NIRS Estimation of Drought Stress on Chemical Quality Constituents of Taro (Colocasia esculenta L.) and Sweet Potato (Ipomoea batatas L.) Flours
Round 1
Reviewer 1 Report
Title is misleading, the Nir acquisition were made on flour and not on whole Taro or Sweet Potato.
Lines 55-56: rewrite this sentence and add bibliographic reference.
Did the nir analysis have been done of flour samples coming from root and shoot? this information is not clear. the experimental plan is quite confused.
Lines 140-147: the description of the PLS model development is quite confused and poorly described.
line 148-169: The description of the statistical indexes used to evaluate the model performance is too long. Some information are redundant. The author should report the method used to select the sample s used to validate the model (Independent set)
Lines 180-188: The section regarding the ANOVA results should be rewritten as more compressible way. It is not clear between those mean was done the analysis. More info should be reported on the ANOVA analysis, for example the type of post-hoc test. Furthermore the ANOVA can be done only if the data are normally distributed and there is the homogeneity of the variance. the author should check this condition by a statistical test (e.g leven test).
Lines 206-209: rewrite this sentence, It is not clear how the PLS models were developed.
Regarding the figure 1, add a quality discussion on the spectra ( e.g. chemical bonds)
lines 218-220: delete
Table 2: For all the quality parameters, R2 values of the validation set are higher of those achieved for the calibration set, this could be a signal of the model overfitting
Lines 221-245: reduce this part, all the reported data are already shown in table2. Furthermore could be interesting insert a discussion of loadings or VIP scores.
The above comments should be considered also for the section on sweet potato.
The sections 3.2 “Variability of quality chemical composition” should be removed because is outside of the scope of the paper.
Author Response
Response to Reviewer 1 Comments
We thank the reviewer for the careful reading of the manuscript, the pertinent comments, and suggestions.
Point 1: Title is misleading, the Nir acquisition were made on flour and not on whole Taro or Sweet Potato.
Response 1: We acknowledge the reviewer’s comment about the title.
To better highlight the subject of the present study, to clarify the NIRS acquisition, and to integrate Point 13 related to the scope of our paper, we reformulated the title to: “NIRS estimation of drought stress on chemical quality constituents of taro (Colocasia esculenta L.) and sweet potato (Ipomoea batatas L.) flours”.
Point 2: Lines 55-56: rewrite this sentence and add bibliographic reference.
Response 2: The suggested correction was made.
Point 3: Did the nir analysis have been done of flour samples coming from root and shoot? this information is not clear. the experimental plan is quite confused. Lines 140-147: the description of the PLS model development is quite confused and poorly described.
Response 3: Yes, NIR analysis was performed on flour samples from underground (tubers, corms) and aboveground (shoots) organs. To better clarify the experimental plan, the NIRS measurements, data pretreatment and analysis, were divided in 3 main steps:
- We obtained the NIR spectrum corresponding to each sample calibration (Lines 135-140).
- Additionally, we determined the mathematical model (e.g., PLS) between NIR spectra and values of corresponding references (calibration samples) for each quality constituent. The chemometric procedures (SNV, derivatives) used for the calibration model robustness goes through the spectral pretreatment that facilitates the calibration process by reducing, eliminating or standardizing spectral variations and oscillations from sample light scattering and intermolecular interactions between components (Lines 140-147).
- And finally, the quality of calibration, prediction and validation of the PLS models were determined through standard statistical tests (SEC, SEP, SECV, r2, RPD), to verify if both reference and NIRS values are statistically correlated (Lines 148-174).
(The line numbers above refer to the original version of the manuscript).
Point 4: line 148-169: The description of the statistical indexes used to evaluate the model performance is too long. Some information are redundant. The author should report the method used to select the sample s used to validate the model (Independent set)
Response 4: We simplified that part of the text from the NIRS measurements, data pretreatment, and analysis, keeping the content that we consider indispensable to discuss the results. We also introduced the information that the method selection of the independent set of samples was made randomly.
Point 5: Lines 180-188: The section regarding the ANOVA results should be rewritten as more compressible way. It is not clear between those mean was done the analysis. More info should be reported on the ANOVA analysis, for example the type of post-hoc test. Furthermore, the ANOVA can be done only if the data are normally distributed and there is the homogeneity of the variance. the author should check this condition by a statistical test (e.g leven test).
Response 5: We added to the statistical analysis the Kolmogorov-Smirnov non-parametric test, to verify the data normal distribution.
The section regarding ANOVA results was described according to Table S1, a comparison of means for the two water regimes (control and drought conditions). No post-hoc test was performed, because the ANOVA was run between control and stress groups, not meeting the minimum three groups required to run post-hoc tests (e.g., Tukey HSD test, Levene’s Test). However, we rewrote the ANOVA results to better clarify the analysis context.
Point 6: Lines 206-209: rewrite this sentence, It is not clear how the PLS models were developed.
Response 6: We simplified that sentence: “The chemical reference values for each plant organ from the 1st trial were used to implement the calibration set. Another set of flour samples from the 1st trial were held and used as an independent validation set”. The relevant part of the PLS implementation was described in the next paragraph.
Point 7: Regarding the figure 1, add a quality discussion on the spectra ( e.g. chemical bonds)
Response 7: The suggested correction was made.
Point 8: lines 218-220: delete
Response 8: The suggested correction was made.
Point 9: Table 2: For all the quality parameters, R2 values of the validation set are higher of those achieved for the calibration set, this could be a signal of the model overfitting
Response 9: Through the validation set robustness, the majority of the models had a robust fitting with SEC and SECV similarity and accuracy with SEP and SEC matching values. Still, in the construction of the calibration models, we had no standardization of samples, preventing the over-fitting that may occur with the addition of non-relevant channels. We acknowledge the reviewer’s comment that r2 values are slightly higher in the independent validation set despite the validation set being made up of independent samples, probably they are more fit for being from the same trial. In fact, this is one of the reasons why we concluded that the present calibration models could be applied in further research on crop quality subjected to water scarcity conditions, but it needs additional data from new drought trials to improve the existing models.
Point 10: Lines 221-245: reduce this part, all the reported data are already shown in table2. Furthermore could be interesting insert a discussion of loadings or VIP scores.
Response 10: We focused mainly on our results and kept their relationship with other literature references. These data report turned out to be extremely important to provide relevant information about the study, and also how they provide a good way to explain the accuracy of the obtained calibration equations between the taro organs under water scarcity conditions, to be used in the prediction of the chemical constituents of the 2nd trial (section 3.2).
Point 11: The above comments should be considered also for the section on sweet potato.
Response 11: Yes, indeed, the suggested reviewer’s comments were performed in the section on sweet potato.
Point 12: The sections 3.2 “Variability of quality chemical composition” should be removed because is outside of the scope of the paper.
Response 12: We acknowledge the reviewer’s suggestion. In fact, what we are discussing in section 3.2 are not exclusively linked to “quality”, being more focused on the variability of chemical constituents. In this section, we show the application of the PLS models constructed from the calibration and external validation sets from the 1st agronomic trial (section 3.1) that allowed the prediction of the quality parameters variability of both crops to drought in the 2nd agronomic trial. Section 3.2 also discusses one of our objectives, which is to find connections within the crop phenotype and its chemotype and other major chemical quality constituent values obtained for drought. So, we consider that section 3.2 is a fundamental part of the scope of the paper and, to better clarify its subject, we reformulated the title section to: “Variability of chemical constituents”.
Author Response File: 
Author Response.docx
Reviewer 2 Report
Dear authors,
I had a great opportunity to review the research manuscript “NIRS Estimation of Taro (Colocasia esculenta) and Sweet Potato (Ipomoea batatas) Quality After Drought” (Manuscript ID applsci-997264) which is considered for publication in Applied Sciences (ISSN 2076-3417) newspaper.
I analyzed the whole manuscript and it showed some interesting insights in topic of NIRS potential for further research on crop quality under drought. In my opinion, this paper needs major revision. Below I list several questions and comments about the manuscript that, in my view, will improve it. I recommend Authors to address them as best as they can.
1) Title: could you improve the title to let it more attractive and original?
2 ) Introduction (lane 47)- Is oxalic acid produced during drought stress? If yes please add « under drought condition » -Please add one sentence to show the originality of this paper! (no study showed ...) [Lanes 84-87] Please rephrase the objective in order to make it very simple. Figure 1 the axes are not visible, the figure needs improvement.
3) Methods [Lanes 90-92] what did you mean by "different water stress levels? how did you manage this stress level I strongly recommend the authors to add a figure that describes the method used in a greenhouse (from the greenhouse until the analysis of the results). This will facilitate the understanding for the reader especially since there is a lot of steps. Thank you
4 ) Discussion In general, in this part, the results are very detailed in a repetitive way (increase decrease, highest significant ....) and the discussion is really missing! the reader is interested in knowing the reasons for which there was an increase or a decrease while referring to the literature! please deepen your discussion!
[Lanes178-185] add the referent figure. [Lanes340-341] detaile these ideas from the literature.
Best regards,
Author Response
Response to Reviewer 2 Comments
Dear authors,
I had a great opportunity to review the research manuscript “NIRS Estimation of Taro (Colocasia esculenta) and Sweet Potato (Ipomoea batatas) Quality After Drought” (Manuscript ID applsci-997264) which is considered for publication in Applied Sciences (ISSN 2076-3417) newspaper.
I analyzed the whole manuscript and it showed some interesting insights in topic of NIRS potential for further research on crop quality under drought. In my opinion, this paper needs major revision. Below I list several questions and comments about the manuscript that, in my view, will improve it. I recommend Authors to address them as best as they can.
- We thank the reviewer for the careful reading of the manuscript, and we acknowledge your comments and suggestions.
Point 1: Title: could you improve the title to let it more attractive and original?
Response 1: We thank the reviewer for the careful reading of the manuscript, and for the pertinent comments and questions. We acknowledge the reviewer’s comment about the title of the present paper. We reformulated the title to: “NIRS estimation of drought stress on chemical quality constituents of taro (Colocasia esculenta L.) and sweet potato (Ipomoea batatas L.) flours”. With this change, we aimed to clarify the NIRS acquisition, and to improve the integration of the scope of our paper.
Point 2: Introduction (lane 47)- Is oxalic acid produced during drought stress? If yes please add « under drought condition » -Please add one sentence to show the originality of this paper! (no study showed ...) [Lanes 84-87] Please rephrase the objective in order to make it very simple. Figure 1 the axes are not visible, the figure needs improvement.
Response 2: The suggested corrections were made. We added the information suggested by the reviewer concerning the oxalic acid production under drought, one sentence mentioning the originality of this paper, and we restructured the objective text to improve its context. Figure 1 has axes visible. They may not be well noticed due to the image size in the manuscript document. We re-upload Figures 1 and 2 with higher resolution.
Point 3: Methods [Lanes 90-92] what did you mean by "different water stress levels? how did you manage this stress level I strongly recommend the authors to add a figure that describes the method used in a greenhouse (from the greenhouse until the analysis of the results). This will facilitate the understanding for the reader especially since there is a lot of steps. Thank you
Response 3: We appreciate the reviewer’s suggestions. In Lines 90-92, we simplified that sentence to improve its context. When we refer to different water stress levels, we tried to mention that different irrigations were applied between control and stress experimental replicates. We added a figure as a supplement (Figure S1) to avoid overloading the content of the present manuscript by representing a short schematization of the drought assays until the analysis of the results.
Point 4: Discussion In general, in this part, the results are very detailed in a repetitive way (increase decrease, highest significant ....) and the discussion is really missing! the reader is interested in knowing the reasons for which there was an increase or a decrease while referring to the literature! please deepen your discussion!
[Lanes178-185] add the referent figure. [Lanes340-341] detaile these ideas from the literature.
Best regards,
Response 4: We acknowledge the reviewer’s comments. In fact, section 3.1 is more technical and focused on our results, showing a brief mention of their relationship with other literature references. These data report turned out to be extremely important to provide relevant information about the accuracy of the obtained calibration equations between the taro and sweet potato organs from the 1st trial under water scarcity conditions, to be used in the prediction of the chemical constituents of the 2nd trial (Section 3.2). However, this last section presented a brief discussion of major constituents’ variation of the plant organs to drought and its correlation between the two agronomic trials through their reference and predicted values, also referring to literature the plausible reasons for the registered variations. Here, we tried to find a reasonable connection within the crops phenotype drought response and its chemotype and other major chemical quality constituent obtained values, using the generated NIR models, to help to monitor these crops according to their tolerance or susceptibility to drought stress.
On Lines 178-185, there is no figure cited in the text. That lines express the results that are present in Table S1.
Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
Response 5.
To evaluate the differences between only two group, t-test should be used, not ANOVA.
Levene-test is not a post-hoc test, but a test useful to check Homoscedasticity that I suggest to evaluate before to use parametric method (ANOVA or t-test).
I suggest to consult this reference: “Observations on the use of statistical methods in Food Science and Technology, Food research International, 55, 137-149.
Author Response
Point 1: Response 5.
To evaluate the differences between only two group, t-test should be used, not ANOVA.
Levene-test is not a post-hoc test, but a test useful to check Homoscedasticity that I suggest to evaluate before to use parametric method (ANOVA or t-test).
I suggest to consult this reference: “Observations on the use of statistical methods in Food Science and Technology, Food research International, 55, 137-149.
Response 1: We appreciate the reviewer’s comment. We consulted the work of Granato et al. [1] and we found it very useful, mainly by Figure 7 from the reference provided by the reviewer. In Granato et al. [1], the One-way ANOVA is used when three or more mean values need to be compared, but we can use it to test if two mean values are significantly different [2,3]. We checked the data homoscedasticity by the Levene’s test [1] to seek the assumption of homogeneity of variance to allow to apply One-way analysis of variance (ANOVA) to determine statistically significant differences (P < 0.05) between the means of control and drought independent groups. We indeed verify that assumption and complemented section 2.3 Statistical Analysis referring to Levene’s test.
References:
- Granato, D.; Calado, V.M.A.; Jarvis, B. Observations on the use of statistical methods in Food Science and Technology. Food Research International. 2014, 55, 137-149.
- SPSS Tutorials: One-Way ANOVA, https://libguides.library.kent.edu/spss/onewayanova, 2020. Accessed at December 1, 2020.
- Bird, K.D. Comparing two means. In Analysis of variance via confidence intervals; Bird, K.D., Ed.; SAGE Publications, Ltd.: London, 2004; pp. 2-27.
Reviewer 2 Report
Dear reviewers,
Your paper could be accepted in the present form. Congratulations and good luck.
I strongly recommend that you insert the suggested figure in the manuscript( not in the supplementary file). thank you for a good collaboration
Best regards.
Author Response
Point 1: Dear reviewers,
Your paper could be accepted in the present form.
Congratulations and good luck.
I strongly recommend that you insert the suggested figure in the manuscript( not in the supplementary file). thank you for a good collaboration
Best regards.
Response 1: The reviewer recommendation was made. We moved the figure representing a short schematization of the drought assays until the analysis from the supplementary file and inserted it into the text as Figure 1. We acknowledge the reviewer’s constructive suggestions and positive comments, which helped us to improve this manuscript.
