Genetic Diversity of Local Wheat (Triticum aestivum L.) and Traceability in the Production of Galician Bread (Protected Geographical Indication) by Microsatellites

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript was read attentively, but sometimes, it was difficult to follow the flow of the text. Below are suggestions to improve the text and its understandability. At some point is difficult with how many genotypes authors are doing their analysis:

• Overall, the English language needs significant improvement, including in the abstract. Please see the text between lines [57-59], though there are other examples as well.
• The meaning of the text in lines [60-62] is unclear. What are the authors trying to convey or say in this sentence? Are they suggesting that the wheat from Galicia has low diversity? The sentence needs to be modified for clarity.
• The authors mention in lines [65-66] “From the last works…” but do not provide any references. Please add them.
• Line 70: Add a reference and clarify the sentence.
• Line 78: Remove the sentence regarding unpublished data. It doesn’t add value to the manuscript, and readers and Editors cannot verify its accuracy.
• Lines [86-97]: It is recommended that the authors summarize the information and improve the language.
• What do the authors mean by "Volunteer wheat"? Please specify whether this refers to wild types, landraces, old varieties, conserved, etc.
• Lines [118-122]: Please rephrase the objective of the paper. It should focus on determining the diversity and structure of Galician wheat, rather than comparing SSRs.
• In the Materials and Methods section: Please add the names or IDs of the ecotypes and specify their type/subspecies/species. Briefly define what an "ecotype" means in the context of this paper.
• The authors seem to mention only 14 ecotypes analyzed. Please clarify/rectify.
• Line 145: Relate the 38 lines used in traceability to the genotypic data obtained in a table.
• Line 207: Please indicate the total number of genotypes from which the 156 unique genotypes were found.
• Line 211: What is a "uniform genetic profile"? Please explain what this means in the context of your results.
• Table 1: It is advised that the authors divide this table into two separate tables—one for the common alleles and another for the exclusive alleles. It is confusing to check the meaning of each number repeatedly.
• Line 240 (Section 3.2): Why was the structure analysis conducted using only exclusive alleles? Why not use both analyses (one with all alleles and another with exclusive alleles) to compare the differences? This would strengthen the results described in the manuscript.
• Please add the Delta K graph to indicate the best K value found, confirming the number of probable groups in the entire dataset.
• Section 2.4 (Data Analysis): Describe the analyses in STRUCTURE, including relevant references. This means the authors need to explain how the structure analysis was conducted in the Materials and Methods section, including references to the software used. The same applies to allele conversion if it was performed.
• The software used for PCA should be properly described with references in the methodology.
• The authors should use the same colors to represent the different groups in the STRUCTURE results, as well as in the phylogenetic tree and PCA. This will make the results clearer and easier to interpret.
• Please provide a more detailed explanation of Figure 4.
• Figure 5: The Galician ecotypes appear to form distinct groups in the graph due to their separation, but they are considered one single ecotype. Please clarify this point.
• There seems to be no explicit relationship or graphical representation connecting the genotypic results with the flour analysis. This should be explored further. What are the practical conclusions derived from this intersection?

Major Revision Required

 

Comments on the Quality of English Language

The English language needs to be improved to the manuscript be understood.

Author Response

Please see the attachment

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The authors aimed to compare the SSRs of Galician ecotypes of wheat and the cultivars to commercial wheats, in order to determine the genetic structure, identify their origin and differentiate them. The results showed that these markers confirmed their utility in tracing genotypes and their derived products. After reviewing, this paper could be accepted after revisions. There are some comments or suggestions as below:

1: give the scientific names of the Galician wheat in the title and abstract part.

2: How did the authors choose the 17 SSR markers? Give more details on the markers, especially on their effectiveness.

3: The tables and the pictures are not well prepared.

Comments on the Quality of English Language

The quality could be improved by revisions.

Author Response

Please see the attachment

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The effort of authors in improving the manuscript quality is highlighted and acknowledged.

Please see my queries/worries/suggestions below:

 a.       Line 235 of the document:

I still with the query to authors in the sentence: In this study, 156 unique genotypes were identified (Table S1).) from a total of 296 plant DNA samples.

Q1. Do the authors want to say that out of 296 genotypes, 156 haplotypes were found? If not explain it in detail.

 

b.      Line 240 of the document:

Where authors say: The genetic profiles for ‘Caaveiro’ and ‘Caaveiro´(prebase) (seed used for certification purposes), ‘Callobre’ and ‘Callobre´(prebase), E16L30 (cv. ‘Castrexo’), and 1910-4 were uniform.each presented a unique genotype. – present a unique fingerprint identity?

Q2. Because the cultivars per se are a genotype. If authors talk about the whole genotype these must undergo Whole genome sequencing of the cultivar/genotype/haplotype. Kindly clarify very briefly in the text.

 

c.       In the methods (line 210 of the document) authors do not insert reference 61 that later is presented at line 274. It should be the opposite: the first time citing the software is where it comes the reference or maintain the reference in both sites.

 

d.      Figure 4. Still not visible, careful.

 

e.       Authors finalise their conclusion saying: ‘As a practical conclusion, we have developed a database employing 17 SSRs to trace the use of Galician wheat from farm to table, ensuring the authenticity of the PGI "Galician 580 bread." 

 

- Authors can say that they manage to get 17 SRRs that are useful for the purpose but not a database. Please, if is a database give the public a link with all information related to these 17 SSRs. Otherwise please moderate the comment and change it, for example … the development of useful SSRs markers that are publicly available to anyone that wants to use. Authors can substitute database by dataset marker.

The link given by authors should have all info related to the SSRs markers as well indicate the conditions to run these either in a laboratory or a genotyping platform.

This gives a more realistic picture of authors research results and doesn’t put MDPI Agronomy in jeopardy due to exaggeration. 17 SSRs are already a very good amount, when markers are excellent even 1 marker suffices. So, no need to say a database because isn’t a database.

 

f.        Comment: The journal shared the supplementary figures now, and as expected, it is clear that samples would need to be run with higher number of iterations and repetitions.

 g.      Regarding the comment: Reviewer 1: What do the authors mean by "Volunteer wheat"? Please specify whether this refers to wild types, landraces, old varieties, conserved, etc. Response: Included in the text: In a study utilising SSRs, Su et al. [27] discovered that volunteer wheat, “a kind of wheat with weed characteristics, distributed widely in the main wheat-producing areas of China”, exhibited greater variability compared to cultivated wheat, with the two displaying rather distant phylogenetic relationships. “Volunteer wheat is a kind of wheat with weed characteristics, distributed widely in the main wheat-producing areas of China.” (Su, W.; Xu, H.; Sun, L.; Lu, C.; Wu, R. Genetic Diversity Analysis of Volunteer Wheat Based on SSR Markers. J Genet 2023, 102, 54, doi:10.1007/s12041-023-01451-9.)

Line 96 of the document.

Still regarding the word ‘volunteer plant’. There are key differences among volunteer plants and spontaneous, please see: 1. volunteer plants" usually refers to plants that grow in cultivated or disturbed areas (gardens, farms), while "spontaneous plants" might grow in both cultivated and wild, natural environments, 2. volunteer plants are often the result of seeds from previously human-planted crops, while spontaneous plants are more about random, natural growth patterns or self-seeding without human involvement.

Query for authors: do they want to maintain the reference Sun et al given, as well the sentence? Because myself, I do not know what type of plant Sun et al are refereeing to.

Alternatively, and if authors want to maintain the reference, is good to have these two definitions in the text, so we all are aware of what we are refereeing to.

Author Response

Please see the attachment

Author Response File: Author Response.pdf