Plant Growth Regulators and Short-Term Irrigation for Berry Maturation Homogeneity and Increased Coffea arabica Bean Quality

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript entitled "Is It Worthy of the Application of Plant Growth Regulators and Irrigation to Homogenize Berry Maturation of Coffea arabica? Yield, Bean Chemical Composition and Virtual Plant Responses" This study explores the effects of plant growth regulators and irrigation on the uniformity of Arabica coffee berry maturation, as well as their influence on chemical composition and overall yield. Given the economic importance of coffee cultivation in Brazil, the topic is both relevant and significant. Overall, manuscript is generally well-written, exhibiting a clear methodology and insightful observations. I commend the authors for their thorough and commendable work. However, I have identified several issues should be improved to enhance the manuscript's clarity.

Title:

I suggested the authors consider a more concise title, such as "Plant Growth Regulators and Irrigation: Impacts on Coffee Berry Maturation and Quality." If the authors wish to emphasize the application potential detailed in the original longer title, you could integrate those into the abstract.

Abstract:

Lines 10-37: The abstract could be strengthened by streamlining the description of treatments and providing a clearer outline of the evaluation metrics. Restructuring the abstract to explicitly separate the background, hypothesis, methodology, key findings, and conclusions would improve reader comprehension. I suggest authors give a more quantitative presentation of key results, for example, specifying the percentage of dry matter and the increase in red fruit and overall fruit yield, it would allow readers to quickly appreciate the significance of the findings.

Authors should expand the conclusions in the abstract to discuss the potential practical applications for coffee cultivation in the region.

I suggest the authors confirm the keywords to ensure they accurately reflect the manuscript's core content. How about considering the following revisions: Arabica coffee; Plant Growth Regulators; Irrigation; Homogenize Berry Maturation; Functional–Structural Plant Modelling.

Introduction:

The introduction effectively presents the research problem, the significance of the study, and the associated hypotheses. However, there appears to be some disconnect between paragraphs. For example:

In line 48: the authors could enhance logical flow by incorporating a statement like, "Understanding which factors influence the plant's physiological processes is crucial for developing strategies to improve berry maturation and overall coffee quality."

In lines 69-100: the authors should provide a more comprehensive conclusion of recent research advancements related to irrigation and plant growth regulators, emphasizing their importance to Arabica coffee quality.

Materials and Methods:

In lines 145-146:  the authors should verify the NPK fertilization amounts and include the appropriate references.

Results:

The results section suffers from inconsistent use of full terms and abbreviations, which affects readability. To improve clarity, abbreviations should be used consistently after the full term has been defined in the methods section. Conversely, certain terms—such as irrigation (IRR), sucrose (SUC), total soluble sugars (TS), and cafestol (CFT)—are clearer when presented in their full form. A more judicious and consistent use of abbreviations will improve the overall efficiency of information transfer.

Line 286: Please confirm whether "n=4" is correct. This issue appears in other figures as well.

Line 315: In Figure 3, the font uniformity should be checked; some elements are bold, while others are not, and some images lack color.

Discussion:

I recommend structuring this section around the three hypotheses presented in the introduction, which would allow for a clearer and more coherent response to each hypothesis.

Conclusions:

I suggest the authors elaborate on the broader implications of this study and its potential applications in the future.

Author Response

Open Review

(x) I would not like to sign my review report
( ) I would like to sign my review report

Quality of English Language

( ) The English could be improved to more clearly express the research.
(x) The English is fine and does not require any improvement.

 

	Yes	Can be improved	Must be improved	Not applicable
Is the content succinctly described and contextualized with respect to previous and present theoretical background and empirical research (if applicable) on the topic?	(x)	( )	( )	( )
Are the research design, questions, hypotheses and methods clearly stated?	(x)	( )	( )	( )
Are the arguments and discussion of findings coherent, balanced and compelling?	( )	( )	( )	( )
For empirical research, are the results clearly presented?	( )	(x)	( )	( )
Is the article adequately referenced?	(x)	( )	( )	( )
Are the conclusions thoroughly supported by the results presented in the article or referenced in secondary literature?	( )	(x)	( )	( )

Comments and Suggestions for Authors

The manuscript entitled "Is It Worthy of the Application of Plant Growth Regulators and Irrigation to Homogenize Berry Maturation of Coffea arabica? Yield, Bean Chemical Composition and Virtual Plant Responses" This study explores the effects of plant growth regulators and irrigation on the uniformity of Arabica coffee berry maturation, as well as their influence on chemical composition and overall yield. Given the economic importance of coffee cultivation in Brazil, the topic is both relevant and significant. Overall, manuscript is generally well-written, exhibiting a clear methodology and insightful observations. I commend the authors for their thorough and commendable work. However, I have identified several issues should be improved to enhance the manuscript's clarity.

Authors: Thank you for your positive opinion, and useful suggestions.

Title:

I suggested the authors consider a more concise title, such as "Plant Growth Regulators and Irrigation: Impacts on Coffee Berry Maturation and Quality." If the authors wish to emphasize the application potential detailed in the original longer title, you could integrate those into the abstract.

Authors: Thank you for your suggestion. It is recommended not to use words as ‘effect’ and ‘impact’ in the title and to be direct, expressing some important points. The PGRs were applied only one time, and irrigation only during berry maturation phenophase. We followed your recommendation in general lines and made one more concise title:

“Plant Growth Regulators and Short-Term Irrigation for Berry Maturation Homogenization and Increased Bean Quality of Coffea arabica”

Abstract:

Lines 10-37: The abstract could be strengthened by streamlining the description of treatments and providing a clearer outline of the evaluation metrics. Restructuring the abstract to explicitly separate the background, hypothesis, methodology, key findings, and conclusions would improve reader comprehension. I suggest authors give a more quantitative presentation of key results, for example, specifying the percentage of dry matter and the increase in red fruit and overall fruit yield, it would allow readers to quickly appreciate the significance of the findings.

Authors: We followed your suggestion in respecting a division but respecting the rule of MDPI to create abstract in only one paragraph. The explicit separation of background, hypothesis, methodology, key findings, and conclusions is usual in some journals, as in Annals of Botany, for example.

Thank you for your suggestion and we improved the key results:

….The 3^rd order axes participation in berry yield was up to ~37% of red and 25% of green berries. The greatest separation between PGRs can be seen in S2, where more berries in the Ethephon plants were found than in the GA3 ones, while the dry mass (DM) percentage was higher in the GA3 than in the Ethephon treatment. The percentage of DM in fresh mass was 17–28% in green berries and 28–36% in red ones. PGRs were worthy of applying for berry maturity homogenization, especially GA3, which also showed the lowest total chlorogenic acid content… (lines 29-35).

Authors should expand the conclusions in the abstract to discuss the potential practical applications for coffee cultivation in the region.

Authors: We have added some more direct conclusions valuable for all similar regions:

NI plants showed reduced red and total berry production compared to irrigated ones, indicating this horticultural measure worthy, even in a sustainably reduced six–week period, due to preserved leaf area and plant photosynthesis, increased lipid and kahweol contents under irrigation when compared to NI, despite the maturation delay. (lines 35-39).

I suggest the authors confirm the keywords to ensure they accurately reflect the manuscript's core content. How about considering the following revisions: Arabica coffee; Plant Growth Regulators; Irrigation; Homogenize Berry Maturation; Functional–Structural Plant Modelling.

Authors: We followed your suggestion, but with restrictions because the two principal rules of keywords are to never repeat the words used in the title, and to mention the parameters used in the Results. We erased ‘bean quality’ because it became a part of a new title, and we added ‘functional–structural plant modelling’, as you recommended, because it is not anymore in the title.

Introduction:

The introduction effectively presents the research problem, the significance of the study, and the associated hypotheses.

Authors: thank you.

However, there appears to be some disconnect between paragraphs. For example:

In line 48: the authors could enhance logical flow by incorporating a statement like, "Understanding which factors influence the plant's physiological processes is crucial for developing strategies to improve berry maturation and overall coffee quality."

Authors: thank you. We added this text of connection to the lines 51-52.

In lines 69-100: the authors should provide a more comprehensive conclusion of recent research advancements related to irrigation and plant growth regulators, emphasizing their importance to Arabica coffee quality.

Authors: thank you. To improve the introduction related to irrigation and PGRs in coffee culture we added:

…Under the climates characterized by one long very dry period, coffee plants grown under rainfed conditions can suffer complete failure of flowering and fruit production in some years [23]. On the other hand,… (lines  83-85)

…The controlled irrigation during the dry period associated with adequate nitrogen NPK fertilization will increase berry yield and promote formation of chemical components such as lipids, chlorogenic acids and caffeine [23]… (lines  91-93)

… For example, the commercial mixture of gibberellic acid, auxin and cytokinin zeatin applied in various phenophases can improve the productivity of Arabica coffee up to 46.9% [32]. (lines  110-111)

 

Materials and Methods:

In lines 145-146:  the authors should verify the NPK fertilization amounts and include the appropriate references.

Authors: The fertilization amounts are OK. It was added:

…high doses necessary for seven-year-old plants [23, 42]. (lines  158-159)

 

Results:

The results section suffers from inconsistent use of full terms and abbreviations, which affects readability. To improve clarity, abbreviations should be used consistently after the full term has been defined in the methods section. Conversely, certain terms—such as irrigation (IRR), sucrose (SUC), total soluble sugars (TS), and cafestol (CFT)—are clearer when presented in their full form. A more judicious and consistent use of abbreviations will improve the overall efficiency of information transfer.

Authors: We improved the use of terms and abbreviations, as suggested, over the whole mnscript.

Line 286: Please confirm whether "n=4" is correct. This issue appears in other figures as well.

Authors: In the line 286 was ‘n=2’, which is correct for the Figures 1-5 (related to 3D reconstructions). In the figures 6-9, n=4 (related to berry collection and chemical analyses).

Line 315: In Figure 3, the font uniformity should be checked; some elements are bold, while others are not, and some images lack color.

Authors: Thank you, the font uniformity was improved. The color is missing in the figures where the impact of water regimes was investigated.

Discussion:

I recommend structuring this section around the three hypotheses presented in the introduction, which would allow for a clearer and more coherent response to each hypothesis.

Authors: Thank you. We followed your recommendations. We included three subtitles to respond to hypotheses and to be coherent, we inverted some paragraph order. For example, the paragraph that discussed PGRs and bean quality is actually in lines 510-527, while previously was in lines 521-539.

Conclusions:

I suggest the authors elaborate on the broader implications of this study and its potential applications in the future.

Authors: Thank you. We added:

…As a general conclusion, in conditions of dry period, as occurs in many coffee growth regions over the world, the short-term sustainable irrigation applied during six weeks of berry maturation is worthy despite it delayed maturation when compared to rainfed conditions, with one-term additional application of PGRs that would increase the uniformity of berry maturation. (Lines 572-576).

 

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The study presents an interesting and novel contribution by extending Functional-Structural Plant Modeling (FSPM) to incorporate the effects of plant growth regulators (PGRs), such as GA3 and Ethephon, on coffee trees. The methods and results are comprehensive, which is a strength of the work. However, I found it challenging to distinguish between the modeled and observed results in several sections, and some aspects of the FSPM’s role and implementation could be clarified. Below are specific comments and questions:

1. Discrepancy in Model Performance (Figure 3):
   The authors validate their 3D plant model by comparing estimated leaf-level assimilation (A) and Leaf Area Index (LAI) with field measurements. According to Figure 3, the model accurately estimates A but performs poorly in capturing LAI variability (e.g., Figure 3B shows the model missing LAI fluctuations entirely). Could you explain why the model behaves so differently for these two parameters?
2. Clarity of Section 2.2:
   Section 2.2 is unclear about whether it describes a field experiment or a modeling exercise. It’s difficult to discern which results stem from empirical measurements and which from model simulations. Please specify the nature of each component in this and other sections to improve readability.
3. Role of FSPM in the Study:
   The PGR and irrigation experiments (Section 2.2) appear to be based on actual fieldwork rather than modeling. If so, it’s not immediately clear how the FSPM is needed to address the research question posed in the title, “Is It Worthy of the Application of Plant Growth Regulators and Irrigation.” The field and lab data alone seem sufficient to answer this. Could you elaborate on the added value of the FSPM? How does it enhance the insights derived from the lab data?
4. Observed vs. Modeled Results:
   Most of the results presented seem to originate from observations rather than modeling. For instance, Figures 1 and 2 appear to be based on gas exchange data, and Figures 5-9 seem to be lab analyses, while only Figures 3 and 4 are tied to modeling outputs. Is this correct? Again, why is FSPM needed?
5. Expanding Model Validation:
   The model is validated using only leaf-level assimilation (A) and LAI. Given the availability of additional field and lab data—such as the percentage of green and red berries and their dry masses—it would be valuable to extend the model to simulate these outcomes as well. Could you generate such modeled results to correspond with the lab results? This would provide a more robust validation and demonstrate the model’s broader utility.
6. Modifications to FSPM for PGR Effects:
   The manuscript lacks detail on how the FSPM was modified to account for the impacts of PGRs like GA3 and Ethephon. What specific changes were made to the model? For example, were any biochemical processes or parameters adjusted to reflect these hormonal applications?

Author Response

Open Review

(x) I would not like to sign my review report
( ) I would like to sign my review report

Quality of English Language

( ) The English could be improved to more clearly express the research.
(x) The English is fine and does not require any improvement.

 

	Yes	Can be improved	Must be improved	Not applicable
Is the content succinctly described and contextualized with respect to previous and present theoretical background and empirical research (if applicable) on the topic?	(x)	( )	( )	( )
Are the research design, questions, hypotheses and methods clearly stated?	( )	( )	(x)	( )
Are the arguments and discussion of findings coherent, balanced and compelling?	( )	(x)	( )	( )
For empirical research, are the results clearly presented?	( )	( )	(x)	( )
Is the article adequately referenced?	( )	( )	( )	( )
Are the conclusions thoroughly supported by the results presented in the article or referenced in secondary literature?	( )	(x)	( )	( )

Comments and Suggestions for Authors

The study presents an interesting and novel contribution by extending Functional-Structural Plant Modeling (FSPM) to incorporate the effects of plant growth regulators (PGRs), such as GA3 and Ethephon, on coffee trees. The methods and results are comprehensive, which is a strength of the work.

Authors: Thank you.

However, I found it challenging to distinguish between the modeled and observed results in several sections, and some aspects of the FSPM’s role and implementation could be clarified.

Authors: That’s true that here we used the existing modelling platform (VPlants) and specific software adapted to coffee plants (CoffePlant3D), to  estimate the effects of PGRs and water regimes on formed leaf area, berry distribution and whole plant photosynthesis. Over the manuscript, we added various short explanations (in blue) to make a text clear, because FSPM was used as a tool, together with various field measurements:

…A combination of field measurements (leaf gas exchanges, berry collection and chemical bean analyses by vertical plant strata) and computing based on existing FSP models was used. In the beginning and the end of BM, coffee trees were coded following VPlants modelling platform and reconstructed using software CoffePlant3D to compute plant leaf area and plant photosynthesis…  (lines 22-26)

…To test those hypotheses, leaf A was integrated at plant scale through FSPM and the distribution of berries over the plant vertical profile was analyzed, together with berry yield and chemical composition of coffee beans. (lines 134-136)

…Line 177

…Line 190

…Lines 193-195

…Line 198

…Lines 218-219

…Lines 231-233

Below are specific comments and questions:

1. Discrepancy in Model Performance (Figure 3):
   The authors validate their 3D plant model by comparing estimated leaf-level assimilation (A) and Leaf Area Index (LAI) with field measurements. According to Figure 3, the model accurately estimates A but performs poorly in capturing LAI variability (e.g., Figure 3B shows the model missing LAI fluctuations entirely). Could you explain why the model behaves so differently for these two parameters?

Authors: We added:

…We chose plants of very similar size, and LAI did not vary significantly during the two phenophases. (lines 327-328)

…The A varied, because of the two strata where it was measured (one light-exposed and the second shaded), which significantly impacted on A intensity (from 2 to 14 μmol CO₂ m^-2 s^-1)  (lines 330-332)

 

2. Clarity of Section 2.2:

Section 2.2 is unclear about whether it describes a field experiment or a modeling exercise. It’s difficult to discern which results stem from empirical measurements and which from model simulations. Please specify the nature of each component in this and other sections to improve readability.

Authors: The section was improved to distinguish between the field experiment and modelling. See lines 177, 190, 193-195, and 198.

1. Role of FSPM in the Study:

The PGR and irrigation experiments (Section 2.2) appear to be based on actual fieldwork rather than modeling. If so, it’s not immediately clear how the FSPM is needed to address the research question posed in the title, “Is It Worthy of the Application of Plant Growth Regulators and Irrigation.” The field and lab data alone seem sufficient to answer this. Could you elaborate on the added value of the FSPM? How does it enhance the insights derived from the lab data?

Authors: The FSPM helped with photosynthesis at plant scale and plant LA estimations, which we added in the abstract, emphasized in M&M, and was existing in Discussion (which was restructured, by demand of reviewer #1).

4. Observed vs. Modeled Results:

Most of the results presented seem to originate from observations rather than modeling. For instance, Figures 1 and 2 appear to be based on gas exchange data, and Figures 5-9 seem to be lab analyses, while only Figures 3 and 4 are tied to modeling outputs. Is this correct? Again, why is FSPM needed?

Authors: That’s correct. Such observations were included in the text to be clear, even in Results. Again, we used FSPM to model plant scale photosynthesis and plant LA.

1. Expanding Model Validation:

The model is validated using only leaf-level assimilation (A) and LAI. Given the availability of additional field and lab data—such as the percentage of green and red berries and their dry masses—it would be valuable to extend the model to simulate these outcomes as well. Could you generate such modeled results to correspond with the lab results? This would provide a more robust validation and demonstrate the model’s broader utility.

Authors: The number of berries is confirmed and are 100% exact, because the reconstruction (using CoffePlant3D) is based on number of berries (see Matsunaga et al., SpringerPlus, 2016). So, it will be simple repetition of reconstructed and counted data. On the other hand, the DM had never been included, only 3D structural reconstruction, and verification with such variable would not be possible.

 

6. Modifications to FSPM for PGR Effects:
   The manuscript lacks detail on how the FSPM was modified to account for the impacts of PGRs like GA3 and Ethephon. What specific changes were made to the model? For example, were any biochemical processes or parameters adjusted to reflect these hormonal applications?

Authors: We included the variations in V_cmax, J_max and R_d variations over the vertical profile and considering each plant:

…For the A_p” computing, the modelled Vc_max, J_max, and R_d were used differing each plant and strata (see section 2.3). (lines 218-219).

 

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

The revised version looks okay.