Exploring the Genetic Variation of Stripe Rust Foliar and Head Infection in Egyptian Wheat as an Effect of Climate Change

Round 1

Reviewer 1 Report

1. It is better to weight  more grains to represent TKW instead of estimated on 100 grains.

2.  L183-184 the references are not in a correct format.

3.  Figure 1 and Figure 2 have additional  "Figure 1" and "Figure 2" in the pictures.

4. L205 Pst italic

5. Figure 9 what genotypes the red highlighted ?

6. Table 1 and 2 what the ** stand  should be mentioned

Minor editing of English language required

Author Response

Dear Dr. Reviewer,

Thank you for spending time reviewing our manuscript. All your comments have been considered and highlighted in yellow in the revised version of the manuscript. Please find a step-by-step response to your comments below.

1. It is better to weight more grains to represent TKW instead of estimated on 100 grains.

Reply: Of course, it is better to weigh more than 100 grains. But the 100 grains used in this study were selected randomly. So, we thought that it will be enough. However, we will consider weighing more grains in our future studies.

2. L183-184 the references are not in the correct format.

Reply: It was corrected.

3. Figure 1 and Figure 2 have additional  "Figure 1" and "Figure 2" in the pictures.

Reply: Sorry, but this comment is not clear. I checked the two figures and not repetition was found. May be something went wrong from the MDPI office while preparing the manuscript in their format.

4. L205 Pst italic

Reply: I think this also the MDPI false as they must change the format of the submitted manuscripts before sending to the reviewers. However, I checked Pst in the version that I submitted and all in italic format. I will check them again in the final version.

5. Figure 9 what genotypes the red highlighted ?

Reply: the red genotypes are those belonging to cluster 2. No genotypes were highlighted. The highlight was for Giza_168 in cluster 1. The figure was corrected.

6. Table 1 and 2 what the ** stand  should be mentioned

Reply: it was mentioned.

Comments on the Quality of English Language

Minor editing of the English language required

The English was revised by Prof. Dr. Stephen Baenziger who is a native English speaker and an expert in wheat.

Reviewer 2 Report

In this study, a set of 34 Egyptian cultivars and 51 isolines were evaluated for their Pst foliar and head infection in two growing seasons (2021 and 2022) under Egyptian conditions. The results show that high genetic variations in head and foliar infections and both stripe rust symptoms are genetically separated. A very weak correlation was found between Pst head and foliar infection in both growing seasons. High significant differences in maximum temperature, minimum temperature, maximum dew point, and average dew point were found between the two growing seasons. This results could help in improving the resistance to both symptoms, and the three resistant genotypes and ten identified genes based on the isolines evaluation should be included in future breeding programs to improve Pst resistance and silence the effect of climate change on such a severe disease under Egyptian conditions. I have some concerns that require the attention of the authors.

1.When the table involving variance analysis appears in the paper for the first time (Table1), the table should be annotated, for example, * and** represent significant differences and highly significant differences, respectively.

2.The serial number of the reference is repeated twice, does the format need to be adjusted?

3.All image quality needs to be improved. For example, the Fig 2 and Fig 3 cannot be seen clearly, Fig5b does not explain the legend clearly (i.e. what horizontal and vertical coordinates represent is not clearly marked).

4.For the foliar evaluation，IT measurement methods should be specified in the Materials and methods section for the reader's convenience.

5.In order to be beautiful and convenient for readers to read, it is suggested to re-typeset the diagram, table and text layout of the article, and the table should not be split;

6.The demarcation of the scale value of the horizontal coordinate is not standard, so it is suggested to unify the scale standard and should label the unit "%"?

7.” Genotype x years interaction” represent? Readers are easily confused and should be explained.

8. Whether “14” in“The remaining genotypes showed different degrees of susceptibility with a number of four, 14, and seven, MS, S, and VS genotypes”needs to be replaced by “fourteen”, and whether “24” in ”All the tested genotypes were grouped in three clusters with three, four, and 24 genotypes in cluster1…”needs to be replaced by”“twenty-four”?

9.What does VR represent in "and five genotypes showed immune, R, and VR response" in Part 3.1.2of the article? Whether it should be VS?

10. I suggest that Part 3.3 should give a more detailed summary of the results about the influence of four climate parameter changes on the occurrence of stripe rust, that is, the relationship between climate parameter and the occurrence of stripe rust, rather than a simple description of data.

11. In this paper, the evaluation of stripe rust infection in the Egyptian wheat germplasm, the relation between stripe rust foliar and head infection, climate parameters that affect stripe rust infection , evaluation of the differential lines to both stripe rust symptoms and effect of PstFI and PstHI on important kernel traits were introduced in detail, but the reader did not clearly read the conclusion about "the effect of climate change on the genetic variation of wheat stripe rust in Egypt", that is, how did climate change affect the genetic variation of wheat stripe rust? It is suggested to redefine the appropriate title.

Extensive editing of English language required

Author Response

Dear Dr. Reviewer,

Thank you for spending time in reviewing our manuscript. All your comments have been considered and highlighted in green in the revised version of the manuscript. Please find step-by-step response to your comments below.

1.When the table involving variance analysis appears in the paper for the first time (Table1), the table should be annotated, for example, * and** represent significant differences and highly significant differences, respectively.

Reply: A legend was added (highlighted in yellow).

2.The serial number of the reference is repeated twice, does the format need to be adjusted?

Reply: this is not my mistake. It was adjusted by the journal should adjust the submitted manuscripts before sending them to the reviewers.

3.All image quality needs to be improved. For example, the Fig 2 and Fig 3 cannot be seen clearly, Fig5b does not explain the legend clearly (i.e. what horizontal and vertical coordinates represent is not clearly marked).

Reply: The quality of the figures is adjusted by the MDPI. We have submitted high-quality figures in our powerpoint file. I would recommend asking the editor to provide the original figure to check their quality.

The coordinates were added to Fig 5b.

4.For the foliar evaluation，IT measurement methods should be specified in the Materials and methods section for the reader's convenience.

Reply: IT was described in detail in Lines: 145-147.

5.In order to be beautiful and convenient for readers to read, it is suggested to re-typeset the diagram, table and text layout of the article, and the table should not be split;

Reply: All legends were revised and adjusted.

6.The demarcation of the scale value of the horizontal coordinate is not standard, so it is suggested to unify the scale standard and should label the unit "%"?

Reply: Your comment is not clear. Which figures do you mean? Each figure represents different category. Some represent number of genotypes and only one (Fig 5b.) represents percentage of infection. It is not possible to unify the scale unit to all figures.

 

7.” Genotype x years interaction” represent? Readers are easily confused and should be explained.

Reply: It was explained in the discussion part (Line 414-416).

 

8. Whether “14” in“The remaining genotypes showed different degrees of susceptibility with a number of four, 14, and seven, MS, S, and VS genotypes”needs to be replaced by “fourteen”, and whether “24” in ”All the tested genotypes were grouped in three clusters with three, four, and 24 genotypes in cluster1…”needs to be replaced by”“twenty-four”?

Reply: Normally number form 0-10 should be written in letter. After 10 all numbers should be written in numbers. Please check this https://www.aje.com/arc/editing-tip-using-numbers-scientific-manuscripts/.

9.What does VR represent in "and five genotypes showed immune, R, and VR response" in Part 3.1.2of the article? Whether it should be VS?

Reply: It should be MR and was corrected.

10. I suggest that Part 3.3 should give a more detailed summary of the results about the influence of four climate parameter changes on the occurrence of stripe rust, that is, the relationship between climate parameter and the occurrence of stripe rust, rather than a simple description of data.

Reply: The effect of climate changes on stripe rust infection in wheat was described previously in previous studies. Therefore, in order to make the manuscript not too long, we thoughts that it will more valuable to focus on the effect of climate factors on head infection as it has been noticed in the last few years.

 

11. In this paper, the evaluation of stripe rust infection in the Egyptian wheat germplasm, the relation between stripe rust foliar and head infection, climate parameters that affect stripe rust infection , evaluation of the differential lines to both stripe rust symptoms and effect of PstFI and PstHI on important kernel traits were introduced in detail, but the reader did not clearly read the conclusion about "the effect of climate change on the genetic variation of wheat stripe rust in Egypt", that is, how did climate change affect the genetic variation of wheat stripe rust? It is suggested to redefine the appropriate title.

Reply: Thanks for your comment. The title has been changed as recommended.

 

Comments on the Quality of English Language

Extensive editing of English language required

The English was revised by Prof. Dr. Stephen Baenziger who is a native English speaker and an expert in wheat.

Reviewer 3 Report

In this manuscript, the authors investigate the high stripe rust head infection in Egyptian wheat across two growing seasons, with a particular focus on comparing it to Pst foliar infection. They determine that Pst foliar and head infections are unrelated, each seems to be controlled by different genetic systems. While the manuscript provides valuable insights and detailed data presentation, it is difficult to read and follow due to repetitive content and a lack of focus.

To improve the manuscript, the authors should reorganize their research findings to clarify the central topic, rather than presenting all data obtained throughout the study. Some data were not confirmed, which is hard to draw any conclusions. Additionally, figures and figure legends require more detailed information. A lot of work is needed before the manuscript can be further evaluated for publication.

Other comments:

1. Lines 49-58: Please expand on the concept of foliar infection in the introduction, including its definition, infection cycle, and symptoms, since it is extensively compared with head infection.

2. Lines 81-84: Streamline the introduction for conciseness.

3. Lines 130-131: Clarify the significance of the "coefficient" and its relevance to the study.

4. Line 140: Address foliar infection, as it is also calculated in the manuscript.

5. Section 2.5: Explain the model's origin, any modifications made, or the rationale behind its development, depending on the circumstances.

6. Lines 197-198 and Figure 1: Include a visual representation of foliar infection symptoms and add a scale bar to facilitate kernel size comparison.

7. Figure 2: Define the coefficient of infection, explain the numbers on the x-axis, and clarify how to distinguish between foliar infections in the two seasons in Figure 2a.

8. Figure 3: Specify the methods and software used to create these graphs and elaborate on the values within the figures.

9. Figure 4: Describe the line representing foliar infection (infection rate?) and provide labels for the x and y axes.

10. Figure 5: Identify the words within the figures and label the x and y axes.

11. Figure 6: Explain the different colors and values in the graphs, and mention the software or method applied to create this figure.

12. Figures 7 and 8: Provide additional information in the figure legends to enhance understanding.

13. Figure 9: Detail the method and data used to construct the phylogenetic tree.

14. Line 408: Clarify the meaning of "old and new cultivars." And this information was not mentioned in method 2.1. Please explain it.

15. Sections 4.5 and 4.3 can be combined for better organization.

16. Lines 550-559 and other instances: Reevaluate the data and reorganize the information to emphasize the research topic, as the current presentation dilutes the focus.

17. Pst foliar and head infections are unrelated, each seems to be controlled by different genetic systems. This is an interesting point. As you discussed in the manuscript, a wider genetic background is needed to investigate which genetic background favors HI or FI.

18. References: Correct the citation format to ensure consistency and traceability throughout the manuscript.

19. Supplementary material was not found in the submission file; please include it if applicable.

 

 

Streamline some sentences for conciseness.

Author Response

Dear Dr. Reviewer,

Thank you for spending time in reviewing our manuscript. All your comments have been considered and highlighted in blue in the revised version of the manuscript. Please find step-by-step response to your comments below.

Comments and Suggestions for Authors

In this manuscript, the authors investigate the high stripe rust head infection in Egyptian wheat across two growing seasons, with a particular focus on comparing it to Pst foliar infection. They determine that Pst foliar and head infections are unrelated, each seems to be controlled by different genetic systems. While the manuscript provides valuable insights and detailed data presentation, it is difficult to read and follow due to repetitive content and a lack of focus.

To improve the manuscript, the authors should reorganize their research findings to clarify the central topic, rather than presenting all data obtained throughout the study. Some data were not confirmed, which is hard to draw any conclusions. Additionally, figures and figure legends require more detailed information. A lot of work is needed before the manuscript can be further evaluated for publication.

Reply: Thank you for your comment. The manuscript, figure legend and figures were revised and adjusted.

Other comments:

1. Lines 49-58: Please expand on the concept of foliar infection in the introduction, including its definition, infection cycle, and symptoms, since it is extensively compared with head infection.

Reply: Foliar infection is well known to wheat farmers and breeders. It has been extensively studied and discussed. Our goal here was to focus on head infection as it didn’t get more concern and is not really known. Therefore, in order to shortness the introduction part, we thought that the comparing the occurrence period of both types of infections as it was mentioned in line 88-89 should be good.

2. Lines 81-84: Streamline the introduction for conciseness.

Reply: introduction was revised and summarized.

3. Lines 130-131: Clarify the significance of the "coefficient" and its relevance to the study.

Reply: I couldn’t get your point here. Coefficient of infection is a known measure of rust infection in adult growth stage of wheat. It has been used widely to measure the infection of rusts. Discussing the significant of this measure will confuse the reader and prolong the manuscript. Not sure what should be mentioned here.

4. Line 140: Address foliar infection, as it is also calculated in the manuscript.

Reply: evaluating foliar infection was added in the materials.

5. Section 2.5: Explain the model's origin, any modifications made, or the rationale behind its development, depending on the circumstances.

Reply: I didn’t get your point here. This is a statistical model depending on our experimental design. No more information should be written in this section. Please see the following link for more details:

https://www2.stat.duke.edu/~banks/111-lectures.dir/lect21.pdf

6. Lines 197-198 and Figure 1: Include a visual representation of foliar infection symptoms and add a scale bar to facilitate kernel size comparison.

Reply: Foliar infection is a widely known symptoms of wheat. It has been extensively studied and many books and manuscripts represented the symptoms and the scale used in evaluating it as it was mentioned in the material (Stakman et al., (1962) and  Roelfs et al., (1992). If the reader doesn’t have enough experience, he can easily search for the foliar symptoms. The aim of the manuscript is to figurehead infection that is not commonly known. Therefore, we thought that presenting the foliar symptoms here will interrupt the reader and make the manuscript hard to follow.

Kernel measures were using a ruler as described in the material part section 2.3.

 

7. Figure 2: Define the coefficient of infection, explain the numbers on the x-axis, and clarify how to distinguish between foliar infections in the two seasons in Figure 2a.

Reply: The coefficient of infection was defined in Figure 2a. The x-axis are the numbers of genotypes. Fig 2a. are the average values of foliar infection in the two seasons as there were no significant differences between foliar infection in both seasons. This was mentioned in the legend of the figure.

8. Figure 3: Specify the methods and software used to create these graphs and elaborate on the values within the figures.

Reply: more details were added in section 2.5. and scale value was added to the figure.

9. Figure 4: Describe the line representing foliar infection (infection rate?) and provide labels for the x and y axes.

Reply: foliar infection was described. X-axes is hard to be described as it represents different categories (percentage of infection and temperatures). Y axes are the date as it was written. More details were added to the legend of the figure.

10. Figure 5: Identify the words within the figures and label the x and y axes.

Reply: The figure was adjusted as recommended.

11. Figure 6: Explain the different colors and values in the graphs, and mention the software or method applied to create this figure.

Reply: these colors are the value of the correlation. There is a guide bar under each figure. Information on calculating the correlation was added in section 2.5.

12. Figures 7 and 8: Provide additional information in the figure legends to enhance understanding.

Reply: legend was revised and adjusted.

13. Figure 9: Detail the method and data used to construct the phylogenetic tree.

Reply: it was mentioned in detail in section 2.6.

14. Line 408: Clarify the meaning of "old and new cultivars." And this information was not mentioned in method 2.1. Please explain it.

Reply: This information was removed from the text as explaining it will prolong the manuscript.

15. Sections 4.5 and 4.3 can be combined for better organization.

Reply: both sections are different. 4.3 discusses the possible resistant genes based on the evaluation of the isoline and 4.5 is mainly discussing the Egyptian genotypes and selecting the most reliable genotypes from them.

16. Lines 550-559 and other instances: Reevaluate the data and reorganize the information to emphasize the research topic, as the current presentation dilutes the focus.

Reply: The manuscript was revised as recommended.

17. Pst foliar and head infections are unrelated, each seems to be controlled by different genetic systems. This is an interesting point. As you discussed in the manuscript, a wider genetic background is needed to investigate which genetic background favors HI or FI.

Reply: I agree, this is why we mentioned: “seems to be”. We are going to evaluate this symptom in another wider-genetic background population.

18. References: Correct the citation format to ensure consistency and traceability throughout the manuscript.

Reply: this is usually done by the MDPI and has been revised again.

19. Supplementary material was not found in the submission file; please include it if applicable.

Reply: It was added in the submission. It seems that this mistakenly forgot by the MDPI office while preparing the manuscript to be sent to the reviewers.

 

Comments on the Quality of English Language

Streamline some sentences for conciseness.

All the manuscript was revised again and long sentences were summarized. Furthermore, the English was revised by Prof. Dr. Stephen Baenziger who is a native English speaker and an expert in wheat.

 

Round 2

Reviewer 2 Report

In this study, a set of 34 Egyptian cultivars and 51 isolines were evaluated for their Pst foliar and head infection in two growing seasons under Egyptian conditions, the results of this study provide candidate genes for wheat resistance to Pst head and foliar infection and it is of great significance for breeding wheat resistance to stripe rust in Egypt. The content of this study is perfect and of great significance，but the abstract does not summarize each part of the article well, which may confuse the readers. I suggest that the author review the abstract, systematically summarize the research content, innovation and significance of this research.

The content of this study is perfect and of great significance，but the abstract does not summarize each part of the article well, which may confuse the readers. I suggest that the author review the abstract, systematically summarize the research content, innovation and significance of this research.

Author Response

Dear Dr. Reviewer,

Thank you for your comment. The abstract was revised and adjusted as recommended. Please find the attached file!

 

Author Response File: Author Response.docx

Reviewer 3 Report

Thanks for the responses and the minor revision from the authors.

I want to clarify three main points of the revision.

1)     Many of your figures (figures 3-9) provide robust information. For me and for readers I believe, it is challenging to comprehend these specific figures based on the concise one to two-sentence figure legends. These figures were created to support your opinions, and I believe that if the authors themselves had created them, they would be able to explain them more effectively. It would be beneficial to refer to other published papers, as it is uncommon to find such brief figure legends when presenting relatively complex figures. I think this is a serious problem in this manuscript.

2)     For the second revision, I didn’t see any figures in the manuscript, and I didn’t see any supplemental material. Since the other reviewer also questioned your figures, why delete all the figures in the manuscript?

 

3)     Based on the reply to my comments and the other reviewers’ comments, it appears that the authors revised a little bit, which is far from a significant improvement. I believe it is the author’s responsibility to deliver a complete and high-quality manuscript, rather than relying on the editor or the journal's office for corrections. Therefore, please ensure that the figures are of high quality and that the citations are correct on your own. The editor's final proofreading of the manuscript occurs during the acceptance phase, and their role is not to complete your job.

The English language is fine.

Author Response

Thanks for the responses and the minor revision from the authors.

I want to clarify three main points of the revision.

1)     Many of your figures (figures 3-9) provide robust information. For me and for readers I believe, it is challenging to comprehend these specific figures based on the concise one to two-sentence figure legends. These figures were created to support your opinions, and I believe that if the authors themselves had created them, they would be able to explain them more effectively. It would be beneficial to refer to other published papers, as it is uncommon to find such brief figure legends when presenting relatively complex figures. I think this is a serious problem in this manuscript.

Reply: All figures in this manuscirpt were created and designed by us. Adding more information to the legend will result in too much text in the figures. More explanation of the figures could be found in the results part. So, we cannot add more explanation in the legend.

2)     For the second revision, I didn’t see any figures in the manuscript, and I didn’t see any supplemental material. Since the other reviewer also questioned your figures, why delete all the figures in the manuscript?

Reply: it is not logical to submit the manuscript without figures or supplementary files. You might have contacted the Editorial office of Agronomy asking about Figures and Tables. How can we delete them after submitting them!! It was surprising to me that you didn't see the figures and had too many comments on them! (e.g. your first comment on 3-9 Figures !!!!!!). Other reviewers didn't ask to provide the figures. They had a few comments on the axis, the legend that we already made and one of them accepted the figures now.

 

3)     Based on the reply to my comments and the other reviewers’ comments, it appears that the authors revised a little bit, which is far from a significant improvement. I believe it is the author’s responsibility to deliver a complete and high-quality manuscript, rather than relying on the editor or the journal's office for corrections. Therefore, please ensure that the figures are of high quality and that the citations are correct on your own. The editor's final proofreading of the manuscript occurs during the acceptance phase, and their role is not to complete your job.

Reply: I know my job as an author very well. This is not my first time to publish in high profile international journals which are 19 articles.

As I told you before, the figures were submitted in a high-quality version. You can ask the journal to send you the PowerPoint file which I submitted. And again, how did you know that these figures in low quality and in the second comment you told that I deleted them from the last version !!!!!!!!!

Furthermore, the manuscript was revised intensely, and major edit was done. I highlighted all specific comments in the text. We also revised the text carefully and we did a lot of changes and it is strange that you did not see the difference between the first and second versions of the manuscript. I invite you to read it again carefully.