL do not really tell anything.
It could be something like: “Genetic and phenotypic characterization of two Triticum aestivum translocations lines” OR “Genetic characterization of two wheat translocations lines and their resistance to xxxx”
Line 18: what you mean by “invalid probes”?
Line 23: add it is powdery mildew
Line 21-22: respectively, please specify. “the translocation lines A303 and B303 have 99.44% and 98.81% identical genotypes to 21 Wan7107, respectively.
Line 51, line 60 and line 71: what are the other agronomic traits that are important to measure? Mention each of them.
line 60: resistance to what diseases??
Lines 77-79: introduce first Wan 7107 And then explain where is coming from.. “ Wan 7107 is a mutation line derived from….
Lines 81-89: Is very confusing. I do not see Nannong 9918 this in fig. is it included in the analysis, because is not explained until this point??
Line 83: is TH3 and allotetraploid? I only see two species
Lines 98-99: “The samples with acceptable 98 measurements for A260/280 and A260/230 without DNA degradation” this is unnecessary information; this is standard protocol.
Lines 100-101: replace by “Genotypic data were extracted and processed using the Axiom Analysis Suite 3.1.51”
Lines 101-103: Each locus was assigned to six types ac- 101 cording to a series of indicators: poly high resolution, nominorhom, mono high resolution, OTV, callratebelow threshold and other” can be deleted.
Lines 105: how did you get 89,167 SNPs?, any filtering strategy?
Lines 109-110: by genotype you mean SNPs throughout?.
Line 103: table legend could be: “Percentage of SNP distribution across the genome in Wan 7107”.
Line 126: is this randomized complete block design?. Your experimental design is not clear? Whay you evaluated 10 and noy the 30 plants?
Line 132-134: How this experiment fits on studying the three lines (A303, B303 and Wan7107). This needs better explanation and mention in material and methods. How many plants planted? experimental design?
Line 141: was a normality test was used?, ANOVA/KRUSKAL?
Lines 144: How many reps?, experimental design?
Line 159: “Chancellor" and Nannong 9918 need to be described in plant materials section and the purpose of using it.
Line 170: replace “The investigation standard” by “screening method was …”. Is this a method access susceptibility/resistance?, because it confusing when you mention scores for isolates in
lines 180-181. Please describe (how many?, where were o) the Bgt isolates somewhere in plant materials or “Reaction to different isolates of the pathogen”.
Line 188: explain describe how you define invalid probes in your set.
Line 189: I do not see this information in Table 3.
Line 222: Please briefly explain what SNP analysis you did, to remind the reader what it is.
Line 288: where are the results from statistical analysis for resistance assays??
Line 297-299: Please show pictures of this in figure 7.
Line 302: In figure 7, it will be appreciated to have better pics with better quality, including a scale bar.
Line 326: crop this figure to remove the extra black background.
Author Response
Q: This manuscript details a genotypic and phenotypic characterization of three lines, and two translocation lines showed strong resistance to PM and very good agronomic trait. Which was the objective of the study and was achieved. This is very important for breeding purposes.
The experiments appear to be robust, but organization and explanation need some improvement.
A: First of all, many thanks for your time and comments.
Addressing the points below would more clearly communicate this research.
Q: I wish, the authors have included the donor Dasypyrum villosum of resistance in all the analysis and assays
A: Thank you for your advice. The two donors have more than one chromosome carrying PM resistance gene, so it is of little significance as a control.
Q: Introduction: I am missing information about the PM disease, severity, yield losses, etc.
A: Thanks for your kind reminder, we have added more information in the introduction, that’s a good advice.
Q: In materials and methods there is information that is missing that once is describes, I think would make this paper better. It needs a better description of the materials/populations used I this study and the experimental design. is missing a lot of details.
A: Thank you for your suggestion. We have added more necessary information in materials and methods section.
Q: Is a bit confusing all the experiments and the purpose of each. A detailed information is well appreciated.
A: That’s really a good point, yes and we have already added more information in the introduction part for understanding. And thanks for your advice.
Q: Probe could be replaced by “SNP” throughout.
A: Thank you for your advice. In some place, we think it’s appropriate to using probe, not SNP, so we didn’t change it throughout.
Q: Statistical analysis for agronomic traits is seem to be robust, but I am missing this for the resistance assays.
A: In fact, in the resistance assays, each line was planted in a pot with 10 plants and inoculating an Bgt strain, then the symptoms on the leaves of the plants were investigated, then scored and graded.
Q: Lines 2-4: tittle is confusing and the names 6V#4S.6DL and 6V#2S.6AL do not really tell anything. It could be something like: “Genetic and phenotypic characterization of two Triticum aestivum translocations lines” OR “Genetic characterization of two wheat translocations lines and their resistance to xxxx”
A: Thanks for your suggestion, we have taken your advice.
Q: Line 18: what you mean by “invalid probes”?
A: Invalid probes mean no genotyping was available by these probes.
Q: Line 23: add it is powdery mildew
A: Thanks for your reminder, we have added now.
Q: Line 21-22: respectively, please specify. “the translocation lines A303 and B303 have 99.44% and 98.81% identical genotypes to 21 Wan7107, respectively.
A: OK, Thanks for your kindness reminder.
Q: Line 51, line 60 and line 71: what are the other agronomic traits that are important to measure? Mention each of them.
A: Yes, we have added. And thanks for your advice.
Q: line 60: resistance to what diseases??
A: We have already listed the target, and thanks for your advice.
Q: Lines 77-79: introduce first Wan 7107 And then explain where is coming from. “ Wan 7107 is a mutation line derived from….
A: Thanks, we have changed this part as your advice.
Q: Lines 81-89: Is very confusing. I do not see Nannong 9918 this in fig. is it included in the analysis, because is not explained until this point??
A: Thank you for your reminder. Nannong 9918 was used as a resistant control in experiment on evaluation of the PM resistance, we have moved it to section 2.5. Evaluation of PM resistance (2) Reaction to different isolates of the pathogen. It doesn’t show in fig1.
Q: Line 83: is TH3 and allotetraploid? I only see two species
A: Actually, TH3 is an allohexaploid (2n=6X=AABBVV), because T. durum is an allotetraploid (2n=4X=AABB) and D. villosum is a diploid (2n=2X=VV).
Q: Lines 98-99: “The samples with acceptable 98 measurements for A260/280 and A260/230 without DNA degradation” this is unnecessary information; this is standard protocol.
A: Ok, we deleted it then. Thanks for your reminder.
Q: Lines 100-101: replace by “Genotypic data were extracted and processed using the Axiom Analysis Suite 3.1.51”
A: OK, we have changed it as your advice.
Q: Lines 101-103: Each locus was assigned to six types ac- 101 cording to a series of indicators: poly high resolution, nominorhom, mono high resolution, OTV, callratebelow threshold and other” can be deleted.
A: Thanks, we have deleted it as you recommend.
Q: Lines 105: how did you get 89,167 SNPs?, any filtering strategy?
A: We select the SNP typing with the highest typing reliability, i.e, Poly High Resolution, and eliminate probes without corresponding physical locations, only retain probes with clear physical locations. Then we got 89,167 SNPs.
Q: Lines 109-110: by genotype you mean SNPs throughout?.
A: In my opinion, genotype refers to a specific line, while single nucleotide polymorphism refers to the comparison between two lines.
Q: Line 103: table legend could be: “Percentage of SNP distribution across the genome in Wan 7107”.
A: Sorry, I don't agree with that.
Q: Line 126: is this randomized complete block design? Your experimental design is not clear? Whay you evaluated 10 and noy the 30 plants?
A: Yes. The translocation lines were BC2F4 and BC8F4, which are genetic stable lines. We think 10 random plants can represents the overall situation, so we set 10 as the minimum sample, and we randomly sampled 10 plants to ensure the accuracy of the data.
Q: Line 132-134: How this experiment fits on studying the three lines (A303, B303 and Wan7107). This needs better explanation and mention in material and methods. How many plants planted? experimental design?
A: Thank you for your suggestion. In fact, we have clearly stated when and where we planting in the materials/methods part, and the number of plantings is also clearly displayed in Table 4. We think that this display is sufficiently clear. And again thanks for your kind reminder.
Q: Line 141: was a normality test was used?, ANOVA/KRUSKAL?
A: We used t-test to compare the averages between the two groups. The statistical differences were obtained by comparing the agronomic traits between the control Wan7107 and each translocation line. Because we have multivariate, the t-test is more applicable.
Q: Lines 144: How many reps?, experimental design?
A: We did this experiment follow the standard, and we describe it at materials/methods. In fact, each line was planted 10 plants in a pot and inoculating an Bgt strain, then investigated the symptom on leaves for scoring and grading.
Q: Line 159: “Chancellor" and Nannong 9918 need to be described in plant materials section and the purpose of using it.
A: Thanks for your reminder, we have added it as your advice.
Q: Line 170: replace “The investigation standard” by “screening method was …”. Is this a method access susceptibility/resistance?, because it confusing when you mention scores for isolates in
A: thanks for your advice, we have changed it now.
Q: lines 180-181. Please describe (how many?, where were o) the Bgt isolates somewhere in plant materials or “Reaction to different isolates of the pathogen”.
A: We did the description in methods/materials part.
Q: Line 188: explain describe how you define invalid probes in your set.
A: As I answered before, Invalid probes mean no genotyping was available by these probes.
Q: Line 189: I do not see this information in Table 3.
A: sorry，it’s our fault, it should be Table 1.Thanks for your reminder.
Q: Line 222: Please briefly explain what SNP analysis you did, to remind the reader what it is.
A: In the next sentence, we explain what SNP analysis we did: The numbers, densities, and proportion of the SNP probes to the total number of the probes per chromosome are listed in Table S3.
Q: Line 288: where are the results from statistical analysis for resistance assays??
A: In Table 3. Each disease grade in Table 3 is the result from statistical analysis of 10 plants.
Q: Line 297-299: Please show pictures of this in figure 7.
A: Indeed, Funo and Nannong9918 were showing at Table 3 as PM resistance spectrum, not in figure 7
Q: Line 302: In figure 7, it will be appreciated to have better pics with better quality, including a scale bar.
A: Thanks for your advice, we added more signs on that picture, including a scale bar.
Q: Line 326: crop this figure to remove the extra black background.
A: Thank you for your detailed suggestions, we have cut it now, and again, many thanks for your time and patient.
Author Response File: Author Response.docx
