Stability Analysis and Multi-Trait Selection of Flowering Phenology Parameters in Olive Cultivars Under Multi-Environment Trials

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

13.4.2025

The manuscript entitled "Stability Analysis and Multi-Trait Selection of Flowering Phenology Parameter in Olive Cultivars under Multi-Environment” was reviewed.

The manuscript delivers novel analysis using holistic methods including BLUP to predict gene values related to olive phenology grown in non-Mediterranean regions, which was visualized using GGE plots. However, predictions and conclusions are risky as major physiological phenomenon in olives, the “alternative bearing” was not mentioned at all, neither in the materials and methods nor in the discussion. Neither did the authors mention the bearing status of the experimental units (trees) in the three influential years (2014 and 2015 experimental years and the 2013 preceding year). Therefore, I do not recommend the publication of this manuscript in "Plants" unless these corrections are made. Please see below additional comments.

1. General:

- The language is good and clear.

 

2. Abstract:

- Line 23: add ”to predict genetic value” after “prediction)”.

- Line 23: write the “GGE” in full “(Genotype + genotype by environment interaction)”.

- Line 23: add “to visualize and assess stability and performance” after “methods”.

- Line 23: remove “to examine GEI and genotype stability”.

 

3. Introduction:

- Very lengthy, please cut short from three pages to 1-2 pages.

 

4. Results:

- Well presented.

- Figure 1: it is better to change the dark blue color to something ligter to be able to read the values in the provided cells.

- Figure 1: you need to indicate the cultivar abbreviations used (genotype codes) listed in Table (5) in used in other figures RATHER than giving numbers of no meaning (1, 2, …16)

- Figures 3, 4, 5, and 6: you need higher resolution figures with enlarged fonts to be visually clear and usable.

 

5. Discussion:

- Moderate, you have novel findings that need to be discussed.

- You seriously need to consider discussing alternative bearing and the bearing status of your experimental unit (trees) across three years (2013, 2014, and 2015) and how this would affect your analysis and conclusions.

- Lines 391-402: this is more an introductory paragraph, please cut short.

- You need rather to show the importance of multiple DEGs as they are related to THE major DEVELPOMENTAL variations observed between the two investigated contrasting soybean varieties. This can cover pages of discussion!

- Lines 433-454: You should be more couscous in your genotype selection and conclusions. You need to consider listed requirements in materials and methods section (please see below), mainly the influential bearing status on your data analysis, which was unfortunately complete ignored

 

6. Materials and Methods:

- Line 484: major influential data is missing and need to be available in the manuscript for the investigated plant material:

 

a) Climate in the two locations and in each year: you need to provide a plot for temperature (showing daily values: mean, upper and lower) for the entire year.

b) Need to provide a plot of received water (both by rain and irrigation showing weekly values and accumulated values in each season).

c) Soil fertility in the two locations.

d) Management practices applied for comparative application: pruning levels, fertilizers and their type and quantity and did they practice any flower or fruit thinning and levels applied and methods used (manual or chemical).

e) Were the trees originated from rooted cutting or grafted on a rootstock?

Where all cultivars also having the same origin or no? and how this would affect the data analysis?

f) The age of experimental units (trees): what was their age? Was it similar between all cultivars and locations?

g) Alternative bearing tendency for the investigated cultivars: please add this information to table (5). For example, Frantoio and Arbequina are low, while Koroneiki is moderate and while Picual is high.

In addition, this should also be considered in the analysis!

h) Bearing status of experimental units: this is very crucial information in your analysis. Authors mentioned using three plots (replicates) each with three trees; this means nine trees per genotype per location.

What was the bearing status of each tress (all on, all off, or percent on and percent off)?

Are the same trees used in the three constitutive years (experimental years 2014 and 2015 in addition to the preceding year 2013)?

If yes, then on trees will be off and vice versa, which should be considered in the analysis!   

Otherwise, if another group was used each year (of course random selection), than again what was the bearing status of each tress (all on, all off, or percent on and percent off)?

Finally, you need to consider the bearing status in ALL three years (2013, 2014 and 2015)!

 

7. References:

- The list needs an update; only 33% of cited articles were published in the last five years (21 out of 61). This needs to go up to 45-50% by citing more recent and related articles.

 

 

Author Response

Dear Reviewer

Thank you very much for your thoughtful and constructive review of our manuscript. We are truly grateful for the time and effort you dedicated to reading our work and for your insightful comments, which have greatly contributed to improving the overall quality of our paper.

Your suggestions have helped us clarify important aspects of the study, and we have addressed each of your points carefully. Below, we provide a detailed, point-by-point response to all of your comments.

The manuscript delivers novel analysis using holistic methods including BLUP to predict gene values related to olive phenology grown in non-Mediterranean regions, which was visualized using GGE plots. However, predictions and conclusions are risky as major physiological phenomenon in olives, the “alternative bearing” was not mentioned at all, neither in the materials and methods nor in the discussion. Neither did the authors mention the bearing status of the experimental units (trees) in the three influential years (2014 and 2015 experimental years and the 2013 preceding year). Therefore, I do not recommend the publication of this manuscript in "Plants" unless these corrections are made. Please see below additional comments.

Reply:

We sincerely appreciate the valuable suggestion to incorporate major physiological phenomenon in olives, the “alternative bearing” in the Materials and Methods, and the Discussion. We fully agree that the bearing status of the observed trees in the three influential years (2014 and 2015 experimental years and the 2013 preceding year may have a significant influence on the results and conclusions derived from this study. However, due to limitation during this phase of the study, evaluating the bearing status of the observed trees in two orchards across three years was not feasible. Additionally, the available time frame to complete the further research was limited and quantitative genetics analysis was utilized for flowering phenology parameters of the observed trees.

1. General:

- The language is good and clear.

Reply:

Thank you for this comment. In response to Reviewer 2, we have gotten the English editing service of MDPI and the manuscript has undergone English language editing by MDPI. The text has been checked for correct use of grammar and common technical terms, and edited to a level suitable for reporting research in a scholarly journal.

2. Abstract:

- Line 23: add “to predict genetic value” after “prediction)”.

- Line 23: write the “GGE” in full “(Genotype + genotype by environment interaction)”.

- Line 23: add “to visualize and assess stability and performance” after “methods”.

- Line 23: remove “to examine GEI and genotype stability”.

Reply:

Thank you for pointing these out. In the revised manuscript, we have revised the sentence of Line 232 in Abstract.

3. Introduction:

- Very lengthy, please cut short from three pages to 1-2 pages.

Reply:

Thank you for this insightful suggestion. In the revised version of the manuscript, we have cut reduced the length of Introduction from three pages to two pages.

4. Results:

- Well presented.

- Figure 1: it is better to change the dark blue color to something ligter to be able to read the values in the provided cells.

- Figure 1: you need to indicate the cultivar abbreviations used (genotype codes) listed in Table (5) in used in other figures RATHER than giving numbers of no meaning (1, 2, …16).

- Figures 3, 4, 5, and 6: you need higher resolution figures with enlarged fonts to be visually clear and usable.

Reply:

Thank you for these valuable observations. In the revised manuscript, we have changed the dark color to lighter, and indicated the cultivar abbreviations than the number (1, 2, ……16) in Figure 1; reconstructed the Figure 3, 4, 5 with much more clarity resolution.

5. Discussion:

- Moderate, you have novel findings that need to be discussed.

Reply:

Thank you for this insightful suggestion. In the revised version of the manuscript, we have expanded the discussion of the results to address the highlight of the innovative approaches and genetic parameter analysis to identify genotypes that would be stable and less affected by environmental variation.

- You seriously need to consider discussing alternative bearing and the bearing status of your experimental unit (trees) across three years (2013, 2014, and 2015) and how this would affect your analysis and conclusions.

Reply:

We sincerely appreciate the recommendation to discuss alternative bearing and the bearing status of the phenology observed trees across three years from 2013 to 2015. We fully agree that alternative bearing may have a significant influence on the analysis results and conclusion derived from the study. However, due to limitation during this phase of the study, evaluating the bearing status of the observed trees in two orchards across three years was not feasible. Additionally, the available time frame to complete the further research was limited.

- Lines 391-402: this is more an introductory paragraph, please cut short.

Reply:

We sincerely appreciate this insightful suggestion. In the revised version of the manuscript, we have cut short Line 392-402.

- You need rather to show the importance of multiple DEGs as they are related to THE major DEVELPOMENTAL variations observed between the two investigated contrasting soybean varieties. This can cover pages of discussion!

Reply:

Thank you for this comment. However, “the multiple DEG and THE major DEVELPOMENTAL variations observed between the two investigated contrasting soybean varieties” were not included in our manuscript and revealed no correlation with this study related to olive flowering phenology.

- Lines 433-454: You should be more couscous in your genotype selection and conclusions. You need to consider listed requirements in materials and methods section (please see below), mainly the influential bearing status on your data analysis, which was unfortunately complete ignored.

Reply:

We sincerely appreciate this insightful suggestion. In the revised version of the manuscript, we have considered the listed requirements in the Materials and Methods section. We fully agree that the bearing status of observed trees may have an impact on the results and conclusion of this study. However, evaluation alternative bearing status of the observed trees was absented in this study and quantitative genetics approach was utilized to analysis flowering phenology parameters of the observed trees.

6. Materials and Methods:

- Line 484: major influential data is missing and need to be available in the manuscript for the investigated plant material:

a) Climate in the two locations and in each year: you need to provide a plot for temperature (showing daily values: mean, upper and lower) for the entire year.

Reply:

We appreciate the recommendation to provide a plot for temperature (showing daily values: mean, upper and lower) for the entire year. In the revised manuscript, we added the plot in Figure 11a for daily average temperature from January to December during the years 1998-2018.

b) Need to provide a plot of received water (both by rain and irrigation showing weekly values and accumulated values in each season).

Reply:

We appreciate the recommendation to provide a plot received water (both by rain and irrigation showing weekly values and accumulated values in each season). In the revised manuscript, we presented the plot in Figure 11c for daily accumulated precipitation from January to December during the years 1998-2018.

c) Soil fertility in the two locations.

Reply:

Thank you for your valuable suggestion. In the revised manuscript, we presented the soil type of the two locations.

d) Management practices applied for comparative application: pruning levels, fertilizers and their type and quantity and did they practice any flower or fruit thinning and levels applied and methods used (manual or chemical).

Reply:

Thank you for your valuable suggestion. In the revised manuscript, we presented that both orchards were maintained with the same olive-growing management aimed at maximizing productivity.

e) Were the trees originated from rooted cutting or grafted on a rootstock?

Where all cultivars also having the same origin or no? and how this would affect the data analysis?

Reply:

Thank you for your valuable suggestion. In the revised manuscript, we presented that olive cultivars were progressively introduced with same origin for same cultivar and propagated at the National Base of Olive Improved Varieties in Longnan and Xichang.

f) The age of experimental units (trees): what was their age? Was it similar between all cultivars and locations?

Reply:

Thank you for pointing this out. In the revised manuscript, we presented that the observed trees aged between 12 and 18 years, which were selected and marked in the orchard at each location. Additionally, the chosen trees were healthy and have similar canopy size.

g) Alternative bearing tendency for the investigated cultivars: please add this information to table (5). For example, Frantoio and Arbequina are low, while Koroneiki is moderate and while Picual is high.

In addition, this should also be considered in the analysis!

Reply:

We sincerely appreciate the recommendation to investigate alternative bearing tendency and add this information to Table 5. We fully agree that alternative bearing may affect our analysis and conclusion derived from the study. However, due to limitation during this phase of the study, evaluating the bearing status of the observed trees in two orchards across three years was not feasible. Additionally, the available time frame to complete the further research was limited. Evaluation alternative bearing status of the observed trees was absented in this study and quantitative genetics analysis was utilized for the observed trees for flowering phenology parameters.

h) Bearing status of experimental units: this is very crucial information in your analysis. Authors mentioned using three plots (replicates) each with three trees; this means nine trees per genotype per location.

What was the bearing status of each tress (all on, all off, or percent on and percent off)?

Are the same trees used in the three constitutive years (experimental years 2014 and 2015 in addition to the preceding year 2013)?

If yes, then on trees will be off and vice versa, which should be considered in the analysis!

Otherwise, if another group was used each year (of course random selection), than again what was the bearing status of each tress (all on, all off, or percent on and percent off)? Finally, you need to consider the bearing status in ALL three years (2013, 2014 and 2015)!

Reply:

We sincerely appreciate the recommendation to discuss alternative bearing and, to evaluate and consider the bearing status of the phenology observed trees across All three years from 2013 to 2015. We fully agree that alternative bearing may affect the analysis and conclusion derived from the study. However, due to limitation during this phase of the study, evaluating the bearing status of the observed trees in two orchards across three years was not feasible. Additionally, the available time frame to complete the further research was limited. Evaluation alternative bearing status of the observed trees was absented in this study and quantitative genetics analysis was utilized for the observed trees for flowering phenology parameters. In the revised manuscript, we described that RCBD was used and each block represented at least one tree, with a total of at least three trees for each cultivar.

7. References:

- The list needs an update; only 33% of cited articles were published in the last five years (21 out of 61). This needs to go up to 45-50% by citing more recent and related articles.

Reply:

We sincerely appreciate the recommendation to update the Reference. In the list reference of revised manuscript, we have added 29, over 45 % of the related articles published in the last five years.

Reviewer 2 Report

Comments and Suggestions for Authors

From a statistical perspective, this demonstrates excellent work, but from an agronomic perspective, I consider it necessary to clarify some points.
It does not detail how the data is collected, whether a branch count or a percentage assessment of the trees is made. It does not detail how many trees are recorded for flowering for each cultivar, since it is clarified that only those with significant flowering are recorded.
Climate records for each area, such as average temperature, frost records, precipitation, winds, and cloud cover, which are important for the activity of pollinating insects, are not provided.
Fruit production results, which are ultimately the most important aspect of this species, are not shown.

Author Response

Dear Reviewer

Thank you very much for your thoughtful and constructive review of our manuscript. We are truly grateful for the time and effort you dedicated to reading our work and for your insightful comments, which have greatly contributed to improving the overall quality of our paper.

Your suggestions have helped us clarify important aspects of the study, and we have addressed each of your points carefully. Below, we provide a detailed, point-by-point response to all of your comments.

From a statistical perspective, this demonstrates excellent work, but from an agronomic perspective, I consider it necessary to clarify some points.

Reply:

Thank you for your comment. We used a novel quantitative genetics approach to analysis olive flowering phenology parameters and select cultivars. Specifically, we have emphasized the potential exploration of MPS and MTMPS for in breeding program, given their earlier flowering dates and extended flowering durations. Likewise, we have addressed the need to implement multi-trait-selection strategies for olive cultivars with stability under changed climate.

It does not detail how the data is collected, whether a branch count or a percentage assessment of the trees is made. It does not detail how many trees are recorded for flowering for each cultivar, since it is clarified that only those with significant flowering are recorded.

Reply:

Thank you for your valuable suggestion. In response, we have incorporated the detail of flowering observation t in the Materials and Methods. In the revised manuscript, we presented the detail of data collect that RCBD was used and each block represented at least one tree, with a total of at least three trees for each cultivar. Inadditionally, the aforementioned data were averaged for each tree, block, cultivar, and used to calculate three phenological parameters. Full bloom was appeared from when Stage 61 to Stage 65, with at least 50% of flowers open, according to the olive BBCH of Sanz-Cortes et al. (2002).

Climate records for each area, such as average temperature, frost records, precipitation, winds, and cloud cover, which are important for the activity of pollinating insects, are not provided.

Reply:

Thank you for your valuable suggestion. In the revised manuscript, we have presented the boxplot of climatic data in the Figure 11, including in (a) average daily temperature; (b) daily sunshine hours; (c) daily accumulated precipitation; (d) average daily windspeed, from January to December during the years 1998-2018.

Fruit production results, which are ultimately the most important aspect of this species, are not shown.

Reply:

We sincerely appreciate the recommendation to evaluate the fruit production of the observed trees in this study. We fully agree that fruit production results are ultimately the most important aspect of this species, specifically in its breeding program. However, due to limitation during this phase of the study, evaluating the fruit yield of the observed trees in two orchards across three years was not feasible. Evaluation fruit yield of the observed trees was absented in this study. A novel quantitative genetics approach to analysis flowering phenology parameters of the observed trees was utilized to explore MPS and MTMPS in breeding program.

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

The paper has been noticeably improved but I insist that it is better to combine fruit production data