Historical Trends Analysis of Main Agronomic Traits in South China Inbred Indica Rice Varieties since Dwarf Breeding

Round 1

Reviewer 1 Report

The study is devoted to the actual problem of the elements of productivity of indica rice in South China. It is a very interesting retrospective analysis of the evolution of the yield structure of rice varieties since the 1960s during the selection of dwarf varieties.

A comprehensive study has been undertaken: 19 (in fact 18) quantitative traits of 231 rice genotypes of different years of breeding in three geographical locations have been studied in 2017. One-factor analysis of variance, correlation and travel analysis for each point was used. The directions of improving the model of a higher grade for obtaining a higher yield are formulated. The conclusions are mainly supported by the research materials.

Comments to the methodology

It is not shown whether the results differ significantly in 3 locations, and why they are different. For each indicator a two-way ANOVA is needed by the period of variety breeding and location. If the locations are just repetitions to demonstrate the basic idea of the difference in the breeding periods, then the data on the locations should be averaged. It is necessary to compare the vegetation conditions in locations in the Materials – soil, temperature, precipitation.

The disadvantage of the article is the heaviness of the presentation results in five huge tables. They should be simplified and visualized in the form of figures. If authors average the data by study points, they can reduce Tables 1-4 into one. The authors themselves mix the dynamics of traits in three locations  (see below) and do not explain them in any way even once.

Comparison of the degree of variability of heading time (3.1.1. Heading date) not confirmed quantitatively. Meanwhile, there are criteria for the reliability of the difference in standard deviations. The range of variability is not discussed anyway in the text and seems superfluous in Tables 1-4.

Minor remarks

Line 25: please decipher the abbreviation International Rice Research Institute (IRRI)

Line 82: please change the dot to a comma

Line 97: please change south China → South China

Line 120: the seed setting rate (SSR) mentioned only once in text, and does not play any role, thus, there are 18 variables in consideration, not 19.

Line 123:”thousand grain weight (TGW), grain length (GL), grain width (GW), and length-to-width ratio (LWR)" – repeat, these traits was in the Lines 121-122.

Lines 137-145: various patterns of HD dynamics in different locations are not explained in any way.

There are discussions of traits trends, when in fact there are no significant differences, please to check everything. For example: Lines 143-144: “the heading days of variations from different decades show a decreasing-then-increasing trend in Pingxiang, while the differences in heading days are not significant in Shenzhen” – incorrect, in Pingxiang there are no significant differences between decades, and in Shenzhen there are; Lines 153-155: “As for the flag leaf area (FLA), it showed a significant decrease only under the conditions of Pingxiang, while varying degrees of increase were observed in Shenzhen and Sanya (Table 1)” - wrong, there is no reliable trend in Pingxiang and Sanya.

Line 156, figure 2: Why do the numbers of accessions in groups of different years of breeding differ from location to location? Why in Fig. 2C 37 landrace genotypes (4+14+18+1=37), if it was originally 36? What is the letter A in Fig. 2B? The figure title is out of place.

Line 159, Table 1. Please indicate what the same letters mean, are they homogeneous groups within each location, or the differences between locations also taken into account?

Line 186, table 2: typo “GD (/cm)”

Line 235: an absolutely incomprehensible representation of the correlation coefficients – in two points in the huge Table 5, in one in the Fig.3. In any case, please to indicate in the table titles, not in notes, where which locations are presented. It is necessary to present all three points equally, in the form of figures like Fig. 3, and explain the differences between the points in the correlation coefficients. If the differences are random, it is better to average the traits on three points and draw one figure with correlations. In Fig.3 it is better to arrange the variables as in Table 5, so that GY comes last.

Line 244: “the regression coefficients" → “The regression coefficients”.

Lines 244-245: “F(PX) = 573.35, F(SZ) = 424.48, F(SY) = 963.99" – what is it? If the value of the test, then you need to specify the critical level. Abbreviated designations of locations should be entered before this phrase.

Author Response

To Reviewer1

The study is devoted to the actual problem of the elements of productivity of indica rice in South China. It is a very interesting retrospective analysis of the evolution of the yield structure of rice varieties since the 1960s during the selection of dwarf varieties.

A comprehensive study has been undertaken: 19 (in fact 18) quantitative traits of 231 rice genotypes of different years of breeding in three geographical locations have been studied in 2017. One-factor analysis of variance, correlation and travel analysis for each point was used. The directions of improving the model of a higher grade for obtaining a higher yield are formulated. The conclusions are mainly supported by the research materials.

Comments to the methodology

It is not shown whether the results differ significantly in 3 locations, and why they are different. For each indicator a two-way ANOVA is needed by the period of variety breeding and location. If the locations are just repetitions to demonstrate the basic idea of the difference in the breeding periods, then the data on the locations should be averaged. It is necessary to compare the vegetation conditions in locations in the Materials – soil, temperature, precipitation.

R: Thanks for your constructive suggestions, and we have performed a two-way ANOVA for each trait separately by decade across three locations. The result has been uploaded as supplementary Table S6, and description of the relevant result has been added to the revised manuscript (Lines 347-354).

The disadvantage of the article is the heaviness of the presentation results in five huge tables. They should be simplified and visualized in the form of figures. If authors average the data by study points, they can reduce Tables 1-4 into one. The authors themselves mix the dynamics of traits in three locations (see below) and do not explain them in any way even once.

R: Thanks for your helpful suggestions, and the Tables 1-4 in the original manuscript have been converted into Figures 3-6 in the revised manuscript. Besides, we performed a two-way ANOVA for each trait and explained the results in the revised manuscript. (Lines 347-351)

Comparison of the degree of variability of heading time (3.1.1. Heading date) not confirmed quantitatively. Meanwhile, there are criteria for the reliability of the difference in standard deviations. The range of variability is not discussed anyway in the text and seems superfluous in Tables 1-4.

R: We totally agree with you, the statement is original draft was inappropriate. So, we have rephrased that in the revised manuscript. (Lines 219-224)

Minor remarks

Line 55: please decipher the abbreviation International Rice Research Institute (IRRI)

Line 82: please change the dot to a comma

Line 97: please change south China → South China

Line 120: the seed setting rate (SSR) mentioned only once in text, and does not play any role, thus, there are 18 variables in consideration, not 19.

Line 123: thousand grain weight (TGW), grain length (GL), grain width (GW), and length-to-width ratio (LWR)" – repeat, these traits was in the Lines 121-122.

R: Thanks for careful review. We have corrected the errors you mentioned above in the revised manuscript.

Lines 137-145: various patterns of HD dynamics in different locations are not explained in any way.

R: We have explained this results in “Results” (Lines 224-227) and “Discussion” (Lines 527-534) in the revised manuscript.

There are discussions of traits trends, when in fact there are no significant differences, please to check everything. For example: Lines 143-144: “the heading days of variations from different decades show a decreasing-then-increasing trend in Pingxiang, while the differences in heading days are not significant in Shenzhen” – incorrect, in Pingxiang there are no significant differences between decades, and in Shenzhen there are; Lines 153-155: “As for the flag leaf area (FLA), it showed a significant decrease only under the conditions of Pingxiang, while varying degrees of increase were observed in Shenzhen and Sanya (Table 1)” - wrong, there is no reliable trend in Pingxiang and Sanya.

R: Thank you for careful review. We have checked the whole text thoroughly and redescribed them in the revised manuscript. (Lines 219-224; Lines 263-266)

Line 156, figure 2: Why do the numbers of accessions in groups of different years of breeding differ from location to location? Why in Fig. 2C 37 landrace genotypes (4+14+18+1=37), if it was originally 36? What is the letter A in Fig. 2B? The figure title is out of place.
R: We apologize for our carelessness and thanks for pointing out these errors. We have checked the raw data and updated the Figure 2 in the revised manuscript. Additionally, we have uploaded the raw data of phenotype for 231 rice accessions as supplementary Table S5 in the new submission.

Line 159, Table 1. Please indicate what the same letters mean, are they homogeneous groups within each location, or the differences between locations also taken into account?

R: Tables 1-4 in the original draft have been converted into histograms in the revised manuscript (see Figure 3-6), and different letters next to the bar chart denote significant difference among decades by Duncan’s multiple range test within each location.

Line 186, table 2: typo “GD (/cm)

R: We have changed it and checked the full text.

Line 235: an absolutely incomprehensible representation of the correlation coefficients – in two points in the huge Table 5, in one in the Fig.3. In any case, please to indicate in the table titles, not in notes, where which locations are presented. It is necessary to present all three points equally, in the form of figures like Fig. 3, and explain the differences between the points in the correlation coefficients. If the differences are random, it is better to average the traits on three points and draw one figure with correlations. In Fig.3 it is better to arrange the variables as in Table 5, so that GY comes last.

R: Thanks for your helpful suggestions. We have uploaded the correlation coefficients between 18 traits in Pingxiang, Shenzhen and Sanya as supplementary tables (see Tables S7-S9). Additionally, the average phenotype of each trait across three different locations was used to analyze the correlation coefficients, which was shown in Figure 7, and the GY comes last in the revised manuscript.

Line 244: “the regression coefficients" → “The regression coefficients”.

R: We have changed it and checked the full text.

Lines 244-245: “F(PX) = 573.35, F(SZ) = 424.48, F(SY) = 963.99" – what is it? If the value of the test, then you need to specify the critical level. Abbreviated designations of locations should be entered before this phrase.

R: It’s the significance testing for multiple linear regression by F-test. We have redescribed it in the revised manuscript. (Lines 418-421)

 

Reviewer 2 Report

The authors used and phenotyped 231 indica rice varieties in South China in three locations.  Although the shifts of phenotypes were observed, the manuscript and the authors’ intention or claim is very hard for me.  I feel that there is a divergence between the results and discussion in this manuscript.

 

“Evolution” in the title is probably inapproptiate.  I think that the period from landrace group to modern varieties is breeding.  Rice evolution usually indicates the domestication from wild rice to landrace group and the breeding to develop modern cultivars.

 

Tables 1 to 4 and 6 should be convert to Figures.  Much data in Tables makes me very very hard to make sense.  I recommend these Tables are as supplementary tables.  

Figure 3 and Table 5 are also hard to watch and understand.

 

For results or discussion in this manuscript, I request the pattern diagram for the associations among the phenotypes.  Also I request another supplementary table for list of cultivars or varieties and all phenotypes.

 

Did the authors conduct English proofreading?

Did the authors conduct English proofreading?  Did the editor receive the certificate for English proofreading?

Author Response

To Reviewer 2:

The authors used and phenotyped 231 indica rice varieties in South China in three locations.  Although the shifts of phenotypes were observed, the manuscript and the authors’ intention or claim is very hard for me.  I feel that there is a divergence between the results and discussion in this manuscript.

R: Thanks for your review. We made a retrospective analysis of the historical trend of the yield structure of rice varieties since the 1960s during the selection of dwarf varieties in “Results”. In “Discussion”, we discussed and explained the historical trend of the important breeding traits, and we formulated the directions of improving the model of a higher grade for obtaining a higher yield in South China based on our research.

 “Evolution” in the title is probably inapproptiate.  I think that the period from landrace group to modern varieties is breeding.  Rice evolution usually indicates the domestication from wild rice to landrace group and the breeding to develop modern cultivars.

R: We totally agree with you. So, we have changed the title to “Analysis on the Historical Trends of Main Agronomic Traits of Inbred Indica Rice Varieties Since Dwarf Breeding in South China”.

 Tables 1 to 4 and 6 should be convert to Figures.  Much data in Tables makes me very very hard to make sense.  I recommend these Tables are as supplementary tables.  

Figure 3 and Table 5 are also hard to watch and understand.

R: Thanks for your helpful suggestions. Tables 1 to 4 have been simplified and visualized in the form of figures (Figures 3 to 6), and the original tables have been uploaded as Table S3-S6 in the revised manuscript. In original draft, Figure 3 has Table 5 showed the correlation coefficient between 18 traits in Pingxiang, Shenzhen and Sanya. In the new submission, we have separately uploaded the correlation coefficients in three locations in supplementary Table S7-9. Additionally, considering there was no differences between the locations in the correlation coefficients, the average phenotype of each trait across three different locations was used to analyze the correlation coefficients, which was shown in Figure 7 in the revised manuscript.

 For results or discussion in this manuscript, I request the pattern diagram for the associations among the phenotypes.  Also I request another supplementary table for list of cultivars or varieties and all phenotypes.

R: Thanks for the reminder. We have performed a two-factor ANOVA and estimate broad sense heritability for each trait separately by decade (Table S6).

In the new submission, we have uploaded supplementary Table S5, in which, all phenotype of 18 agronomic traits of 231 rice accessions across three locations was included.

Did the authors conduct English proofreading?

R: we have invited an English-speaking expert in this field to polish the language and we have proofread the full text.

Round 2

Reviewer 1 Report

A few small comments are given in the attached text

Comments for author File: Comments.pdf

Author Response

1. Line 84, “19 agronomic traits” should be changed into “18 agronomic traits”.

R: Thanks very much for your careful review, we have changed it and checked the full text.

2. Line111, how about temperature and precipitation conditions during vegetation?

R: We have added more information about these three ecological regions (Lines 113-114, Lines 117-118), besides we have uploaded the temperature and precipitation conditions as supplementary Table S1 in the new submission.

3. Line 131, There is no SD in this version of main text, only in Supplements.

R: We have rephrased the sentence in the revised manuscript. (Lines 135-137)

4. Line 154, The figure title is out of place.

R: We have changed it (Line 164).

 

 

Reviewer 2 Report

I think the revised version is improved.  For Table S5, English names for variety names are required.

Author Response

I think the revised version is improved.  For Table S5, English names for variety names are required.

R: Thank you very much for the careful review, and we have added the English names for these rice varieties in the new submission.