Impact of Allelic Variation in Maturity Genes E1–E4 on Soybean Adaptation to Central and West Siberian Regions of Russia

Round 1

Reviewer 1 Report (New Reviewer)

Dear Authors

The manuscript entitled: Impact of Allelic Variation of Maturity Genes E1–E4 to 2 Soybean Adaptation to Central and West Siberian regions of 3 Russia represents good work and interesting information, offering valuable insights in soybean research. However, there are a few minor suggestions that need to be addressed:

Comparison with European germplasm: Considering the significant geographical distance of the locality (Novosibirsk and Orel) discussed in your manuscript, it would be interesting to make a comparison with European germplasm. This would provide a broader perspective on soybean adaptability and enhance the significance of your findings. We encourage you to explore the available literature and include relevant publications that support your research.

It is suggested incorporating the contents of Supplement 3 into Supplement 1. This consolidation would streamline the supplementary materials and improve the overall organization of your manuscript.

I recommend adding the classification of genotypes in accordance with Figure 1 to Supplement 1. This addition will provide readers with a comprehensive understanding of the genotypes and their classification, supporting the visual representation provided in the figure. Please ensure that the combined supplement clearly presents the necessary information and supports the findings discussed in Figure 1.

Overall, manuscript is good written, representing interesting topic and provide scientific important data and interpretations related to soybean adaptability and genetic diversity.

Author Response

Dear reviewer,

Thank you very much for your comments and suggestions.

Reviewer: Comparison with European germplasm: Considering the significant geographical distance of the locality (Novosibirsk and Orel) discussed in your manuscript, it would be interesting to make a comparison with European germplasm. This would provide a broader perspective on soybean adaptability and enhance the significance of your findings. We encourage you to explore the available literature and include relevant publications that support your research.

Authors: In the article, we partially compare the frequency of established alleles with European germplasm according to Kursch et al. (2017) (https://doi.org/10.1111/pce.12896). We also know of only one other paper on E1-E4 genotypes in European varieties by Miladvonic et al. (2018) (https://doi.org/10.3389/fpls.2018.01286). But this article focuses on the Serbian germplasm collection from the Institute of Field and Vegetable Growing of Novi Sad, Serbia (IFVCNS) and only contains information about 12 European varieties. We believe that this is not enough for a good comparison.

Reviewer: It is suggested incorporating the contents of Supplement 3 into Supplement 1. This consolidation would streamline the supplementary materials and improve the overall organization of your manuscript.

Authors: We changed Supplement 1 according you suggestion.

Author Response File: Author Response.docx

Reviewer 2 Report (New Reviewer)

Comments to the authors:

Authors have studied the allele variation of soybean E1–E4 genes, both flowering and maturity time under natural day length conditions of Central Russia and Western Siberia in collection of 176 soybean accessions, The results can provide important germplasm materials for breeding local soybean varieties in Russia. The MS should be published after revised.

All my questions about this article are as follows：

1.      Neither the authors nor me are native speaker. However, There are numerous other smaller issues, but it would be easier to address these once this paper is in better shape.

2. in Figure1, authors should add the percentage to each part.

 

 

 Minor editing of English language required

Author Response

Dear reviewer,

Thank you very much for your comments and suggestions.

Reviewer: Neither the authors nor me are native speaker. However, There are numerous other smaller issues, but it would be easier to address these once this paper is in better shape.

Authors: We don't understand the question, please clarify.

Reviewer: in Figure1, authors should add the percentage to each part.

Authors: We added the percentage to each part in our piecharts (Figure1 attached to doc file)

Author Response File: Author Response.docx

Reviewer 3 Report (New Reviewer)

In this study, the authors investigated the allele variation of soybean E1-E4 genes in  collection of 176 soybean accessions, which play a key role in controlling the flowering and maturity time of soybean. It was found that there is a high frequency of previously reported E1-E4 alleles in the accessions and the genotype with all recessive alleles e1-nl/e2/e3/e4 and e1-as/e2/e3/e4 provide an effective adaptation of soybean to the mentioned conditions. However, soybean is a typical photoperiod-sensitive crop, such that photoperiod determines its flowering time, maturity, grain yield, and phenological adaptability. Therefore, it was not convincible that the cultivars with these genotypes are considered to be most suitable for cultivation in Central Russia and Western Siberia, just based on the DTF and DTM. The authors should provide additional field experiment data for the yields traits, such as plant height, the number of nodes and grain weight per plant. I suggest acceptance of the manuscript after the major reversion.

In this study, the authors investigated the allele variation of soybean E1-E4 genes in  collection of 176 soybean accessions, which play a key role in controlling the flowering and maturity time of soybean. It was found that there is a high frequency of previously reported E1-E4 alleles in the accessions and the genotype with all recessive alleles e1-nl/e2/e3/e4 and e1-as/e2/e3/e4 provide an effective adaptation of soybean to the mentioned conditions. However, soybean is a typical photoperiod-sensitive crop, such that photoperiod determines its flowering time, maturity, grain yield, and phenological adaptability. Therefore, it was not convincible that the cultivars with these genotypes are considered to be most suitable for cultivation in Central Russia and Western Siberia, just based on the DTF and DTM. The authors should provide additional field experiment data for the yields traits, such as plant height, the number of nodes and grain weight per plant. I suggest acceptance of the manuscript after the major reversion.

Author Response

Dear reviewer,

Thank you very much for your comments and suggestions.

Reviewer: However, soybean is a typical photoperiod-sensitive crop, such that photoperiod determines its flowering time, maturity, grain yield, and phenological adaptability. Therefore, it was not convincible that the cultivars with these genotypes are considered to be most suitable for cultivation in Central Russia and Western Siberia, just based on the DTF and DTM. The authors should provide additional field experiment data for the yields traits, such as plant height, the number of nodes and grain weight per plant. I suggest acceptance of the manuscript after the major reversion.

Authors: We agree with you that photoperiod affects other traits as well. But, only the maturity time is major trait, limiting the soybean cultivation in different latitude. Only cultivars with the most appropriate maturity time can maximum realize their biological potential in the target region. For example, in our case, in the conditions of Western Siberia, not all varieties can reach maturity before frost damage to seeds. It doesn't matter what other characteristics a variety has if it cannot produce the final product - a seeds. Therefore, we have concentrated our work on maturity time and its component – flowering time. The effect of E1-E4 genes on yields traits is also an interesting issue that requires particular studies. We would like to keep the structure of our article.

Author Response File: Author Response.docx

Round 2

Reviewer 3 Report (New Reviewer)

The authors gave the response in addressing my comments overall.  

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

The authors studied the E gene combinations of soybeans that cultivated in Russian regions.

The results analyzed in this paper provide important information when growing soybeans in high latitudes.

However, there are some mistakes in interpreting the results, and corrections are needed.

1.     DTM data generated from Orel 2022 is not understandable. For example, SNK-282 have 26 DTF and 27 DTM in 2022. I don’t understand how it reached maturity one day after flowering. Some data is reversed. Authors should check again all data from Orel in 2022.

2.     Table 2 and Figure 2 represent the same data differently. So authors should only use one of the two.

3.     Table 3 and Figure 3 represent the same data differently. So authors should only use one of the two.

4.     Both Table 2 and Table 3 or Figure 2 and Figure 3 require statistical analysis.

5.     Authors did two year x two location tests with genotypes. Therefore need to do ANOVA for this.

6.     If authors know pedigree of soybean lines such as Sel. Lines and SNK lines, better add their e gene combination in table S1.

All interpretation and consideration of results should be based on the results of statistical analysis. .

Author Response

Thank you very much for your comments and suggestions.

Reviewer: 1) DTM data generated from Orel 2022 is not understandable. For example, SNK-282 have 26 DTF and 27 DTM in 2022. I don’t understand how it reached maturity one day after flowering. Some data is reversed. Authors should check again all data from Orel in 2022.

Authors: Our mistake, we added and uploaded the correct data in Table S1.

Reviewer: 2) Table 2 and Figure 2 represent the same data differently. So authors should only use one of the two; 3) Table 3 and Figure 3 represent the same data differently. So authors should only use one of the two.

Authors: We removed the tables.

Reviewer: 4) Both Table 2 and Table 3 or Figure 2 and Figure 3 require statistical analysis.

Authors: We do not understand what exact statistical analysis is still needed on the tables and figures. For example, a multiple comparison of genotypes (add on the figure ANOVA/Kruskal Wallis test followed by post hoc test), add additional descriptive statistics for the genotypes (CV, ME, min, max, kurtosis), or something else? We believe that ANOVA is a sufficient statistical analysis for our data. We also made multiple comparisons of genotype (for which this is possible), and the results supported our conclusions. We believe that adding comparison bars to Figures 2 and 3 is redundant. We attach the result of a multiple comparison for the major genotypes e1-nl/e2/e3/e4, e1-as/e2/e3/e4, e1-nl/e2/e3/E4 and e1-as/e2/e3/E4 (in the Word file).

Reviewer: 5) Authors did two year x two location tests with genotypes. Therefore need to do ANOVA for this.

Authors: We added two year x two location test to Table 2.

Reviewer: 6) If authors know pedigree of soybean lines such as Sel. Lines and SNK lines, better add their e gene combination in table S1.

Authors: Unfortunately, we do not know the exact pedigree of the lines. In part, we are going to shed light on this issue in our future work using SNP array data.

Author Response File: Author Response.docx

Reviewer 2 Report

The study investigated the impact of allele variation of maturity genes E1-E4 on the adaptation of soybean to the natural day length conditions of Central Russia and Western Siberia. The manuscript demonstrates clear writing and strong logic throughout. The language used is concise, well-organized, and easy to follow, making it accessible to a wide audience. This manuscript is acceptable for publication after revision and clarification:

 

Major comments.

1.     In table 4, the “year” seems to be a more important factor than genotype of E4 and/or E1 in 3 of four “Trait x Location”. Would you like to add discussion on this?2.     For your conclusion: “Cultivars with these and mono-dominant genotypes e1-nl/e2/e3/E4 and e1-as/e2/e3/E4 as well are considered to be most suitable for cultivation in Central Russia and Western Siberia.” Frequency of genotypes e1-nl/e2/e3/E4 and e1-as/e2/e3/E4 is much lower than those recessive ones. To support this conclusion, it would be helpful if the authors could provide a clearer discussion of why these genotypes are considered the most suitable. It is my understanding that allelic variations of E1-E4 genes determine the adaptability of soybean cultivars to the duration of the germination to maturity phases, ultimately affecting yield with longer flowering and maturity times.

 

Minor comments for typos:

1. “Cultivars from regions located between 58-52°N mainly carry the e1-as/e2/e3/e4 and e1-nl/e2/e3/e4 genotypes, but there are also varieties with e1-nl/e2/e3 /E4.” please note that there is a redundant space in this sentence.

2. “providedby” should be “provided by”

3. Bottom line of Table 4.

Author Response

Thank you very much for your comments and suggestions.

Major comments.

Reviewer: 1.In table 4, the “year” seems to be a more important factor than genotype of E4 and/or E1 in 3 of four “Trait x Location”. Would you like to add discussion on this?

Authors: We have added a discussion of the results of ANOVA. Here is the added text:

“According to the ANOVA results, all the studied factors influence on DTF and DTM. For each region separately, the “year” factor affects on DTF and the DTM more strongly than the E1 and E4 genes, apparently due to the atypical weather conditions in Orel in 2022 and drought in early June in Novosibirsk in 2022. The result of the "two years x location" model shows that the E1 and E4 genes are the main factors influencing on DTM. DTF is most dependent on the "location" factor (Table 2)”.

Reviewer: 2. For your conclusion: “Cultivars with these and mono-dominant genotypes e1-nl/e2/e3/E4 and e1-as/e2/e3/E4 as well are considered to be most suitable for cultivation in Central Russia and Western Siberia.” Frequency of genotypes e1-nl/e2/e3/E4 and e1-as/e2/e3/E4 is much lower than those recessive ones. To support this conclusion, it would be helpful if the authors could provide a clearer discussion of why these genotypes are considered the most suitable. It is my understanding that allelic variations of E1-E4 genes determine the adaptability of soybean cultivars to the duration of the germination to maturity phases, ultimately affecting yield with longer flowering and maturity times.

Authors: We agree with you and have rephrased our conclusion as: “The field experiment showed that genotypes with all recessive alleles e1-nl/e2/e3/e4 and e1-as/e2/e3/e4 provide an effective adaptation of soybean to the mentioned conditions. Cultivars with these genotypes are considered to be most suitable for cultivation in Central Russia and Western Siberia.”

Minor comments for typos:

Reviewer: 1. “Cultivars from regions located between 58-52°N mainly carry the e1-as/e2/e3/e4 and e1-nl/e2/e3/e4 genotypes, but there are also varieties with e1-nl/e2/e3 /E4.” please note that there is a redundant space in this sentence.

Authors: We corrected

Reviewer: 2. “providedby” should be “provided by”

Authors: We corrected

Reviewer: 3. Bottom line of Table 4.

Authors: We corrected

Author Response File: Author Response.docx