QTL×QTL×QTL Interaction Effects for Total Phenolic Content of Wheat Mapping Population of CSDH Lines under Drought Stress by Weighted Multiple Linear Regression

Round 1

Reviewer 1 Report

Line No 54. Metabolites – m will be small letter and not capital letter, please check

Line No 56. In wordv phenols p will be small letter and not capita, please check

Line No 72-73, The tolerance is more appropriate than resistant, please check the correctness

Line  No 82.  Coma will be deleted and ‘and’ will be inserted after [28] and there shall be no coma after [29].

Line No 108. There will be were instead of was after the word pots

Line No 110. There will be contents instead of content

Line No .185 . threes- what does it mean, please check the correct word

Line No. 214- threes, please check its correctness (two times present)

Line no 234- word threes, please check its correctness

Line no-239- word threes, please check its correctness

Author Response

Response to Reviewer 1 Comments

Reviewer #1

Point 1: Line No 54. Metabolites – m will be small letter and not capital letter, please check.

Response: This sentence has been corrected.

Point 2: Line No 56. In wordv phenols p will be small letter and not capita, please check.

Response: This sentence has been corrected.

Point 3: Line No 72-73, The tolerance is more appropriate than resistant, please check the correctness.

Response: This sentence has been corrected.

Point 4: Line  No 82.  Coma will be deleted and ‘and’ will be inserted after [28] and there shall be no coma after [29].

Response: This sentence has been corrected.

Point 5: Line No 108. There will be were instead of was after the word pots.

Response: This sentence has been corrected.

Point 6: Line No 110. There will be contents instead of content.

Response: This sentence has been corrected.

Point 7: Line No .185 . threes- what does it mean, please check the correct word.

Response: This sentence has been corrected. We used word ”Triples”.

Point 8: Line No. 214- threes, please check its correctness (two times present)

Response: Response: This sentence has been corrected. We used word ” triples interaction”.

Point 9: Line no 234- word threes, please check its correctness

Response: Response: This sentence has been corrected. We used word ” triples interaction”.

Point 10: Line no-239- word threes, please check its correctness

Response: Response: This sentence has been corrected. We used word ” triples interaction”.

Author Response File: Author Response.pdf

Reviewer 2 Report

The work entitled "QTL×QTL×QTL Interaction Effects for Total Phenolic Content of Wheat Mapping Population of CSDH Lines under Drought Stress by Weighted Multiple Linear Regression" is an original and interesting contribution to science, in the field of genetics and plant breeding. The authors gave the first report on the use of weighted regression to estimate of aaa interaction of wheat. Appropriate material and modern methods were used. The proposed weighted regression method for estimation of the QTL´QTL´QTL interaction effect can contribute to the improvement of the plant selection process, not only for drought resistance and tolerance, but also for many other traits of interest. I propose to the Editor to accept this work without changes.

Author Response

Response to Reviewer 2 Comments

Reviewer #2

Point 1: The work entitled "QTL×QTL×QTL Interaction Effects for Total Phenolic Content of Wheat Mapping Population of CSDH Lines under Drought Stress by Weighted Multiple Linear Regression" is an original and interesting contribution to science, in the field of genetics and plant breeding. The authors gave the first report on the use of weighted regression to estimate of aaa interaction of wheat. Appropriate material and modern methods were used. The proposed weighted regression method for estimation of the QTL´QTL´QTL interaction effect can contribute to the improvement of the plant selection process, not only for drought resistance and tolerance, but also for many other traits of interest. I propose to the Editor to accept this work without changes.

Response: Thank you very much.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comment

This work describes a method for estimating the three-way interaction effects, and is a brief story about statistical model. After reading through, I have some major and minor comments.

Firstly, I don’t think the dataset containing 94 lines, with each lines evaluated in two treatments is a good dataset for proving your methods. Many public data could be used to test your methods. There is no need to use such a small population. Moreover, the stress treatment is unexploited in this story. Normal data without stress treatment is enough to prove your method, which I think is unrelated to stress treatment.

Secondly, the abstract should be more concise. For example, the sentence “Plants have evolved innate adaptations to stress conditions through a series of biochemical 16 and physiological interventions involving the function of many stress-related genes” seems unrelated to this genetic story. Such description should be avoided: There is no published evidence on the study of the use of weighted regression to 19 assess triple interaction. To our knowledge, this is the first report on the use of weighted regression 20 to estimation of aaa interaction of wheat. Moreover, from your abstract, it seems that your methods is not better than conventional phenotypic method, do you mean this story is meaningless?

Thirdly, the introduction should be more concise. The first paragraph should concisely raised why drought stress is important. The second and third paragraphs should be combined. As for the fifth paragraph, there seems no gwas analysis in this story, why you mention it in the introduction. In the last two paragraph, you said that high-order interaction is very important, but why you only mention AAA interaction? Why not DDD, AAD, ADD, etc. I think it is needed to added all possible interactions.

Forthly, for the method part, should briefly adds the formula presented by Kaczmarek et al. [41]. Moreover, if epistatic and three-way epistatic interaction effects show only loci with significant additive gene action effects, why not firstly provide a comprehensive GWAS analysis to found significant loci?

Author Response

Response to Reviewer 3 Comments

Reviewer #3

Point 1: This work describes a method for estimating the three-way interaction effects, and is a brief story about statistical model. After reading through, I have some major and minor comments.

Response: Thank you very much.

Point 2: Firstly, I don’t think the dataset containing 94 lines, with each lines evaluated in two treatments is a good dataset for proving your methods. Many public data could be used to test your methods. There is no need to use such a small population. Moreover, the stress treatment is unexploited in this story. Normal data without stress treatment is enough to prove your method, which I think is unrelated to stress treatment.

Response: We agree that a data set with more than 94 lines would be better to test the proposed estimation methods. It should be mentioned, however, that the dataset used in the manuscript was a very good mapping population, which was used previously to locate and estimate the main effects of QTLs. Many public data exist, however, all of them (the ones we reviewed) contained only mean phenotypic values. The method proposed in this paper requires replicating and observing individuals to estimate variance for individual genotypes. Hence the use of the available dataset containing 94 DH lines. We also agree with the statement that normal data without stress treatment would be sufficient to prove our method. The data associated with the stress treatment were used as additional features (independently of the normal data without the stress treatment), which allowed a broader opportunity to observe the beneficial aspects of the proposed method.

Point 3: Secondly, the abstract should be more concise. For example, the sentence “Plants have evolved innate adaptations to stress conditions through a series of biochemical 16 and physiological interventions involving the function of many stress-related genes” seems unrelated to this genetic story. Such description should be avoided: There is no published evidence on the study of the use of weighted regression to 19 assess triple interaction. To our knowledge, this is the first report on the use of weighted regression 20 to estimation of aaa interaction of wheat. Moreover, from your abstract, it seems that your methods is not better than conventional phenotypic method, do you mean this story is meaningless?

Response: The summary has been shortened. Two passages have been removed: “Plants have evolved innate adaptations to stress conditions through a series of biochemical and physiological interventions involving the function of many stress-related genes.” And “There is no published evidence on the study of the use of weighted regression to assess triple interaction. To our knowledge, this is the first report on the use of weighted regression to estimation of aaa interaction of wheat.”. The proposed weighted regression method for triple interaction estimation is far superior to the conventional phenotypic method and unweighted regression. To confirm this, the results obtained in the abstract are included in the form of coefficients of determination. We added sentence: “The coefficients of determination for the weighted regression model were significantly higher than for the unweighted regression and ranged from 46.2% (C in 2010) to 95.0% (C in 2011).”

Point 4: Thirdly, the introduction should be more concise. The first paragraph should concisely raised why drought stress is important. The second and third paragraphs should be combined. As for the fifth paragraph, there seems no gwas analysis in this story, why you mention it in the introduction. In the last two paragraph, you said that high-order interaction is very important, but why you only mention AAA interaction? Why not DDD, AAD, ADD, etc. I think it is needed to added all possible interactions.

Response: We corrected manuscript. The second and third paragraphs were combined. GWAS analysis was mentioned because it is a very important step leading to the estimation of the triple interaction. It was assumed that three-way epistatic interaction effects show only loci with significant additive gene action effects as a result of GWAS analysis. We added: “(additive×additive×additive, additive×additive×dominance, additive×dominance×additive, dominance×additive×additive, addi-tive×dominance×dominance, dominance×additive×dominance, domi-nance×dominance×additive and dominance×dominance×dominance)”. In the presented manuscript, only the parameter connected with the additive×additive×additive interaction effect was estimated, because the study material was doubled haploid lines, and for homozygous material only this triple interaction can be analyzed.

Point 5: Forthly, for the method part, should briefly adds the formula presented by Kaczmarek et al. [41]. Moreover, if epistatic and three-way epistatic interaction effects show only loci with significant additive gene action effects, why not firstly provide a comprehensive GWAS analysis to found significant loci?

Response: We added the formula presented by Kaczmarek et al. [41]. Loci with significant additive effects of genes were located and estimated previously by Czyczyło-Mysza et al. [42].

Author Response File: Author Response.pdf

Reviewer 4 Report

The manuscript SJBS-D-23-00263 entitled "QTL×QTL×QTL Interaction Effects for Total Phenolic Content of Wheat Mapping Population of CSDH Lines under Drought Stress by Weighted Multiple Linear Regression" sets out to estimate parameters connected with the additive×additive×additive (QTL×QTL×QTL) interaction effects for total phenolic content of wheat mapping population from the cross Chinese Spring×SQ1 doubled haploid (CSDH) lines under drought stress by weighted multiple linear regression. The study is on a topic of relevance and general interest to the journal's readers. However, I have several concerns that should be addressed before publication.

·         The title of the manuscript is long and should be shortened.

·         The authors are highly recommended to avoid using a personal pronoun (e.g., We, our, etc.); they can use the third party in the past tense's passive voice.

·         The authors need to carefully read the manuscript to correct typos and grammar to improve the manuscript. Also, use one font type throughout the manuscript.

·         Any abbreviation must be associated with the full name at the first mention in the manuscript to allow the reader to follow up because not all readers are familiar with the abbreviated terminology

·         The first two sentences in the abstract fit more into the introduction; in the abstract, please go directly to the current study. There is no need to provide any background in abstract

·         In the material and methods section, lines 10-103, what was the temperature? In lines 105-109, it is unclear whether the authors used the same or different pots each time. Line 107 ‘Every few days’ please be specific

·         In table 1 and table 3, define each abbreviation in the table footnote

·         In table 3, expand the first three columns to fit in one line to make it easy to follow. The current format is hard to follow and understand.

·         Add more information to the conclusion section

Author Response

Response to Reviewer 4 Comments

Reviewer #4

Point 1: The manuscript SJBS-D-23-00263 entitled "QTL×QTL×QTL Interaction Effects for Total Phenolic Content of Wheat Mapping Population of CSDH Lines under Drought Stress by Weighted Multiple Linear Regression" sets out to estimate parameters connected with the additive×additive×additive (QTL×QTL×QTL) interaction effects for total phenolic content of wheat mapping population from the cross Chinese Spring×SQ1 doubled haploid (CSDH) lines under drought stress by weighted multiple linear regression. The study is on a topic of relevance and general interest to the journal's readers. However, I have several concerns that should be addressed before publication.

Response: Thank you very much. We have incorporated several changes into the manuscript and carefully reviewed your suggestions.

Point 2: The title of the manuscript is long and should be shortened.

Response: Thank you for the suggestion to shorten the title. Indeed, the length was too long. We propose a new title which is shorter.

Point 3: The authors are highly recommended to avoid using a personal pronoun (e.g., We, our, etc.); they can use the third party in the past tense's passive voice.

Response: Thank you very much. We corrected manuscript.

Point 4: The authors need to carefully read the manuscript to correct typos and grammar to improve the manuscript. Also, use one font type throughout the manuscript.

Response: We corrected the manuscript.

Point 5: Any abbreviation must be associated with the full name at the first mention in the manuscript to allow the reader to follow up because not all readers are familiar with the abbreviated terminology.

Response: We have added full names to all abbreviations at the first mention in the manuscript.

Point 6: The first two sentences in the abstract fit more into the introduction; in the abstract, please go directly to the current study. There is no need to provide any background in abstract.

Response: We have removed the first two sentences from the abstract.

Point 7: In the material and methods section, lines 10-103, what was the temperature? In lines 105-109, it is unclear whether the authors used the same or different pots each time. Line 107 ‘Every few days’ please be specific.

Response: We have used the same experimental setup during all the experimental years, this included also the pot size. A sentence was added to clarify this. Plants were subjected to the drought stress in the natural conditions, this is being mentioned in the manuscript. We didn’t include the information regarding the exact temperature because this is not the subject of this study. All other parts of methods sections have been corrected.

Point 8: In table 1 and table 3, define each abbreviation in the table footnote.

Response: We added abbreviations in Tables 1 and 3.

Point 9: In table 3, expand the first three columns to fit in one line to make it easy to follow. The current format is hard to follow and understand.

Response: We corrected Table 3.

Point 10: Add more information to the conclusion section.

Response: Additional conclusions were added to the section.

Author Response File: Author Response.pdf

Round 2

Reviewer 3 Report

I don't have any questions.

Reviewer 4 Report

Thank you, the authors responded to all of my comments!