the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 11 Jul 2024
A modeling System for Identification of Maize Ideotypes, optimal sowing dates and nitrogen fertilization under climate change – PREPCLIM-v1
Abstract. The impact of climate change on crops and agricultural yield is an actual threat while being a challenging issue due to the high complexity of factors that intervene at the local scale of the crop. Assessing it, requires the use of coupled models climate-phenology, meanwhile methods to identify management and genotypes suitable for local future conditions, in order to sustain adaptation strategies. We present the implementation and use of a new integrated climate-phenology adaptation support modeling system based on regional CORDEX climate models and the CERES Maize model from DSSAT platform, with new modules for optimal management and genotype identification using a hybrid method: deterministic modeling and -ML/ genetic algorithms. It was run as a regional pilot over Romania, operating in real-time in interaction with users, performing agro-climate projections (combination of fertilization, sowing date, soil) and providing best crop management simulated under climate change projections. Multi-model ensemble simulations for two climate scenarios RCP4.5 and RCP8.5 and twelve management scenarios show new results for the region.
For the actual genotype we find a projected mean decrease in yield in both climate scenarios for all sowing dates and fertilization levels tested, response shown to be sensitive to initial soil parameters. This response was linked to two factors: a shorter growing season by up to 10 % and a loss of fertilization efficiency in a warmer climate. A warning points to results showing a narrowing of agro-management opportunities for crop yield but in opposite it is shown a significant role of optimal genotype-range identification that may provide crop solutions under climate change even in extreme years. Identifying best genotype under warmer climate along sets of six cross-parameter simulations show systematic lower values of the maximal yields, but emphasizes genotype windows of increases in the intermediate yield values in scenarios compared to actual climate. The highest harvest sensitivity to genotype is shown to be to changes in the thermal time to juvenil respectively to maturity stage under warmer climate. The results sustain using a deterministic coupled modeling system combined with data-driven modeling for identifying optimal adaptation including fertilization paths that contribute to climate change mitigation.
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Status: final response (author comments only)
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CEC1: 'No compliance with the policy of the journal', Juan Antonio Añel, 16 Jul 2024
Dear authors,
Unfortunately, after checking your manuscript, it has come to our attention that it does not comply with our "Code and Data Policy".
https://www.geoscientific-model-development.net/policies/code_and_data_policy.html
You have archived your code on GitHub. However, GitHub is not a suitable repository for scientific publication. GitHub itself instructs authors to use other alternatives for long-term archival and publishing, such as Zenodo. Therefore, please, publish your code in one of the appropriate repositories, and reply to this comment with the relevant information (link and and permanent identifier for it (e.g. DOI)) as soon as possible, as we can not accept manuscripts in Discussions that do not comply with our policy. Therefore, the current situation with your manuscript is irregular.However, this is not the only problem. For your manuscript, from your manuscript, you state that you use the DSSAT model. Therefore, it is mandatory that you publish its DSSAT code too in a suitable repository.
Also, you must include in a potentially reviewed manuscript the modified 'Code and Data Availability' section, the DOI of the code (and another DOI for any dataset necessary).
Additionally, the GitHub repository does not contain a BSD license, despite what you state in your manuscript. You need to fix this.
Please, reply to this comment as soon as possible addressing these issues. Otherwise, we could have to reject your manuscript because of lack of compliance with our policy.
Thanks,
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/gmd-2024-105-CEC1 -
AC1: 'Reply on CEC1', Mihaela Caian, 31 Jul 2024
Response Letter to the Editor
Juan A. Añel
Geosci. Model Dev. Executive Editor
You have archived your code on GitHub. However, GitHub is not a suitable repository for scientific publication. GitHub itself instructs authors to use other alternatives for long-term archival and publishing, such as Zenodo. Therefore, please, publish your code in one of the appropriate repositories, and reply to this comment with the relevant information (link and and permanent identifier for it (e.g. DOI)) as soon as possible,
(A.:) The code is now archived and published on Zenodo.
The permanent identifier to the code (DOI) is 10.5281/zenodo.13132588
However, this is not the only problem. For your manuscript, from your manuscript, you state that you use the DSSAT model. Therefore, it is mandatory that you publish its DSSAT code too in a suitable repository.
(A.:) Yes, we use the DSSAT model as stated, as part of the modeling chain implemented.
(A.:) We initially published on GitHub only the code parts developed in this work: 1) a weather pre-processor tool for a range of climate models (this code is needed for computing inputs for DSSAT models from: CORDEX models climate scenarios, reanalysis and from forecast systems e.g. SEAS5-ECMWF seasonal forecasts) 2) The DSSAT build-in ML code for ideotype identification across multiple genotype parameters (cultivar dependent coefficients); 3) post-processing optimization code for off-line optimal configurations selection for cross parameters: genotype- sowing dates - fertilisation. This third module is necessary due to the fact that ideotype configuration for the new climatic conditions may be strongly influenced by agrotechnological options.
(A.:) Now, we conformed to the Editor request and uploaded at the code location ZENODO, also the DSSAT model version used in this work: Fortran model code version dssat-csm-os-4.8.0.15 compiled and run on Linux platform.
(A.:) The official site for obtaining DSSAT source code is https://dssat.net/3853/ with a GitHub repository at https://github.com/DSSAT/dssat-csm-os.
Also, you must include in a potentially reviewed manuscript the modified 'Code and Data Availability' section, the DOI of the code (and another DOI for any dataset necessary).
(A.:) After your approval, we will include in the 'Code and Data Availability' section the following statements: the DOI of the code is 10.5281/zenodo.13132588, and DOI for the archive with the sample dataset is 10.5281/zenodo.13133108.
Additionally, the GitHub repository does not contain a BSD license, despite what you state in your manuscript. You need to fix this.
(A.:) We included BSD 2 licenses inside the zip files, but also Zenodo provided a Creative Commons Attribution 4.0 International license each object with a DOI.
Please, reply to this comment as soon as possible addressing these issues.
(A.:) We remain open and anticipated grateful for further suggestions and requests.
Otherwise, we could have to reject your manuscript because of lack of compliance with our policy.
Thanks,
(A.:) We thank you for the asked corrections, with consideration,
Mihaela Caian and Lazar Catalin on behalf of the coauthors.
31.07.2024
Citation: https://doi.org/10.5194/gmd-2024-105-AC1 -
CEC2: 'Reply on AC1', Juan Antonio Añel, 31 Jul 2024
Dear authors,
Thanks for your reply. Unfortunately, it comes two weeks after my comment, when we were requesting urgent action on the code-sharing issues pointed out. I have to note again that your manuscript should not be under review or Discussions because of this no compliance with the policy of the journal. We should have desk rejected it before even getting to this point. Also, unfortunately, your answer does not solve the issues that I pointed out in my previous comment to your manuscript, as you continue to fail to share in an acceptable repository the DSSAT model that you made only available through two unreliable websites. Someway, the situation regarding the accessibility to the code has improved, but it is not what our policy requests. Also, one of the Zenodo repositories you shared with data contains many empty directories. I would like you to double-check and fix it.
Therefore, if you do not fix the issue regarding the correct sharing of DSSAT in a repository we can accept, we will have to reject your manuscript. As you can understand, we can not ask reviewers to spend their valuable time reviewing a manuscript we can not publish. And this is already happening.Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/gmd-2024-105-CEC2 -
CC1: 'Reply on CEC2', Catalin Lazar, 31 Jul 2024
Now, the DATA folder has been completed with Input and Output data from
all three models and all simulations: Historical, RCP45, and RCP85, for both Input and Output. The DOI is 10.5281/zenodo.13145786.
Now, we uploaded in a separate ZENODO repository the DSSAT model used in the work,
and this received a separate DOI (10.5281/zenodo.13145521).Citation: https://doi.org/10.5194/gmd-2024-105-CC1 -
CEC3: 'Reply on CC1 - compliance solved', Juan Antonio Añel, 31 Jul 2024
Dear authors,
Thanks for the quick reply. For the records, I have checked the repositories and now we can consider this manuscript in compliance with our code and data policy. Please, if in potentially reviewed versions you have to contribute additional code or data as it is necessary for the review process, remember to update the repositories accordingly.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/gmd-2024-105-CEC3
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CEC3: 'Reply on CC1 - compliance solved', Juan Antonio Añel, 31 Jul 2024
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CC1: 'Reply on CEC2', Catalin Lazar, 31 Jul 2024
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CEC2: 'Reply on AC1', Juan Antonio Añel, 31 Jul 2024
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AC1: 'Reply on CEC1', Mihaela Caian, 31 Jul 2024
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RC1: 'Comment on gmd-2024-105', Anonymous Referee #1, 23 Oct 2024
This paper develops a modelling system for adaptation support that can clarify the optimal genotype and cultivation management for maize cultivation under climate change in Romania. In recent years, research into climate change impact and its adaptation has advanced highly, and it has been becoming increasingly important to consider how to implement the findings of this research into society. The system developed in this paper is expected to be effectively used by the related stakeholders in Romania. However, there are some significant points that should be improved in this paper. Firstly, although a sensitivity analysis was carried out on various factors in relation to yield, the developed system's predictive reality and effectiveness could not be fully convinced me due to the lack of explanation of the details of the processes considered by the crop model and the lack of sufficient biological background to the results. Secondly, there are many basic mistakes throughout the paper, so I hope the authors will check it carefully.
[Specific comments]
3.a.1:How general is the index used in this study?
3.a.2:Without an explanation of the agrometeorological background in Romania, the importance of these indices is not understood.
Fig.5:
Please write the vertical axis of the graph. Though the meteorological data since 1976 were used, from what year were yield data obtained? Please illustrate the missing years so that they are clear (it seems that at least the years 1992, 93 and 94 are missing).
The prediction in 1995 does not seem to match the observations. What is the reason for this? The variability of the predictions seems to be greater than that of the observations. This would lead to over-underestimation in future predictions. Which of the 12 management scenarios is the closest to reality?
L423-425:I doubt whether it can be explained by rainfall. Yield is affected by various weather factors. For example, when the photosynthesis period is shortened due to a shortened growing season, the increase in biomass may not be sufficient.
L426-428:From Fig. 7c, it was not possible to confirm whether fertilizer efficiency decreases due to global warming.
L430-423:This may be due to an increase in photosynthetic products.
3.b.3:Is it practically possible to change N and C without adding fertilizer?
L483-4:Why does soil fertility delay maturity?
L492-3:I can't understand the sentence.
L516-520:Why were these six parameters chosen? What are the values of each? What is the validity of the values that were adopted?
[Minor comments]
It is better to explain what an abbreviation stands for when it first appears.
RCP45 and RCP85 → RCP4.5 and RCP8.5
Please standardize terminology (e.g. yield and harvest, sowing and planting)
Ｌ28:RCP scenario is an emission scenario, not a climate scenario.
L51:“)” is needed after Hatfield et al, 2021.
L56:“,” before Xie et al, 2023 is needed to be corrected to “;”.
L319:“;” after Miyawaki, 2024 is needed to be removed.
L361:peack→peak
L375:Yield→yield
L651:tis→this
Table1:I think that Fx0 is correct for Fertilazation in TR2 and 3.
Table1:I think that for the sowing date in TR2, 6 and 10 15.04 is correct.
Citation: https://doi.org/10.5194/gmd-2024-105-RC1 -
CC2: 'Reply on RC1', Catalin Lazar, 23 Oct 2024
Dear Reviewer,
Thank you very much for your valuable comments and suggestions. We have started analyzing each comment, and we will prepare and submit the answers as soon as possible.
We are sure that your remarks will help us improve the paper's new version, and we are grateful for this.
Citation: https://doi.org/10.5194/gmd-2024-105-CC2 -
AC2: 'Reply on RC1', Mihaela Caian, 18 Nov 2024
Dear Reviewer,
Thank you very much for your extremely valuable observations and suggestions, we are very grateful and we hope we could address it.
Please find attached the document with the answers (are marked by color light green) and for each answer there is a Comment containing:
the reference to the Reviewer question and explanation about the answer.
Thank you very much for your extremely valuable observations, we are very grateful and we hope we could address it.
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CC2: 'Reply on RC1', Catalin Lazar, 23 Oct 2024
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RC2: 'Comment on gmd-2024-105', Anonymous Referee #2, 30 Oct 2024
In this manuscript, the authors describe a model system—including a graphical user interface (GUI)—that can be used to help decisionmakers understand what sort of crop planting practices will be optimal in the future. These practices include sowing date, fertilization level, and genotype selection. The latter is especially interesting, with the authors using a genetic algorithm in addition to a more deterministic method. The system is demonstrated for maize in Romania as a case study, but such tools are of much broader interest.
Unfortunately, the paper is hampered by poor organization, unclear use of language, and low-quality figures. An extensive rewrite is required to address everything from separating methods and results, to improving the way experiments are referenced, to more minor language and typo issues. I thus recommend this paper be reconsidered only after major revisions.
See attached PDF for detailed comments.
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CC3: 'Reply on RC2', Catalin Lazar, 30 Oct 2024
Thank you for your observations and suggestions. We will revise the paper extensively, considering the analyses of both referees.
Regarding one of our poor formulations in L 483-4, "How exactly would richer soil lead to the model simulating slower maturity?" We should instead show that in our simulations with the new weather conditions, genotypes with a longer vegetation period performed better than genotypes with a shorter vegetation period when they benefited from favorable nutrition conditions, but under low nitrogen conditions genotypes with earlier maturity may escape from late summer stress conditions, stress that otherwise may be just too hard for plants that already suffered by a nutritional stress.
Regarding your question "What is the purpose of the analysis in Sect. 3.b.3 (“Sensitivity to changes to nutrients”)?
How can farmers choose inherent characteristics of their soil?" - We are concerned about the extent of the impact of soil variability from a given soil type on our simulations (and recommendations for corn breeders that target larger areas, even if only a few soil types are present there). But you are right that the paper is already too large and some analyses may go to another paper.The Zenodo/DOI problem was already solved.
Now, after submission, it is clear that the paper needs a careful major revision and all the suggestions are welcome.
Citation: https://doi.org/10.5194/gmd-2024-105-CC3 -
AC3: 'Reply on RC2', Mihaela Caian, 18 Nov 2024
Dear Reviewer,
Thank you very much for your extremely valuable observations, we are extremely grateful and we hope we could address it.
Please find attached the document with the answers (are marked by color light green) and for each answer there is a Comment in the doc document containing:
the reference to the Reviewer question and explanation about the answer.
Thank you very much indeed and we are awaiting to complete any further requirement,
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CC3: 'Reply on RC2', Catalin Lazar, 30 Oct 2024
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