Genome-Wide Association Study for Agronomic Traits in Wild Soybean (Glycine soja)

Round 1

Reviewer 1 Report

The submitted manuscript entitled “Genome-wide association study for agronomic traits in wild soybean (Glycine soja)” with the aimed to explore the genetic diversity of soybean using data from a high-density SNP chip for 203 wild soybean accessions and also to identify potential genes associated with key agronomic traits that influence soybean yield through a genome-wide association study. The study is interesting and discuss important agronomic traits, however authors need to address some minor points before accepting for publication as follows:

 

Line 19 and 36: change (Glycine max) to (Glycine max (L.) Merr.)

Line 48-49:  Please insert little extra word to describe why flowering is important, with references.

Line 81: wild soybean accessions

Line 100: why days to maturity was not assumed from sowing date?

Line 103: The 100SW was measured by randomly selecting 100 mature seeds…. What you did after that for those selected seeds.

Figure 3,a,c,d is not clear and poorly informative , please edit this figure to increase its resolution and clarity , for example what different colors indicate to?

Figure 4: so bad quality of figure I have ever seen.

Table 4: title is not correct…..please consider the correct title.

Conclusion is so short and lacks to more facts about the current findings.

 

 

 

 

 

Author Response

The revised manuscript is attached.

Response to Reviewer 1 Comments

Thank you so much for your suggestion. After considering this suggestion and reviewing the manuscript, we have amended the manuscript to your suggestion.

My comments and questions to authors are as follows:

Point 1: Line 19 and 36: change (Glycine max) to (Glycine max (L.) Merr.)

Response 1: Thank you for pointing out, the correction has been completed.

Point 2: Line 48-49:  Please insert little extra word to describe why flowering is important, with references.

Response 2: Based on the suggestions of the reviewer, references were added and written in the main text.

Point 3: Line 81: wild soybean accessions

Response 3: Thank you for pointing out, the correction has been completed.

Point 4: Line 100: why days to maturity was not assumed from sowing date?

Response 4: When measured from the sowing date, it was thought that the ability to detect traits could be insufficient because the coefficient of variation could be small.

Point 5: Line 103: The 100SW was measured by randomly selecting 100 mature seeds…. What you did after that for those selected seeds.

Response 5: For 100SW mature seeds were dried in a dry oven at 30 ° C for 72 hours, and then randomly selected 100 of them and weighed them.

Point 6: Figure 3,a,c,d is not clear and poorly informative , please edit this figure to increase its resolution and clarity , for example what different colors indicate to?

Response 6: As the reviewer pointed out, the resolution and sharpness of the figure were increased, and a legend was added. Also, the colors here represent separate groups with different levels of admixture.

Point 7: Figure 4: so bad quality of figure I have ever seen.

Response 7: As the reviewer pointed out, the resolution and sharpness of the figure were increased.

Point 8: Table 4: title is not correct….please consider the correct title.

Response 8: Thank you for pointing out, the correction has been completed.

Point 9: Conclusion is so short and lacks to more facts about the current findings.

Response 9: The reviewer's suggestions were collected and added to the text.

Reviewer 2 Report

The main issue is to assess the possibility of searching for molecular markers for polygenic agronomic traits in soybeans. The topic is an original and relevant area of research. The results of the work showed new data on the detection of effective molecular markers. The main improvement of the work consists in conducting additional experiments in the field to study the relationship of the markers with seed yield. The conclusions are consistent with the evidence and arguments. The references are appropriate. 

 

Is it correct to name the two sections the same 2.4 (125) and 2.5 (137)?

Is it doubtful whether the term “strong” negative correlation is used correctly with the coefficient values of -0.390 and -0.345 (179)?

Author Response

The revised manuscript is attached.

Response to Reviewer 2 Comments

Thank you so much for your suggestion.After considering this suggestion and reviewing the manuscript, we have amended the manuscript to your suggestion.

My comments and questions to authors are as follows:

Point 1: Is it correct to name the two sections the same 2.4 (125) and 2.5 (137)?

Response 1: Thank you for pointing out, the correction has been completed.

Point 2: Is it doubtful whether the term “strong” negative correlation is used correctly with the coefficient values of -0.390 and -0.345 (179)?

Response 2: I used the expression strong because the significance level was significant at 0.01, but I will change it because I think the reviewer's point is correct.

Reviewer 3 Report

The presented manuscript entitled "Genome-wide association study for agronomic traits in wild soybean (Glycine soja)" tries to detect phenotype-genotype associations for important agronomic traits in wild soybean as a new genetic resource to improve soybean breeding programs. In general, the manuscript is well written and covers the important literature. Further, the methodology is understandable. Unfortunately, I have some concerns with the candidate gene detection. Despite the chosen method has been used before in the literature, it is not as precise as other methods based on local LD estimations. Additionally, I think the discussion lacks depth in the interpretation of the generated results. Line-by-line commends can be found below.

LL 123: Citation for R software is missing

LL126: Citation for ADMIXTURE software is missing

LL132: Citation for MEGA11 is missing

LL134: Citation for PLINK is missing

LL137: Subchapter header "2.5. Population structure and genetic diversity" has been used forthe subchapter 2.4 as well

LL138: Citation for TASSEL is missing

LL177-183: How is the correlation between the two environments for the same trait? Does year significantly affect different traits? Since you use the mean later on in your analysis, I think it would make sense to report that too.

LL208-211: Color legend is missing in figure 3 and Figure 3c is to small

LL219-222: Figure 4 is to small

LL270-291: Candidate gene detection using a widow size defined from global LD-Decay is a common way to do but it is less precise than the method where local LD is calculated among markers surrounding the significant marker and then using a window size based on these local LDs. The authors should consider redoing the candidate gene detection using local LDs.

LL292-411: In general, the discussion in sparse. The authors should add more depth to their discussion especially the candidate gene part. They mention the identified gene and that it might have been detected in other species, but they don't add much detail to it.

LL311: The authers say "it can be inferred that Korea is the origin of wild soybean." I don't think this statement is possible based on only 200 accessions. You can hypothesis that Korea might be the center of origin but the way it is state here indicates that Korea has to be the center of origin, but the present manuscript doesn't provide an actual prove. 

LL358-359: The statement of the heritability of NoP to be low and therefore greatly influenced by the environment is partially true since the low heritability also indicates a strong effect of gene-gene interactions on NoP.

LL383-384: It is not clear to me why the authors added this statement. Do they expect that transcription factors have no effect on gene expression in soybean? Isn't that their main function, to influence gene transcription?

LL391-393: I don't understand this statement. Would we expect flowering-related genes to be detected in a wild population due to local adaptation since it is an important mechanism of survival. Which has just been stated by the authors (lines 388-389).

Author Response

The revised manuscript is attached.

Response to Reviewer 3 Comments

Thank you so much for your suggestion. After considering this suggestion and reviewing the manuscript, we have amended the manuscript to your suggestion.

My comments and questions to authors are as follows:

Point 1~4 and 6: missing citation

Response 1~4 and 6: All missing citations pointed out by the reviewers have been added.

Point 5: LL137: Subchapter header "2.5. Population structure and genetic diversity" has been used for the subchapter 2.4 as well

Response 5: Thank you for pointing out, the correction has been completed.

Point 7: LL177-183: How is the correlation between the two environments for the same trait? Does year significantly affect different traits? Since you use the mean later on in your analysis, I think it would make sense to report that too.

Response 7: The mean values of both environments showed a significant correlation. However, we tried to show that it may not be significant in some circumstances. In addition, in the subsequent association analysis, the merged method (151-152) was analyzed according to the cited literature, and this is not an average value. Year was treated as replication.

Point 8: LL208-211: Color legend is missing in figure 3 and Figure 3c is to small

Response 8: A color legend was added to Figure 3, and Figure 3c was modified.

Point 9: LL219-222: Figure 4 is to small

Response 9: Figure 4 has been modified.

Point 10: LL270-291: Candidate gene detection using a widow size defined from global LD-Decay is a common way to do but it is less precise than the method where local LD is calculated among markers surrounding the significant marker and then using a window size based on these local LDs. The authors should consider redoing the candidate gene detection using local LDs.

Response 10: In our results, the size of LD in the wild soybean accessions was 6K, which was too small to search for candidate genes. Therefore, candidate genes were searched in a wider range.

Point 11: LL292-411: In general, the discussion in sparse. The authors should add more depth to their discussion especially the candidate gene part. They mention the identified gene and that it might have been detected in other species, but they don't add much detail to it.

Response 11: As suggested by the reviewers, partial additions have been made to the manuscript.

Point 12: The authers say "it can be inferred that Korea is the origin of wild soybean." I don't think this statement is possible based on only 200 accessions. You can hypothesis that Korea might be the center of origin but the way it is state here indicates that Korea has to be the center of origin, but the present manuscript doesn't provide an actual prove. 

Response 12: As the reviewer pointed out, it can be difficult to perfectly estimate the country of origin with only 200 accessions. However, it was a guess, and it was changed because it was thought that it would be better to change it to the Korean Peninsula rather than the expression Korea.

Point 13: The statement of the heritability of NoP to be low and therefore greatly influenced by the environment is partially true since the low heritability also indicates a strong effect of gene-gene interactions on NoP.

Response 13: I agree with reviewer

Point 14: LL383-384: It is not clear to me why the authors added this statement. Do they expect that transcription factors have no effect on gene expression in soybean? Isn't that their main function, to influence gene transcription?

Response 14: I misunderstood the sentence about whether the candidate gene would have an effect. Edited in text.

Point 15: LL391-393: I don't understand this statement. Would we expect flowering-related genes to be detected in a wild population due to local adaptation since it is an important mechanism of survival. Which has just been stated by the authors (lines 388-389).

Response 15: There are reports that wild soybeans can have unique alleles because they are found in a variety of climates and geographies, and that's what I'm talking about.