QTL Mapping for Seed Quality Traits under Multiple Environments in Soybean (Glycine max L.)
Round 1
Reviewer 1 Report
For the visibility of the article by the researchers, the Latin of soybean should be added to the title.
The summary is very short and can be elaborated a little.
In the first paragraph of the introduction, a few sentences should be written about the world production value of soybeans.
line 35: add literature to the first sentence of the second paragraph.
In the introduction, long sentences that are difficult to understand were preferred. In addition, most sentences do not use references.
Line 59: In this paragraph, write the full expansion where the abbreviations are first used. For example RFLP.
Line 138: Write down the specifications of the SPSS package program, such as the manufacturer, country, etc.
The correlation analysis made in the parameters examined in Table 1 and given in Figure 2 should be given as an understandable table.
What program was the QTL map drawn with? please explain in detail.
It is insufficient to use only 29 references in an article with so much data.
Take a look at the bibliography. Generally, studies in far eastern countries are given as reference.
Author Response
For the visibility of the article by the researchers, the Latin of soybean should be added to the title.
Reply: Corresponding changes have been made in the article
The summary is very short and can be elaborated a little.
Reply: Corresponding changes have been made in the article
In the first paragraph of the introduction, a few sentences should be written about the world production value of soybeans.
Reply: The relevant information has been consulted and referenced in the article
line 35: add literature to the first sentence of the second paragraph.
Reply: The relevant literature has been consulted and quoted in the article
Singh, P., Kumar, R., Sabapathy, S.N., and Bawa, A.S. Functional and edible uses of soy protein products. Compr. Rev. Food Sci. Food Saf. 2008, 7, 14–28.doi: 10.1111/j.1541-4337.2007.00025.x
In the introduction, long sentences that are difficult to understand were preferred. In addition, most sentences do not use references.
Reply: Amendments have been made as required
Line 59: In this paragraph, write the full expansion where the abbreviations are first used. For example RFLP.
Reply: Corresponding changes have been made in the article
Line 138: Write down the specifications of the SPSS package program, such as the manufacturer, country, etc.
Reply: The SPSS® Statistics 24 used in this paper is a data mining software developed by IBM®, an American company.
The correlation analysis made in the parameters examined in Table 1 and given in Figure 2 should be given as an understandable table.
Reply: Heatmap of this correlation, the numbers in the upper right part are the correlation coefficients between the individual quality traits, the colours indicate the degree of correlation and the lower left part indicates its significance. Currently, there are a large number of studies whose correlation analyses are represented by heat maps
Cardoni, M., Mercado-Blanco, J., and Villar, R. Functional Traits of Olive Varieties and Their Relationship with the Tolerance Level towards Verticillium Wilt. Plants 2021, 10, 1079.
Hu, L., Luo, G., Zhu, X., Wang, S., Wang, L., Cheng, X., and Chen, H. Genetic Diversity and Environmental Influence on Yield and Yield-Related Traits of Adzuki Bean (Vigna angularis L.). Plants 2022, 11, 1132.
What program was the QTL map drawn with? please explain in detail.
Reply: The graphic representation of the linkage groups were created using MapChart 2.0
It is insufficient to use only 29 references in an article with so much data.
Take a look at the bibliography. Generally, studies in far eastern countries are given as reference.
Reply: Subsequently, a number of references were reviewed and included in the article.
Reviewer 2 Report
The authors performed a QTL mapping project for soybean seed quality traits in multiple environments and got valuable results. The manuscript is worth publishing in the Agronomy Journal. However, the manuscript has the following minor and major concerns before acceptance of the article for publication.
Abstract: Please add R2 (coefficient of determination) for the major or important QTLs
Keywords: Keywords should be in alphabetical order and different from title words.
Introduction
Lines 27-31: The used Reference is old (2009). Please use the latest statistics from FAO
Material and methods:
Lines 100-105:
Please note we can use the Fx:y population for QTL mapping. which x is the used generation for constructing the genetic map and y is the used generation for phenotyping. You used this population for QTL mapping and the cultivated generations in the field are F3, F4 not F2:3, or F2:4.
Results:
Figure 1: Please add the parents’ position on the frequency charts. Segregation distortion would be visible easily.
Table 2: Why Gen.Env interaction is missing? It is so important in ANOVA
All Figures and Tables: Each separate table/figure should 'stand alone', according to scientific writing rules.
Please add more information about the plant name! marker type and number of primers etc
Please perform for all Tables and Figures
Lines 210-212: Please move to the material and method section!
Table 3 and in the text: The second number in the QTL names, only when it is needed that you have more than one QTL on the Chromosome. When you have only one QTL you must mention only the first number=Chr. number
For example, qOIL01.1 indicates you have more than 1 QTL on chromosome 1 and the reader expects to see the next one!!
Line 247: Please rewrite.
Line 250: Please add the R2 value here in the parenthesis.
Reference: References should be adjusted according to the format of the Agronomy Journal. For example, the Abbreviated Journal name must be Italic and the year should be bold.
Comments for author File: 
Comments.pdf
Minor editing of English language required
Author Response
Abstract: Please add R2 (coefficient of determination) for the major or important QTLs
Reply: PVE in this article is the R2 mentioned, that is, the phenotypic contribution rate, and has been modified in the abstract to solve this problem
Keywords: Keywords should be in alphabetical order and different from title words.
Reply: The keywords in this article are sorted according to the order of research
Introduction
Lines 27-31: The used Reference is old (2009). Please use the latest statistics from FAO
Reply: Statistical data from the FAO has been added later in the article.
Material and methods:
Lines 100-105:
Please note we can use the Fx:y population for QTL mapping. which x is the used generation for constructing the genetic map and y is the used generation for phenotyping. You used this population for QTL mapping and the cultivated generations in the field are F3, F4 not F2:3, or F2:4.
Reply: The purpose of writing F2:3 and F2:4 in this paper is to make it clear that the mapping population in this study is selected by F2 generation single plant. The phenotypic data of F2:3 and F2:4 in this article were the average values of several seeds randomly selected from each lines F2:3 and F2:4 for phenotypic detection, respectively, which can be corresponding to the phenotypic data of single plant F2.
Results:
Figure 1: Please add the parents’ position on the frequency charts. Segregation distortion would be visible easily.
Reply: Corresponding changes have been made in the article
Table 2: Why Gen.Env interaction is missing? It is so important in ANOVA
Reply: Sorry, no repeated tests were carried out for the determination of phenotypic traits in this study, and the experimental design will definitely pay attention to this problem in the future.
All Figures and Tables: Each separate table/figure should 'stand alone', according to scientific writing rules.
Reply：We are also concerned about this problem，in our opinion, these issues will correct after typesetting.
Please add more information about the plant name! marker type and number of primers etc. Please perform for all Tables and Figures
Reply: The genetic map used in this experiment was constructed by laboratory predecessors and has been described in the paper. Details of the number and types of primers can be found in the following paper
Jiang A, Liu J, Gao W, Ma R, Tan P, Liu F and Zhang J (2023), Construction of a genetic map and QTL mapping of seed size traits in soybean. Front. Genet. 14:1248315. doi: 10.3389/fgene.2023.1248315
Lines 210-212: Please move to the material and method section!
Reply: This part of the expression has been described in the previous section on materials and methods, so it has been deleted
Table 3 and in the text: The second number in the QTL names, only when it is needed that you have more than one QTL on the Chromosome. When you have only one QTL you must mention only the first number=Chr. Number
For example, qOIL01.1 indicates you have more than 1 QTL on chromosome 1 and the reader expects to see the next one!!
Reply: The nomenclature of the qtl in this study is based on previous research.
Hina, A., Cao, Y., Song, S., Li, S., Sharmin, R. A., Elattar, M. A., et al. (2020). High-resolution mapping in two RIL populations refines major QTL “hotspot” regions for seed size and shape in soybean (Glycine max l.). Int. J. Mol. Sci. 21 (3), 1040. doi: 10.3390/ijms21031040
Kumar, R., Saini, M., Taku, M., Debbarma, P., Mahto, RK., Ramlal, A., Sharma, D., Rajendran, A., Pandey, R., Gaikwad, K., Lal, SK., and Talukdar, A. (2023) Identification of quantitative trait loci (QTLs) and candidate genes for seed shape and 100-seed weight in soybean [Glycine max (L.) Merr.]. Front. Plant Sci. 13:1074245. doi: 10.3389/fpls.2022.1074245
Line 247: Please rewrite.
Reply: Corresponding changes have been made in the article
Line 250: Please add the R2 value here in the parenthesis.
The PVE mentioned in this article is R2, that is, the phenotypic contribution rate, which has been indicated in Table 3 and Table 4.
Reference: References should be adjusted according to the format of the Agronomy Journal. For example, the Abbreviated Journal name must be Italic and the year should be bold.
Reply: Changes and adjustments have been made as required.
Reviewer 3 Report
In line 184, ‘environment’ should be ‘environments’.
I table, the p-value for F-statistic is better to be added.
The authors mentioned multiple-QTL model (MQM) mapping method was adopted in this study. The related references for this method should be added. Please explain why this method was used. There are many QTL mapping methods (e.g. CIM and ICIM). Do you think if it is better to include more mapping methods in the analysis?
There are many grammar errors in the paper. Please correct them.
In line 195, the authors wrote “indicating that suitable varieties can be selected according to this law in breeding”. I am confused about it. Is there any analysis based on this law? Are there any results that give evidence to it?
Moderate editing of English language required.
Author Response
In line 184, ‘environment’ should be ‘environments’.
Reply: Corresponding changes have been made in the article
I table, the p-value for F-statistic is better to be added.
Reply: Thank you for your suggestion. The addition of * to the F value of the difference analysis in the article means its significance
The authors mentioned multiple-QTL model (MQM) mapping method was adopted in this study. The related references for this method should be added. Please explain why this method was used. There are many QTL mapping methods (e.g. CIM and ICIM). Do you think if it is better to include more mapping methods in the analysis?
Reply: A multiple-QTL mapping approach is expected to increase detection power, enable separation of linked QTL, and provide the basis for studying QTL interaction (epis.tasis).
Pereira, G., da, S., Gemenet, D. C., Mollinari, M., Olukolu, B. A., Wood, J. C., et al. (2020). Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-Sib population. Genetics 215, 579–595. doi: 10.1534/genetics.120.303080.
There are many grammar errors in the paper. Please correct them.
Reply: Grammar errors and other issues have been corrected in the article
In line 195, the authors wrote “indicating that suitable varieties can be selected according to this law in breeding”. I am confused about it. Is there any analysis based on this law? Are there any results that give evidence to it?
Reply: The literature listed below is a selection of studies on target traits based on correlations between certain quality traits.
Cober, E. R., and D Voldeng, H. Developing High-Protein, High-Yield Soybean Populations and Lines. Crop Science, 2000.40(1), 39. doi:10.2135/cropsci2000.40139x
Kim Hyun Tae., Ko Jong Min., Baek In Youl., Jeon Meong Ki., and Han Won Young, et al.Soybean Cultivar for Tofu, ‘Saedanbaek’ with Disease Resistance, and High Protein Content. Korean Journal of Breeding Science 46.3(2014). doi:10.9787/kjbs.2014.46.3.295.
Shi, Z., Bachleda, N., Pham, A. T., Bilyeu, K., Shannon, G., Nguyen, H., and Li, Z. (2015). High-throughput and functional SNP detection assays for oleic and linolenic acids in soybean. Molecular Breeding, 35(8). doi:10.1007/s11032-015-0368-4.
Round 2
Reviewer 1 Report
Ms is ready for publication
