PONE-D-20-08197

Diversity of nutritional content in seeds of Brazilian common bean germplasm

PLOS ONE

Dear Dr. Azeredo Gonçalves,

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Reviewers' comments:

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Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: No

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Diversity of nutritional content in seed of Brazilian common bean germplasm

The authors presented a study on mineral nutrients (P, K, Ca, Mg, Cu, Zn, Mn, Fe and S) and protein content in a collection of 1,512 common bean accessions consisting on local, commercial and improved varieties. A total of 4 environments in 2 crop seasons were evaluated. The aim of the study is to evaluate the diversity regarding to these traits within this germplasm collection in order to identify some parental lines that can be used in future breeding programs.

The study is original and the topic is interesting since the biofortification is one the target for breeding programs nowadays. Nevertheless, some points specially regarding to the material and methods need to be clarify in order to understand better the study.

Abstract:

The abstract is well written and summarizes the information included in the work.

Introduction:

In the introduction, the authors presented the problematic and the objective of the study is clearly established.

Material and Methods:

Line 109: different center of origin…Describe how many of the 1512 accessions are Mesoamerican and how many Andean since this data is later used in the results and it is useful information for the reader.

Line 138: the factor 6.25 is used to convert total seed N to protein content. Reference this conversion factor for common bean.

According to I.E. Ezeagu et al. / Food Chemistry 78 (2002) 105–109. Crude protein analysis conventionally based on multiplying the total nitrogen (N) (Kjeldalh N) by a factor of 6.25 has been suspect. Different conversion factors recommended for cereals and grain products range between 5.70 and 5.83; for dry grain legumes 5.46–5.71 is recommended; while 5.18–5.46 is for nuts and seeds (FAO, 1982).

Considered this reference. François Mariotti, Daniel Tomé, Philippe Mirand. Converting Nitrogen into Protein – Beyond 6.25 and Jones’ Factors. Critical Reviews in Food Science and Nutrition, Taylor & Francis, 2008, 48 (2), pp.177-184. ff10.1080/10408390701279749ff. ffhal-02105858f

Please discuss this and reference the conversion factor used in this study for common bean.

Line 145 -146: the authors said: with these data, a Tukey test and boxplot were performed to show the distribution of the accessions grouped by the criteria using R packages….

Some points are needed to be clarify in this sentence in order to explain better the methods.

Please specify what data is used for the contrast test in order to follow better the methods…. the mean values for each analyzed trait per accession, per seed color group or per genetic material.

Regarding the Tukey test is this multiple means comparison test supporting another global mean test (ANOVA or Krukall wallis etc)?

Specify also in the text the alpha level for the statistical test.

Line 148: Ward-MLM. Specify the complete name of these test. Ward- Modified Location Model.

Lines 159-160: This sentence is a bit confusing; the authors presented a correlation network made with qgraph, but which data is correlated? the dissimilarity coefficients, the distance coefficients, the mean values. Please specify in order to specify this issue.

It would be also interesting to specify what method do you use for correlating the data with qgraph, (cor_auto?)

Results:

Line 182: Positive and median correlations, what do you mean with median correlations?. Are all these correlations significant? Please include in the results the signification level of the correlations to better interpretation the results.

Lines 190-192: This sentence is a bit confusing please rewrite.

Line 197: add (Figure 2)

Line 227-241: In this section of the results the composition of the groups obtained by Ward-MLM method is describe, but the table 2 just reflects the total number of accessions of each group but not the characteristics of the accessions included in each one. It might be interesting to include this information the supplementary material since it is presented as results.

Line 243: It might be Figure 5 instead of Table 2

Line 247: table 2 instead of Fig 5

Lines 258- 263: this paragraph is not easy to follow. Please re-write it.

Discussion:

In general, the discussion is well written and it adresses the main points of the results.

line 336: proper bibliography format [36]

Tables and figures:

Table 1: please review the legend of the table, the superindex a and the cross might be changed.

Figure 1: correlation network, please include the significance level for each correlation or at least for those that are significant.

Figure 2: include significant level considering for the tukey test (plabeled with different letters in the plot indicate differences between group means?

Figure 3. Might be interesting to include the plots for pseudo-t2 and pseudo-F in the supplementary materials as it is the criteria used for the grouping. Suplementary material.

Table 2: in the legend (line 225) delete CV

In general, for all the figures, improve printing quality for seeing details.

The bibliography is well formated

Reviewer #2: In general the study is interesting: the Abstract provide a first insight into the results obtained, giving importance to commercial varieties widely diffused in Brazil as carioca and black beans, arising major interest for partecipatory breeding and breeding strategies in the next future. The Introduction is complete and well structured with references righlty reported. Materials and Method are well organized as the workflow strategy is highly reccomended for these type of experiment and confirmed by previous studies applying the same methodology. Results are clear as they follow the order of the analysis conducted as explained in materials and methods.

In general the study is well conducted and explained but maybe some slight adjustments could be done. I’ve resumed some points below (with reference to manuscript lines).

Line 35 – 39: not clear the distinction among gene pools… I would specify in line 35 that carioca and black market group is characterized by mesoamerican accessions.

Line 91 : maybe some very fast highlights on the conclusions reached by these two authors (very fast because you already explain this in the conclusions, but could be useful to touch the topic in the introduction)… for example: “the mesoamerican gene pool gave higher lectin, clacium,phosphorus,sulfur and zinc than the andean but lower phaseolin and iron” or “The major gene pools differed significantly in almost all grain constituents… (Discussion of Islam, 2002), or see Cominelli et al., 2019.

Line 106: In material and method: will you provide a table with the list of the accessions with the relative gene pool, seed color and genetic material specified? (this is the MAJOR IMPORTANT POINT!!!!)

Line 142: maybe would be nice to make a simple PCA to see how accessions behave considering variables that you use to create your preliminary groups. I would add also the belonging to a gene pool that at the end gives also a correlation with the dimensions of the seeds

Line 146: Tukey test and boxplot could be done also separating by gene pools?

Line 220: In Table 2, you show the different groups with the relative contribution of the first two canonical variables of each nutrient and means/st.dev of the nutrient contents in each group. However, while describing the groups (just below the table) you specify the descriptors of each group but without a rational order. Eventually, would be nice to have descriptors cited always in the same order for all the groups and I would give a world to each category you considered at the beginning, thus: seed color, genetic material and I would add also the belonging to the gene pool. (Eventually a pCoA for each group would be useful to see how accessions in each group distribute in relation to the categories mentioned above?)

Line 304: maybe a fast citations of the co-segregation evidences of Fe and Zn too?

Line 311: rightly you talk about gene pools but in your experiment seems that you skip the belonging to a gene pool as an important factor. Maybe it has a sense considering your experiment but it is not clear to the reader… this should be specified somewhere as I’ve showed in the comments above.

Line 356: a reference when you say “increased indirectly by human selection”.

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Reviewer #1: Yes: Ester Murube Torcida

Reviewer #2: No

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Diversity of nutritional content in seeds of Brazilian common bean germplasm

PONE-D-20-08197R1

Dear Dr. Azeredo Gonçalves,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Roberto Papa, PhD

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PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: After considering all the changes suggested by the reviewers, I think the manuscript improves in terms of clarity and ease of understanding the study. As I already included in my first review, I consider that the printing quality of the images is not very good and I urge the journal editing team to check this issue in the final publication.

It seems to be a very interesting study that highlight the importance of studying nutritional characteristics in a crop as important as the common bean.

Reviewer #2: Authors have efficiently addressed the doubts arose by the reviewers in an exhaustive way. Tables and figures have been updated as suggested. The new submitted document is more legible and understandable by readers, in particular for the part relative to matherials and methods. Authors gave complete explanations to reviewers on decisions and modifications made after the first review. The article is now complete and ready for submission.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: Ester M. Murube Torcida

Reviewer #2: No