Opportunities to Improve the Recommendation of Plant Varieties under the Recommended List (RL) System

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Dear Editor and responsible author,

Thank you for your invitation to review this article.

Plant breeding programs continue rapidly all over the world to find solutions to nutrition problems. The new varieties obtained in these programs are shared with the public through various means. The data used in these disclosures are obtained from trials conducted in different regions. End-users should be sure of the reliability of this data so that they can make their own production plans with the right choices. There are various plant variety recommendation practices developed for different countries. 

This paper examines some data from the Recommended List (RL) system for the United Kingdom. The purpose of the study is described in the sentence “Here we evaluate the current RL system in the UK and identify possible areas for improvement.” The topic of the study is quite original. However, no clear hypothesis was put forward. Spring barley was chosen as the model plant. Why this species was chosen should be explained.

 The title is sufficient to reflect the content of the study. The study utilized 18 years of data (2002 to 2019) of 153 unique varieties from 80 different trial sites.  This data pool is sufficient to achieve the objective. The results are shared in a clear and understandable way. The writing language is quite fluent. However, while explaining the results, the suggestions for improving the system should be more detailed. The references used in the study are relevant and up-to-date.

Author Response

Comment 1: This paper examines some data from the Recommended List (RL) system for the United Kingdom. The purpose of the study is described in the sentence “Here we evaluate the current RL system in the UK and identify possible areas for improvement.” The topic of the study is quite original. However, no clear hypothesis was put forward. Spring barley was chosen as the model plant. Why this species was chosen should be explained.

Response 1: Thank you for raising this. We have updated the text in Line 77-80 and 82-84 with a clear hypothesis and reason for choosing spring barley as the model plant.

 

Comment 2: The title is sufficient to reflect the content of the study. The study utilized 18 years of data (2002 to 2019) of 153 unique varieties from 80 different trial sites.  This data pool is sufficient to achieve the objective. The results are shared in a clear and understandable way. The writing language is quite fluent. However, while explaining the results, the suggestions for improving the system should be more detailed. The references used in the study are relevant -and up-to-date.

Response 2: Thank you. We have updated the text in Line 262-264, 287-288 and 393-398 with more details on the suggestions for improving the system.

Reviewer 2 Report

Comments and Suggestions for Authors

The main question addressed by this research is to evaluate the current recommended list system in the UK and to identify possible areas for improvement. The topic of the study “Opportunities to improve the recommendation of plant varieties under the Recommended List (RL) system” is original and includes the main question. The study addresses a specific gap because the RL system was incepted in the UK in 1944, for supporting growers when choosing the right variety. The current RL system is heavily focused on single-trial analyses developed in the 1980s without full use of information across varieties and trial sites. The study reviews and updates methods for data analysis in RL that could be used to predict the variety of performance in future environments. Based on this study better variety recommendations, particularly for matching varieties to specific environments can be achieved through improved modelling of effects from genetics, environments and gene-environment interactions. Grain yield data from 153 spring barley varieties were trialled for RL from 2002 to 2019. The current RL system produces poor and inconsistent predictions on variety of performances across environments.

The Materials and Methods section is well described and visualized.

The figures/tables should be inserted into the main text close to their first citation.

Some of the abbreviations are not defined. The abbreviations should be defined the first time they appear in each section. Once defined, the abbreviations should be added in parentheses after the written-out form. 

 The section Discussion is incomplete. My suggestion for this section is to compare your results with the findings from other (similar/contradictory) studies or use other studies to support your claim.

The conclusions of this large-scale and long-term work are consistent with the evidence and arguments presented and address the main question: to evaluate the current recommended list system in the UK and to identify possible areas for improvement.

The conclusion of this study is better presented in the abstract. The authors suggested that:

1-The improvement in RL could be achieved by mixed models that include the genetic relationships among varieties.

2- If genetic and environmental interaction could be modelled accurately additional improvement is possible.

 3-The importance of genomics in both variety registration and recommendation.

 It would be better if lines 91-101 were added in the conclusion part or at the end of the discussion part.

Based on the main question posed the authors’ conclusions are the following:

1-The current RL system provides a poor and inconsistent variety of recommendations across environments.

2-While simple means from more trial sites lead to higher prediction accuracies on variety performance, one-year means outperform five-year means due to inaccurate variety ranks involving new and old varieties.

3-The alternative methods using Genomic BLUP (GBLUP) address the shortcomings in the existing variety selection methods by producing better and more consistent variety performance predictions.

4- GBLUP with a five-year variety trial data outperforms all considered metrics among eight studied methods.

5-The use of genomic marker data for variety recommendation fits perfectly with a previously proposed system for variety registration known as genomic Distinctness, Uniformity and Stability (DUS).

 

 

Author Response

Comment 1: The figures/tables should be inserted into the main text close to their first citation.

Response 1: Thank you. We have made sure to have the figures and tables immediately after their first citation in the main text. In some cases, the figures and tables are too long to fit within the remaining space and may get pushed into the next page.

 

Comment 2: Some of the abbreviations are not defined. The abbreviations should be defined the first time they appear in each section. Once defined, the abbreviations should be added in parentheses after the written-out form.

Response 2: Thank you for catching these. We have added the full definitions of all abbreviations in Line 99-100, 114, 116, 154, 378-379, 384 and 402-403.

 

Comment 3: The section Discussion is incomplete. My suggestion for this section is to compare your results with the findings from other (similar/contradictory) studies or use other studies to support your claim.

Response 3: Thank you. We have added a new paragraph in Line 411-430 to summarize the findings from relevant studies.

 

Comment 4: The conclusions of this large-scale and long-term work are consistent with the evidence and arguments presented and address the main question: to evaluate the current recommended list system in the UK and to identify possible areas for improvement. The conclusion of this study is better presented in the abstract. The authors suggested that: 1-The improvement in RL could be achieved by mixed models that include the genetic relationships among varieties. 2- If genetic and environmental interaction could be modelled accurately additional improvement is possible. 3-The importance of genomics in both variety registration and recommendation. It would be better if lines 91-101 were added in the conclusion part or at the end of the discussion part.

Response 4: Thank you for pointing this out. We have improved the conclusions in Line 451-460.

Reviewer 3 Report

Comments and Suggestions for Authors

Row 14 (In Abstract):

Authors wrote: Lastly, we highlight the relevance and importance of genomics....

Reviewer: This sentence could start without " Lastly ". Remove this two words and start with: "We highlight the relevance and importance of genomics..."

Please correct.

 

Rows 119-120 (In 2. Materials and Methods 2.1. Data Collection):

Authors wrote: The data included monthly average of maximum temperature (C), minimum temperature (C), number of frost days and rainfall (mm) from 2002 to 2019. Temperature range (C)...

Reviewer: Because in Table 1. Authors wrote: ...Tmax (°C) Tmin (°C) Trange (°C)... maybe the better look of indicated sentence could be: "The data included monthly average of maximum temperature (Tmax (°C)), minimum temperature (Tmin (°C)), number of frost days and rainfall (mm) from 2002 to 2019. Temperature range (Trange (°C)) was estimated as the..."

Please correct

 

Rows: Between Rows 257-258 (Chapter: 3.3. Comparison across methods in predicting variety yield):

Authors wrote: Figure 2. Comparison of eight different methods for predicting variety performance. Each boxplot contains correlations between predicted and observed yield ranks from 29 unique trial sites and 13 years (2007 to 2019). The lower, middle and upper hinges of the boxplots represent the first, second (median) and third quartiles of the data points. The whiskers extend from the boxes to the furthest data points within 1.5 times of the interquartile range. The vertical red line serves as a reference based on the largest median correlation from method A5B.

Reviewer: The Title of Figure 2. is too long (without rows numbering and between Rows 257-258). For Title of the Figure 2. write one short sentence (Possible Title of Figure 2.: Comparison of eight different methods for predicting variety performance.).

Rest of the text from Authors Title of Figure 2 enter in the text of the Manuscript where you refer to this Figure 2.

Please correct

 

Rows: Between Rows 288-289 (Chapter: 3.4. Site-specific comparison of methods):

Authors wrote: Figure 3. Correlations between predicted and observed yield ranks in six trial sites. (A) Heatmap of correlations for eight methods and 13 years. These six trial sites are highlighted here because they have the greatest number of trials across the years. (B) Scatter plot of correlations for eight methods and 13 years. Significant difference in mean correlations between methods after applying Bonferroni correction is indicated by a black vertical line.

Reviewer: The Title of Figure 3. is too long (without rows numbering and between Rows 288-289). For Title of the Figure 3. write one short sentence (Possible Title of Figure 3.: Correlations between predicted and observed yield ranks in six trial sites with (A) Heatmap and (B) Scatter plot of correlations for eight methods and 13 years.).

Rest of the text from Authors Title of Figure 3 enter in the text of the Manuscript where you refer to this Figure 3.

Please correct

 

Rows: Between Rows 317-318 (Chapter: 3.5. Year-specific comparison of methods):

Authors wrote: Figure 4. Correlations between predicted and observed yield ranks over 13 years. (A) Scatter plot of correlations for eight methods and trial sites within each year. Significant differences in mean correlations between methods after applying Bonferroni correction are indicated by black vertical lines. (B) Line plot of mean correlations for eight methods shown from 2007 to 2019.

Reviewer: The Title of Figure 4. is too long (without rows numbering and between Rows 317-318). For Title of the Figure 4. write short sentence (Possible Title of Figure 4.: Correlations between predicted and observed yield ranks with (A) Scatter plot of correlations and (B) Line plot of mean correlations for eight methods shown from 2007 to 2019.).

Rest of the text from Authors Title of Figure 4 enter in the text of the Manuscript where you refer to this Figure 3.

Please correct

 

Rows: Between Rows 346-347 (Chapter: 3.6. Quantifying deficits in yield):

Authors wrote: Figure 6. Cumulative Percent Deficits (CPD) in yield over the years. PD is averaged across all trial sites within each year to obtain the annual mean PD, which is then summed over the years from 2007 to 2019 to highlight the CPD in yield for each method.

Reviewer: The Title of Figure 6. is too long (without rows numbering and between Rows 346-347). For Title of the Figure 6. write short sentence (Possible Title of Figure 6.: Cumulative Percent Deficits (CPD) in yield over the years from 2007 to 2019.).

Rest of the text from Authors Title of Figure 6 enter in the text of the Manuscript where you refer to this Figure 6.

Please correct

 

Rows: Between Rows 415-420 (Chapter: 5. Conclusions):

Authors wrote: Very simple and short Conclusion.

Reviewer: Very important Chapter of Manuscript is "Conclusion" and in this Manuscript is Very simple and short. Conclusion must contain direct Authors findings from their research and not only general notes. Conclusions must be consistent with the evidence and arguments presented in Results and Discussion. In Conclusion write the specific Improvements in RL that are suggest in Manuscript. Conclusions must be rewrite again based on Results and Discussion.

Please correct

Comments for author File: Comments.docx

Author Response

Comment 1: Row 14 (In Abstract): Authors wrote: Lastly, we highlight the relevance and importance of genomics.... Reviewer: This sentence could start without " Lastly ". Remove this two words and start with: "We highlight the relevance and importance of genomics..." Please correct.

Response 1: Thank you. We have made the suggested change in Line 14.

 

Comment 2: Rows 119-120 (In 2. Materials and Methods 2.1. Data Collection): Authors wrote: The data included monthly average of maximum temperature (C), minimum temperature (C), number of frost days and rainfall (mm) from 2002 to 2019. Temperature range (C)... Reviewer: Because in Table 1. Authors wrote: ...Tmax (°C) Tmin (°C) Trange (°C)... maybe the better look of indicated sentence could be: "The data included monthly average of maximum temperature (Tmax (°C)), minimum temperature (Tmin (°C)), number of frost days and rainfall (mm) from 2002 to 2019. Temperature range (Trange (°C)) was estimated as the..." Please correct

Response 2: Thank you. We have made the suggested changes in Line 123-127.

 

Comment 3: Rows: Between Rows 257-258 (Chapter: 3.3. Comparison across methods in predicting variety yield): Authors wrote: Figure 2. Comparison of eight different methods for predicting variety performance. Each boxplot contains correlations between predicted and observed yield ranks from 29 unique trial sites and 13 years (2007 to 2019). The lower, middle and upper hinges of the boxplots represent the first, second (median) and third quartiles of the data points. The whiskers extend from the boxes to the furthest data points within 1.5 times of the interquartile range. The vertical red line serves as a reference based on the largest median correlation from method A5B. Reviewer: The Title of Figure 2. is too long (without rows numbering and between Rows 257-258). For Title of the Figure 2. write one short sentence (Possible Title of Figure 2.: Comparison of eight different methods for predicting variety performance.). Rest of the text from Authors Title of Figure 2 enter in the text of the Manuscript where you refer to this Figure 2. Please correct

Response 3: Thank you for raising this. We intend for the first sentence to be the main title of Figure 2, and the remaining sentences to be subtitles/short description. Format-wise, we are aware that Agronomy does not distinguish between title and subtitle but there are similar examples for figure subtitles in Agronomy (https://www.mdpi.com/2073-4395/14/9/2075, https://www.mdpi.com/2073-4395/14/9/2071).

 

Comment 4: Rows: Between Rows 288-289 (Chapter: 3.4. Site-specific comparison of methods): Authors wrote: Figure 3. Correlations between predicted and observed yield ranks in six trial sites. (A) Heatmap of correlations for eight methods and 13 years. These six trial sites are highlighted here because they have the greatest number of trials across the years. (B) Scatter plot of correlations for eight methods and 13 years. Significant difference in mean correlations between methods after applying Bonferroni correction is indicated by a black vertical line. Reviewer: The Title of Figure 3. is too long (without rows numbering and between Rows 288-289). For Title of the Figure 3. write one short sentence (Possible Title of Figure 3.: Correlations between predicted and observed yield ranks in six trial sites with (A) Heatmap and (B) Scatter plot of correlations for eight methods and 13 years.). Rest of the text from Authors Title of Figure 3 enter in the text of the Manuscript where you refer to this Figure 3. Please correct

Response 4: Thank you for raising this. We intend for the first sentence to be the main title of Figure 3, and the remaining sentences to be subtitles/short description. Format-wise, we are aware that Agronomy does not distinguish between title and subtitle but there are similar examples for figure subtitles in Agronomy (https://www.mdpi.com/2073-4395/14/9/2075, https://www.mdpi.com/2073-4395/14/9/2071).

 

Comment 5: Rows: Between Rows 317-318 (Chapter: 3.5. Year-specific comparison of methods): Authors wrote: Figure 4. Correlations between predicted and observed yield ranks over 13 years. (A) Scatter plot of correlations for eight methods and trial sites within each year. Significant differences in mean correlations between methods after applying Bonferroni correction are indicated by black vertical lines. (B) Line plot of mean correlations for eight methods shown from 2007 to 2019. Reviewer: The Title of Figure 4. is too long (without rows numbering and between Rows 317-318). For Title of the Figure 4. write short sentence (Possible Title of Figure 4.: Correlations between predicted and observed yield ranks with (A) Scatter plot of correlations and (B) Line plot of mean correlations for eight methods shown from 2007 to 2019.). Rest of the text from Authors Title of Figure 4 enter in the text of the Manuscript where you refer to this Figure 3. Please correct

Response 5: Thank you for raising this. We intend for the first sentence to be the main title of Figure 4, and the remaining sentences to be subtitles/short description. Format-wise, we are aware that Agronomy does not distinguish between title and subtitle but there are similar examples for figure subtitles in Agronomy (https://www.mdpi.com/2073-4395/14/9/2075, https://www.mdpi.com/2073-4395/14/9/2071).

 

Comment 6: Rows: Between Rows 346-347 (Chapter: 3.6. Quantifying deficits in yield): Authors wrote: Figure 6. Cumulative Percent Deficits (CPD) in yield over the years. PD is averaged across all trial sites within each year to obtain the annual mean PD, which is then summed over the years from 2007 to 2019 to highlight the CPD in yield for each method. Reviewer: The Title of Figure 6. is too long (without rows numbering and between Rows 346-347). For Title of the Figure 6. write short sentence (Possible Title of Figure 6.: Cumulative Percent Deficits (CPD) in yield over the years from 2007 to 2019.). Rest of the text from Authors Title of Figure 6 enter in the text of the Manuscript where you refer to this Figure 6. Please correct

Response 6: Thank you for raising this. We intend for the first sentence to be the main title of Figure 6, and the remaining sentences to be subtitles/short description. Format-wise, we are aware that Agronomy does not distinguish between title and subtitle but there are similar examples for figure subtitles in Agronomy (https://www.mdpi.com/2073-4395/14/9/2075, https://www.mdpi.com/2073-4395/14/9/2071).

 

Comment 7: Rows: Between Rows 415-420 (Chapter: 5. Conclusions): Authors wrote: Very simple and short Conclusion. Reviewer: Very important Chapter of Manuscript is "Conclusion" and in this Manuscript is Very simple and short. Conclusion must contain direct Authors findings from their research and not only general notes. Conclusions must be consistent with the evidence and arguments presented in Results and Discussion. In Conclusion write the specific Improvements in RL that are suggest in Manuscript. Conclusions must be rewrite again based on Results and Discussion. Please correct

Response 7: Thank you for pointing this out. We have improved the conclusions in Line 451-460.

Round 2

Reviewer 3 Report

Comments and Suggestions for Authors

Row: 456 (Chapter: 5. Conclusions):

Authors wrote: …improve variety registration [23] and recommendation…

Reviewer: In Conclusion Authors use Citation (number 23). Conclusion must contain only Authors results without any type of citations numbers.

 

Please correct