Geometric Analysis of Seed Shape Diversity in the Cucurbitaceae

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The paper addresses a significant gap in the literature by applying quantitative methods to describe seed shape diversity in the Cucurbitaceae family. The background is well-established, emphasizing the lack of such methods despite the family's agronomic importance. The study employs general morphological analysis, curvature analysis in the poles, and symmetry analysis to quantitatively assess seed shape. While the methods are suitable, a more detailed description of each technique would enhance understanding. The results and discussions hint at differences in seed shape but lacks an in-depth discussion of their implications. A more detailed exploration of the practical and theoretical significance of these differences would strengthen the paper. The conclusion succinctly summarizes the study's main outcomes. However, it would benefit from a statement on the broader implications of the research and potential avenues for future studies. Overall, the paper is well-written and logically structured, effectively presenting the key elements of the study. Some specific comments for your consideration:

- More detail on specific morphological measurements used in the analysis would enhance clarity.

- Consider discussing the limitations of the study and areas for further investigation.

- Clarify the geometric figures used for the overall description of seed shape.

- Explore the broader significance of the research for the field of plant science or agriculture.

- Starting from L104, the line space is changed for no apparent reasons?

- Table1, observe significant numbers

- what is the statistics method used to deal with uneven number of samples?

- Figures 3-11, please have the figures scaled so the 1-mm bar is standardized and identical across the figures

Author Response

Dear Reviewer,

Thank you very much for your comments that have contributed to improve the clarity and quality of the article.

According to your recommendation, more detailed descriptions have been given in the methods section. Subsection 2.3 that was entitled Fourier transform (EFT) in the previous version is now entitled Model design by Elliptic Fourier Transform (EFT). It describes the method used to acquire the model that was used for shape comparison in Cucumis species and varieties. Symmetry index has been defined in section 2.5, and the corresponding equation has been included in this section.

The contents of the results section have been summarized in a new paragraph at the beginning of the section, indicating that Cucumis species and varieties are the object of a detailed analysis in sub-section 3-4. The results of shape comparison with the model for Cucumis are presented in Table 4 and those of symmetry analysis for species and varieties of this genus, in Table 5. The later were applied in a dendrogram that is now shown in Figure 12, indicating in the text that similar results were obtained with the results of shape comparison.

Following your advice, a more in-depth discussion on the implications of the quantitative morphological methods is given now in the discussion, considering the limitations of the study and areas for further investigation. An exploration of the practical and theoretical significance of the results found is also included now in the discussion.

The conclusion has been rewritten following your advice and considering now the broader implications of the research and potential avenues for future studies.

Since the samples had different size, the statistical method used was used Kruskall-Wallis test.

Figures have been scaled and other minor changes suggested have been done.

Looking forward to your answer, on behalf of the authors,

Emilio Cervantes

Reviewer 2 Report

Comments and Suggestions for Authors

This manuscript introduced a seed shape analysis method. I have the following concerns.

1. Keyword, 'models' was mentioned. It seem that some models should be established in this study. However, it was hard to find explicit models in the materials or results section. Please kindly make a clear explaination about the 'Model'.

2. This special issue is 'Application of Imaging and Artificial Intelligence in Seed Research'. In this manuscript, there were no artificial intelligence-related content. As for imaging-related content, the image processing method was relatively weak.

3. How many seed samples of each variety were analyzed? this important information was missing in the manuscript.

4. Line 131, Line 146, '2.4' are duplicated.

5. The conclusion was very weak. Please stated the main results with performance index of the methods. Please highlight the main discoveries and new technologies provided by this study.

6. Please kindly pay attention to the self-citation problem.

Comments on the Quality of English Language

None.

Author Response

Dear Reviewer,

Thank you very much for your comments to our article that have contributed to improve the clarity and quality of the presentation in this new version.

According to your recommendation, subsection 2.3 that was entitled Fourier transform (EFT) in the previous version is now entitled Model design by Elliptic Fourier Transform (EFT). In this subsection it has been specified that the model used for shape comparison of Cucumis species and varieties resulted from the EFT expansion with six harmonics corresponding to 25 points taken regularly along a seed silhouette of C. sativus. The model used is also described in the results section: 3.4.2. Morphological comparison by models based on EFT curves reproducing the seed silhouettes and may be downloaded from the web site indicated in the supplementary materials section.

We agree that there were not any specific artificial intelligence-related protocols in the elaboration of data or images in this article. Nevertheless, the work described fits well with the special issue entitled 'Application of Imaging and Artificial Intelligence in Seed Research' because the techniques proposed for image analysis, being relatively easy to apply and requiring basic equipment, may be implemented to operate under automated control, providing new quantitative morphological data required for biological analysis.

The number of seeds analyzed in each experiment are indicated in the corresponding tables.

According to your commentary number 5, the discussion and conclusion sections have been modified to include now highlight the main discoveries and new technologies provided by this study.

Unnecessary self-references have been deleted.

Other minor changes suggested have been done.

Looking forward to your answer, on behalf of the authors,

Emilio Cervantes

Corresponding author

Reviewer 3 Report

Comments and Suggestions for Authors

Martín-Gómez et al., made an attempt to present a method for geometric analysis of seed shape diversity in the Cucurbitaceae family, which may help in the identification of agronomic varieties and discrimination different species based seed shape. The manuscript can be improved by addressing the following concerns.

Cucurbitaceae family consists about 965 species in around 95 genera. Identification of agronomic varieties and taxonomic classification based on 11 species is very less in my opinion.

Application of the method in taxonomical classification has to be more elaborative in the introduction.

I find many self citations, however I feel references from 22-31 can be reduced to  maximum two recent citations.

Page no 5 line 163: Present measurement of symmetry in a equation form.

Authors must justify why they have chosen Kruskal Walis test among many non parametric tests to identify significant difference between populations.

Authors used morphological measurements, curvature analysis and symmetry variables. Among all the considered variable which parameters are most important for characterization of the seed. Authors should present a dendrogram based on their parameters which should justify biological relationships within and between genera of the family Cucurbitaceae.

Heading of 3.1 and 3.4 seems similar, and headings 3.2 &3.4.1 and 3.3 &3.4.3 are exactly same in the Results section. However these sections should be combined to avoid repetition and enhance easy understanding.

Subheading 4.1 for the discussion section is not necessary. Further, authors should descriptively discuss the wider applicability of their findings with corroboration to sufficient citations.

Minor Comments

Grammar has to be rechecked

Species names are to be in italics

Page no 4 line 138: small x should be replaced with multiplication symbol in the equation

Line 168: according to [39]should be replaces with "according to Scaefer, [39]"

Line 356: Change "were comprised between" to "were observed between"

Comments on the Quality of English Language

Authors should check grammar before re-submission.

Author Response

Dear Reviewer,

Thank you very much for your comments article that have contributed to improve the readability and overall quality of the article.

We agree that 11 species is a short amount for a work on taxonomy of the family Cucurbitaceae. Nevertheless, our objective was more to describe new quantitative morphological methods that may contribute to the description of seed shape, and in consequence, be useful for taxonomic purposes. Also, the elaboration of the article has included the observation of seeds belonging to almost hundred species, of which 63 are presented in Supplementary Figures S1 and S2, as indicated in the Supplementary material section.

The application morphological methods of seed description in taxonomical classification has now been expanded both in the introduction and in the discussion.

Unnecessary self-references have been deleted.

According to your indication, in the materials and Methods section, the measurement of symmetry is expressed in a formula.

As indicated in M&M, given the heterogeneity in sample sizes or in their distributions, Kruskal-Wallis test was used to identify significant differences between populations for the measured variables.

Following your advice and for shake of clarity, the contents of the results section have been summarized at the beginning of the section, indicating there that Cucumis species and varieties are the object of a detailed analysis in sub-section 3-4. The results of the shape comparison with the model are here presented in Table 4 and those of symmetry analysis in Table 5. The later were applied in a dendrogram that is now shown in Figure 12, indicating that similar results were obtained with the results of shape comparison.

A dendrogram with the results of symmetry analysis in Cucumis species and varieties in now given in Figure 12, with the indication that similar results were obtained by the quantitative shape comparison by models. These aspects are now discussed in the Discussion section.

The discussion is now expanded on the relative relevance, drawbacks and benefits, of each of the parameters considered for species characterization and taxonomical application.

Other minor changes suggested have been done.

Looking forward to your answer, on behalf of the authors,

Emilio Cervantes

Corresponding author

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Thanks for the revision

Reviewer 2 Report

Comments and Suggestions for Authors

The authors have revised the manuscipt. It can be accepted.

Comments on the Quality of English Language

None.

Reviewer 3 Report

Comments and Suggestions for Authors

The manuscript may be accepted after minor English editing

Comments on the Quality of English Language

The manuscript may be accepted after minor English editing