Phenotypic Variation and Molecular Marker Network Expression of Some Agronomic Traits in Rice (Oryza sativa L.) RIL_S of Gr 89-1×Shuhui 527

Round 1

Reviewer 1 Report

This article aims to relate rice phenotypic traits to the molecular markers. A lot of work has been done for many years. I would like to share my points of view for this article as followed.

Introduction

According to the tile, the term “molecular marker network expression” is quite unclear. This must be improved by providing the information and the impact of this matter in the introduction section.

Materials and Methods

1. There is the repeated sentence in 2.3, “Ten extreme lines were selected for each agronomic trait, gene pools were established, and differential molecular markers were identified”. Please revise.

2. Please clarify how molecular marker network expression has been done.

3. Please clarify how the correlation between molecular marker and traits was performed and how the correlation degrees were calculated.

Results

1. In 3.1 Phenotypic variation and trait distribution of RILs, line 105 – 106 do not make sense according to Table 1. Please recheck the meaning and revise.

2. Figure 1 (b), what is the trait of these data, PL (in graph) or SL (in legend)?

3. Please clarify Table 2 in the result. What are A, B, C? What is the meaning of red and grey colors? What does “code” mean? 89-1 should be written as Gr 89-1 in the table2.

4. Figure 3 does not provide any information to the readers. Please revise and provide more explanation of this impact of these data.

Discussion

The first paragraph does not seem to be related to this work. Please revise.

Comments for author File: Comments.docx

Author Response

Dear reviewer,

Thank you for your comments and suggestions of the manuscript. We revised the manuscript with red and blue colored words in accordance with the reviewer’s comments, and carefully proof-read. After careful consideration, we absolutely agree with your opinion. The following are the point-by-point responses:    

Response to Reviewer #1 Comments

Introduction:

1. According to the tile, the term “molecular marker network expression” is quite unclear. This must be improved by providing the information and the impact of this matter in the introduction section.

Response 1: We have added relevant content to explain the problem. (Line 45-46)

Materials and Methods:

1. 1.There is the repeated sentence in 2.3, “Ten extreme lines were selected for each agronomic trait, gene pools were established, and differential molecular markers were identified”. Please revise.

Response 1: We have deleted the redundant sentences (Line 68)

2. Please clarify how molecular marker network expression has been done.

Response 2: The F₉ generation recombination inbred line population of 309 lines constructed by crossing Gr 89-1 with Shuhui 527 was used to select 10 extreme lines of eight agronomic traits, including plant height, panicle length, grain number per panicle, seed setting rate, thousand-grain weight, flag leaf length, grain length and grain width, respectively, to establish a gene pool. Different molecular markers were graded according to the number of which showed polymorphism in the eight agronomic traits, then 309 F₉-generation RILs were tested by the gradient molecular markers. According to the test results, the corresponding relationship between molecular markers and agronomic traits was clarified, and the relationship was displayed by the network diagram.

3. Please clarify how the correlation between molecular marker and traits was performed and how the correlation degrees were calculated.

Response 3: Correlations between molecular markers and traits were analyzed by the number of total markers of each level versus the number of associated markers of the corresponding level for each agronomic trait. The correlation degrees were calculated as follows:

 

Results:

1. In 3.1 Phenotypic variation and trait distribution of RILs, line 105 – 106 do not make sense according to Table 1. Please recheck the meaning and revise.

Response 1: We have revised the manuscript in accordance with the reviewer’s comments. (Line 102-109)

2. Figure 1 (b), what is the trait of these data, PL (in graph) or SL (in legend)?

Response 2: Figure1 (b) represents the distribution of panicle length at multiple points and years. The “SL” in the legend has been changed to “PL”. (Line 117)

3. Please clarify Table 2 in the result. What are A, B, C? What is the meaning of red and grey colors? What does “code” mean? 89-1 should be written as Gr 89-1 in the table2.

Response 3: The “A”, “B”, and “C” in Table 2 represent the molecular markers ^aRM85，^aRM274 and ^aRM5414, respectively. The gray, red, and black boxes denote the genotype of Gr 89-1, shuhui527, and heterozygote, respectively. The "code" represents the field planting code. These have been marked at the lower end of the table2. And the “89-1” has been changed to “Gr 89-1”. (Line 140-141)

4.Figure 3 does not provide any information to the readers. Please revise and provide more explanation of this impact of these data.

Response 4: The network diagram expressed correspondence between the eight agronomic traits and the eight graded molecular markers (Figure 3). The 3 first-level markers showed polymorphism in all eight agronomic traits. As the level of markers increased, fewer agronomic traits showed polymorphism in each molecular marker. in the eighth-level markers, only one agronomic trait showed polymorphism in each molecular marker.

Discussion:

1. The first paragraph does not seem to be related to this work. Please revise.

Response 1: We have made a lot of changes to the first paragraph(Line 185-197)

 

Thanks very much!

Yours sincerely,

Lu Gan, Zhengwu Zhao

Author Response File: Author Response.docx

Reviewer 2 Report

Dear Authors,

MS needs improvement before acceptance, general points needs attention are listed below and for specific comment please see the sticky notes in pdf file.

1)      The materials and methods section needs slight modifications as per suggestion

2)      The results required some clarification for fig 2 and fig 3. Table 4 need a look for its completion.

3)      Discussion section should be improved by aligning with the results.

Author Response

Dear reviewer,

Thank you for your comments and suggestions of the manuscript. We revised the manuscript with red and blue colored words in accordance with the reviewer’s comments, and carefully proof-read. After careful consideration, we absolutely agree with your opinion. The following are the point-by-point responses:    

Response to Reviewer #2 Comments

1.The materials and methods section needs slight modifications as per suggestion

    Response 1: We have revised this part.(Line 65-82) 

2. The results required some clarification for fig 2 and fig 3. Table 4 need a look for its completion.

Response 2: We have required this part for fig 2(Line 120-127) and fig 3(Line 150-155) The network expression relationship map was constructed to explain correspondence between agronomic traits and molecular markers. The 3 first-level markers showed polymorphism in all eight agronomic traits with corresponding network lines. As the level of markers increased, fewer agronomic traits showed polymorphism in each molecular marker. In the eighth-level markers, only one agronomic trait showed polymorphism in each molecular marker, and there was a single network line between markers and agronomic traits, which corresponded one to one( Figure 3).

Table 4  Correlations between molecular markers and traits were analyzed by the number of total markers of each level versus the number of associated markers of the corresponding level for each agronomic trait. The correlation degrees were calculated as follows:

 

3. Discussion section should be improved by aligning with the results.

 Response 3: We have required this part(Line 185-197) 

 

Thanks very much!

Yours sincerely,

Lu Gan, Zhengwu Zhao

Author Response File: Author Response.docx

Reviewer 3 Report

Dear Prof. Dr. Editor of Agronomy Journal,

 

I write you regarding Manuscript Number: agronomy-2005274 entitled "Study on Phenotypic Variation and Molecular Marker Network Expression of Agronomic Traits in Gr 89-1 / Shuhui 527 RILS " which was submitted to the Agronomy journal.

In this manuscript, the authors studied the Phenotypic Variation and Molecular Marker Network Expression of Agronomic Traits in Gr 89-1 / Shuhui 527 RILS. The manuscript is suitable for publication in Agronomy.

I have gone through this work. My decision is accepted with minor revisions for this work. The reason for that is as follows:

The manuscript deals with " Phenotypic Variation and Molecular Marker Network Expression of Agronomic Traits in Gr 89-1 / Shuhui 527 RILS.

 I hope explain the allele size of promising markers used for these 8 traits that may be used as markers assisted  selection.

First: Title: It should change to the following:

1)  Phenotypic Variation and Molecular Marker Network Expression of Some Agronomic Traits in Rice (Oryza sativa L.) RILS of Gr 89-1 x Shuhui 527

 

Second Abstract, keywords and Introduction:

2) has some minor corrections as in the attached file.

 

Third: The objectives of the study

3) is ok.

 

Fourth: Materials and Methods

4) has some minor corrections as in the attached file.

 

Results and discussion

5)  has some minor corrections as in the attached file.

 

References

6) Please remove the Journal name from the beginning of all references. It has some minor corrections as in the attached file.

 

Thank you for suggesting me as a reviewer for this paper.

 

with best regards

 

Comments for author File: Comments.pdf

Author Response

Dear reviewer,

Thank you for your comments and suggestions of the manuscript. We revised the manuscript with red and blue colored words in accordance with the reviewer’s comments, and carefully proof-read. After careful consideration, we absolutely agree with your opinion. The following are the point-by-point responses:    

Response to Reviewer #3 Comments

First:Title: It should change to the following: 

1) Phenotypic Variation and Molecular Marker Network Expression of Some Agronomic Traits in Rice (Oryza sativa L.) RILS of Gr 89-1 x Shuhui 527

 Response 1: We have revised the Title in accordance with the reviewer’s comments. (Line 1-3)

Second ：Abstract, keywords and Introduction:

2) has some minor corrections as in the attached file. 

Response 2: Abstract: We have changed “glutinnous” to “Glutinous”. (Line 9)

Keywords: Since the first letters of keywords are lowercase in articles published in the journal Agronomy, no changes have been made. 

Introduction:

We have changed “select for superior” to “select superior”. (Line 36)

We have changed “(Oryza sativa L.)” to “(Oryza sativa L.)”. (Line 43)

Third: The objectives of the study

3) is ok.

Response 3: Thank reviewer very much for your approval of the article.

Fourth: Materials and Methods

4) has some minor corrections as in the attached file.

Response 4: We have changed “by the only” to “by only”. (Line 78) 

We have changed “among” to “in”. (Line 82)

Results and discussion

5)  has some minor corrections as in the attached file.

Response 5: Results:

“110.85-123.09 cm” is shown in Figure 1a, the plant height of 309 lines is divided into 10 intervals from low to high, and then the interval with a relatively concentrated number of distributed trees (i.e. 110.85-123.09 cm) is counted.   

We have added a space in the middle of “0.783and”. (Line 93) 

We have changed “different years and different locations” to “different years and locations in F₉ RILs of Gr 89-1 x Shuhui 527”. (Line 98)

We have changed “(Figure 1(a))” to “(Figure 1a)”, and changed “(Figure 1(b))” to “(Figure 1b)”, and changed “(Figure 1(c))” to “(Figure 1c)”, and changed “(Figure 1(d))” to “(Figure 1d)”, and changed “(Figure 1(e))” to “(Figure 1e)”, and changed “(Figure 1(f))” to “(Figure 1f)”, and changed “(Figure 1(g))” to “(Figure 1g)”, and changed “(Figure 1(h))” to “(Figure 1h)”. (Line 104-109)

We have changed “traits” to “traits in F₉ RILs of Gr 89-1 x Shuhui 527”. (Line 116)

We have changed “/” to “x”. (Line 136-138)

We have changed “markers” to “markers in F₉ RILs of Gr 89-1 x Shuhui 527”. (Line 143-144)

We have changed “/” to “x”. (Line 185)

Discussion: 

We have made a lot of changes to the first paragraph.(Line 185-197)

References

6) Please remove the Journal name from the beginning of all references. It has some minor corrections as in the attached file.

Response 6: We have revised the manuscript in accordance with the reviewer’s comments and format of Agronomy journal .(Line 248-350)

 

Thanks very much!

Yours sincerely,

Lu Gan, Zhengwu Zhao

Author Response File: Author Response.docx

Reviewer 4 Report

Dear Sir

I study the article Study on Phenotypic Variation and Molecular Marker Network 2 Expression of Agronomic Traits in Gr 89-1 / Shuhui 527 RILS. This article has actually investigated the relationship between molecular markers and agricultural traits based on the single marker analysis method. This method is the first method introduced to investigate such relationships. This method had some problems that were later solved by other methods (interval mapping, composite interval mapping, inclusive composite interval mapping, and genome-wide composite interval mapping, recently). If these methods are also investigated, I recommend this article for further investigation. For this, I suggest this paper for study. https://doi.org/10.1016/j.csbj.2019.11.005, But currently, the article does not have the quality data analysis

Regards

Author Response

Only three reviewers

Round 2

Reviewer 4 Report

This article has actually investigated the relationship between molecular markers and agricultural traits based on the single marker analysis method. This method is the first method introduced to investigate such relationships. This method had some problems that were later solved by other methods (interval mapping, composite interval mapping, inclusive composite interval mapping, and genome-wide composite interval mapping, recently). If these methods are also investigated, I recommend this article for further investigation. For this, I suggest this paper for study. https://doi.org/10.1016/j.csbj.2019.11.005, But currently, the article does not have the quality data analysis

Author Response

Dear reviewer,

Thank you for your comments and suggestions of the manuscript. We revised the manuscript with red and blue colored words in accordance with the reviewer’s comments, and carefully proof-read. After careful consideration, we absolutely agree with your opinion. The following are the point-by-point responses:    

Response to Reviewer #4 Comments

This article has actually investigated the relationship between molecular markers and agricultural traits based on the single marker analysis method. This method is the first method introduced to investigate such relationships. This method had some problems that were later solved by other methods (interval mapping, composite interval mapping, inclusive composite interval mapping, and genome-wide composite interval mapping, recently). If these methods are also investigated, I recommend this article for further investigation. For this, I suggest this paper for study. https://doi.org/10.1016/j.csbj.2019.11.005, But currently, the article does not have the quality data analysis

Response : According to the comments of the reviewers, we carefully read the "QTL.gCIMapping.GUI v2.0: An R software for detecting small-effect and linked QTLs for quantitative traits in bi-parental segregation populations" article, consulted the relevant literature, made a lot of amendments to the first paragraph of the discussion, and added 4 references.

 

 

Thanks very much!

Yours sincerely,

Lu Gan, Zhengwu Zhao

Author Response File: Author Response.docx