Breeding Dual-Purpose Maize: Grain Production and Biofuel Conversion of the Stover

Round 1

Reviewer 1 Report

The authors of this article conducted a two-year evaluation of a subset of the Ames Association Panel using an augmented block design. They assessed grain yield, stover yield, and saccharification efficiency of the genotypes under investigation. Additionally, they performed basic descriptive statistical analysis on these phenotypes, and conducted GWAS analysis using previously published GBS data. This study holds significance due to the global importance of corn and its potential for dual use as a grain crop and biofuel production. However, I have a few suggestions/questions:

The authors need to clarify, which version of the genome was used to call the GBS SNPs.

Are the genotypes used in this study overlap with the newly published resequencing data on thousands of genotypes? "https://doi.org/10.1111/tpj.16163." If yes then the marker information published in this study could have been used to perform GWAS. With the high number of high-quality markers, you might get better and more confident hits. re-sequencing data is better than GBS because GBS has a lot of missing data points.

Have you checked if the QTLs detected in your study overlap with the genomic regions detected in a comprehensive analysis of hundreds of phenotypes with a common marker set as described in this study: "https://doi.org/10.1093/gigascience/giac080"? This might help you to understand if grain yield, stover yield, and saccharification efficiency is associated with the genomic regions also associated with some other phenotypes.

Lastly, I don't see any Manhattan plots or QQ plots to quickly visualize the GWAS results. I recommend authors include them in the article.

There are a few grammatical mistakes that need to be fixed.

Author Response

Responses to the reviewer are italicized and in blue

The authors need to clarify, which version of the genome was used to call the GBS SNPs. The version 4 of B73 genome was used. It was included in material y methods section.

Are the genotypes used in this study overlap with the newly published resequencing data on thousands of genotypes? "https://doi.org/10.1111/tpj.16163." If yes then the marker information published in this study could have been used to perform GWAS. With the high number of high-quality markers, you might get better and more confident hits. re-sequencing data is better than GBS because GBS has a lot of missing data points. We agree that the use of high-quality markers are the best to perform GWAS, but the overlap between our genotypes and those used in this study is small, so we cannot carry out the analysis.

Have you checked if the QTLs detected in your study overlap with the genomic regions detected in a comprehensive analysis of hundreds of phenotypes with a common marker set as described in this study: "https://doi.org/10.1093/gigascience/giac080"? This might help you to understand if grain yield, stover yield, and saccharification efficiency is associated with the genomic regions also associated with some other phenotypes. We have now checked for significantly associated QTL in our work with the study by Mural et al (2022). There is a snp on chromosome 3 related to grain yield that is 3243 bp away from a snp associated with the character BulliformColWidth2_E, which a priory does not seem to have a direct relationship with yield. Another snp associated with ears per plant is 50,000 bp from a snp that we found associated with grain yield. This would have a biological significance, but the linkage disequilibrium decays very quickly in the line panels, especially if it consists of many lines, as is the case in the Mural panel. Since it is not the same trait   we consider that we should include this comparison in the article.

Lastly, I don't see any Manhattan plots or QQ plots to quickly visualize the GWAS results. I recommend authors include them in the article. The Q-Q and Manhattan plots of the three analyzed traits have been included in a supplementary figure.

Reviewer 2 Report

ABSTRACT

Describe what it is and then put the acronym in parentheses. QTL. Quantitative trait loci.

INTRODUÇÃO

Line 31 - Is it really that the cultivated area of corn is falling, decreasing? I can't believe it's true. I suggest removing that part or referencing this statement with a larger number of solid references.

Describe what it is and then put the acronym in parentheses. RIL.

In the second paragraph the acronym QTL is repeated six times. It's a repetitive read.

Check for the remainder of the article - there are several acronyms without a description of them.

Line 47 - Dear authors, I do not consider this to be the case. In Brazil, there are numerous efforts and researches for the development of corn silage for animal feed. This effort aims at greater straw yield. Therefore, one cannot generalize.

MATERIAL AND METHODS

2.1.1 - add number (1) in equation 1.

Keep the same formatting pattern of equations 1 and 2

2.1.3 - When citing authors in full text, do not insert the date of publication.

RESULTS

3.2 - The citation Yi et al. (2023), lacked to be numbered. Also, in running text, do not insert a date, just the first author, followed by "et al.." (when there are several authors).

In the Figure 1 , it is not possible to read what is in column "Y" nor what is written in column "x". It would be interesting to increase the font of the Figure's axes.

DISCUSSION

Line 230 - I believe that some work with corn silage - quality and yield in different regions of the world could serve as a reference to support your results. At least in relation to yield of green mass that reflects in straw. There are many jobs.

4.2 - Several citations without the reference number [??].

I missed the conclusions. I believe that in a simple and direct way, it would close the article with a golden key. 3 or 4 short sentences.

REFERENCES

I will introduce ALL authors.

Comments for author File: Comments.pdf

Author Response

Responses to the reviewer are in blue and italics

ABSTRACT

Describe what it is and then put the acronym in parentheses. QTL. Quantitative trait loci. The proposed change has been made

 INTRODUÇÃO

Line 31 - Is it really that the cultivated area of corn is falling, decreasing? I can't believe it's true. I suggest removing that part or referencing this statement with a larger number of solid references. This part has been removed

Describe what it is and then put the acronym in parentheses. RIL.The proposed change has been made

In the second paragraph the acronym QTL is repeated six times. It's a repetitive read.  The proposed change has been made

Check for the remainder of the article - there are several acronyms without a description of them. Now all the acronyms have been described when they are first named.

Line 47 - Dear authors, I do not consider this to be the case. In Brazil, there are numerous efforts and researches for the development of corn silage for animal feed. This effort aims at greater straw yield. Therefore, one cannot generalize. We have changed the sentence

MATERIAL AND METHODS

2.1.1 - add number (1) in equation 1.

Keep the same formatting pattern of equations 1 and 2. The proposed change has been made

2.1.3 - When citing authors in full text, do not insert the date of publication. The publication date was removed

RESULTS

3.2 - The citation Yi et al. (2023), lacked to be numbered. Also, in running text, do not insert a date, just the first author, followed by "et al.." (when there are several authors). The proposed change has been made

In the Figure 1 , it is not possible to read what is in column "Y" nor what is written in column "x". It would be interesting to increase the font of the Figure's axes. To avoid this problem we write in the legend ' The X-axis shows the rank of each gene effect value; the Y-axis shows the value of the enrich-ment score (ES) running sum statistic as each consecutive gene effect value is processed. The x-intercept line indicates the highest point of the ES. Small hatch marks at the top of the image in-dicate the rank position of the effect of all genes in the pathway’.

DISCUSSION

Line 230 - I believe that some work with corn silage - quality and yield in different regions of the world could serve as a reference to support your results. At least in relation to yield of green mass that reflects in straw. There are many jobs. We have include the reference :”           I. García-Chávez, E. Meráz-Moreno, O Castelán-Ortega, J. Zaragoza-Esparza, J. Osorio Avalos, L.E. Robles Jime-nez and M. González-Ronquillo. “Corn silage, a systematic review of the quality and yield in different regions around the world” Cienc. Tecnol. Agropecuaria, 23(3): e2547, 2022, https://doi.org/10.21930/rcta.vol23_num3_art:2547”

4.2 - Several citations without the reference number [??]. The proposed change has been made

I missed the conclusions. I believe that in a simple and direct way, it would close the article with a golden key. 3 or 4 short sentences. The conclusion has been emphasized

REFERENCES

I will introduce ALL authors. All authors have been added