Identification of Genomic Loci Controlling Grain Macro and Micronutrient Variation in a Wild Barley (Hordeum vulgare spp. spontaneum) Diversity Panel

Round 1

Reviewer 1 Report

Barley was the fourth largest cereal crop on the world. Barley is rich in nutrients, such as β-glucan and grain protein content, et al. Variation in seed of macronutrient and micronutrient content were important for high-quality and nutrient-dense foods. In the present study, diversity of micro and macro nutrient content, GWAS  and candidate gene were analyzed by authors. Here, I have several contens that should be addressed before acceptance.

 

Major

1.The quality  of Figure 1,3 need improved, it’s not enough clear. What is the “a-i”, they should be explained. The same appears in Table 1, 3.

2.In the table 3.  The gene ID is incomplete.

3.The reference list should change to be satisfied with the demands of the Agronomy.

4.In the MS, how many wild barley accessions were used for analysis, line 94, Of the 318 accessions, 297 accessions yielded sufficient samples in the two replicate experiments., but line 156, “Two hundred thirty-two wild barley accessions were represented in analyses for the 2006-2007 and 2015-2016 crop years.”

5.In the table 2, “H2 = Vg/(Vg+Ve) Vg = (meansqr(Accession) - meansqr(residuals))/(# Trials) Ve = meansqr(residuals))/(# Trials)”,  this was in  Materials and Methods part.

Minor

1.Line 123, colon should be deleted.

2.Line 190, “Mg2+ and K+” should be “Mg²⁺ and K⁺” , please check the whole MS.

3.line 344, ‘.” Is missing?

4.Line 498, “5. Patents” should be deleted

Author Response

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Author Response File: Author Response.docx

Reviewer 2 Report

1. Although the author think that the phenotypic results of nutrient concentrations were consistent across two different years, but from the table 1, we found that nutrient concentration of 2015-16 are all higher than that of 2006-07. So is it associated with the Seed storage time? And for one accession,What is the range of change between the two years?

2. In this experiment, two methods were used in genotyping association analysis. So the advantage of GWASpoly methodology and FarmCPU model is ? which one is more suitable for association analysisi of micronutrient elements ?

3. The heritability of Boron is only 0.11, and there were two significant SNPs were detected. The heritability of P is 0.35,but there were no obvious MTAs identified. So is there any relationship between the heritable and MTAs? And how to explain this phenomenon? The two candidate locus are credible or not?

4. While analysis of the candidate MTA (line438-439), surpass the confidence threshold of -log(p)>4.79 and repeat in two years, which one is more confident ? And why?

5. Please check the numbers of candidate MTAs of B in Line356-357. 

Author Response

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Reviewer 3 Report

1.    H. vulgare in title should be in full name

2.    Hordeum vulgare should be in italic throughout all the manuscript  

3.    The font in Figure1 is not clear

Author Response

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Reviewer 4 Report

Review of „Identification of genomic loci controlling grain macro and micronutrient variation in a Wild Barley (H. vulgare spp spontaneum) Diversity Panel”

Jillian A Abendroth, Ahmad H Sallam, Brian J Steffenson, Marcus A Vinje, Ramamurthy Mahalingam,* and Jason G Walling

1.Introduction:

The magnitude and forms of hunger occurring in the world were described in detailed, but I miss the description of the micronutrients character of cultivated barley and other cereal grains, The authors mention that such experiments have been carried out in the introduction to association studies. Summarizing this result in one or two sentences would help to form a more complete picture of the role of barley in human nutrition.

The aim of study:  should be described more clearly, separately from the results so far.

2. Material and method:

2.1 Plant material: The composition of the grain depends on the growing conditions, so it is necessary to specify them both years together with the soil composition.

line 117: cube root transformation reference is missing

3. Results and Discussion

3.1. Macro and Micronutrient content and correlation analysis”

line 160 figure 1: boxplots are missing from the figure

The different presentation of data in figure 1 and table 1 makes difficult to compare its.

Figure 2: I recommend using the same colours, both years when presenting the correlations between traits, because then it is easier to compare the stability of the correlation. The placement of the colour scale is misleading. Using the same colours in both years makes enough to use one colour scale.

line 187-191: The explanation of positive correlation between K and Mg quite short. The relationship between the two elements is very complex, so I recommend supplementing this section with the results of other studies

The results of MTA analysis is the last part of “3.1. Macro and Micronutrient content and correlation analysis” subsection. I recommended an independent subsection of MAT analysis because it is not belong to the 3.1 subsection topics.

3.2. Primary Macronutrients: Phosphorus and Potassium

line 271: the 6H chromosome is missing from the list.

3.3. Secondary Macronutrients: Calcium and Magnesium

lines 280-289 and 308-318 belong to the Introduction chapter

line 319: “In barley seeds, the observed range was 1279-2547 mg/Kg-1.” were the results of WDBC panel?

 

3.4. Micronutrients: Boron, Manganese, Copper, Iron, and Zinc

line 334-344 belong to the Introduction chapter

line 356-358: The authors state that there are two significant boron associated SPN then listed three: two on chromosome 7, one on chromosome three. Please clarify this contradiction.

line 369-380 belong to the Introduction chapter

line 386: The authors state that there are three significant Mn associated MTA then listed four. Please clarify this contradiction.

line 404-418 belong to the Introduction chapter

line 433: The authors state that there are six significant Cu associated MTA by FarmCUP. There are seven in table 1. Please clarify this contradiction.

line 456-463 belong to Introduction chapter

Sometimes it is difficult to follow whether it is about plant or human needs. Results of other and recent study is also hard to follow. It should be highlighted.

4. Conclusions

I recommend adding the following to the conclusion: Is Hordeum spontaneum suitable for breeders to use it to improve the micro- and macronutrient content of barley grains? Were there any accession with outstanding macro- or micronutrients, which are useful as parent in barley breeding program?

Comments for author File: Comments.pdf

Author Response

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Round 2

Reviewer 1 Report

I agree to accept the article for publication.