Enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity in maize
Quantitative genetics states that phenotypic variation is a consequence of the interaction between genetic and environmental factors. Predictive breeding is based on this statement, and because of this, ways of modeling genetic effects are still evolving. At the same time, the same refinement must b...
| Autores principales: | , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
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Frontiers Media
2021
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| Acceso en línea: | https://hdl.handle.net/10568/164183 |
| _version_ | 1855525006804516864 |
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| author | Costa-Neto, Germano Crossa, José Fritsche-Neto, Roberto |
| author_browse | Costa-Neto, Germano Crossa, José Fritsche-Neto, Roberto |
| author_facet | Costa-Neto, Germano Crossa, José Fritsche-Neto, Roberto |
| author_sort | Costa-Neto, Germano |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Quantitative genetics states that phenotypic variation is a consequence of the interaction between genetic and environmental factors. Predictive breeding is based on this statement, and because of this, ways of modeling genetic effects are still evolving. At the same time, the same refinement must be used for processing environmental information. Here, we present an “enviromic assembly approach,” which includes using ecophysiology knowledge in shaping environmental relatedness into whole-genome predictions (GP) for plant breeding (referred to as enviromic-aided genomic prediction, E-GP). We propose that the quality of an environment is defined by the core of environmental typologies and their frequencies, which describe different zones of plant adaptation. From this, we derived markers of environmental similarity cost-effectively. Combined with the traditional additive and non-additive effects, this approach may better represent the putative phenotypic variation observed across diverse growing conditions (i.e., phenotypic plasticity). Then, we designed optimized multi-environment trials coupling genetic algorithms, enviromic assembly, and genomic kinships capable of providingin-silicorealization of the genotype-environment combinations that must be phenotyped in the field. As proof of concept, we highlighted two E-GP applications: (1) managing the lack of phenotypic information in training accurate GP models across diverse environments and (2) guiding an early screening for yield plasticity exerting optimized phenotyping efforts. Our approach was tested using two tropical maize sets, two types of enviromics assembly, six experimental network sizes, and two types of optimized training set across environments. We observed that E-GP outperforms benchmark GP in all scenarios, especially when considering smaller training sets. The representativeness of genotype-environment combinations is more critical than the size of multi-environment trials (METs). The conventional genomic best-unbiased prediction (GBLUP) is inefficient in predicting the quality of a yet-to-be-seen environment, while enviromic assembly enabled it by increasing the accuracy of yield plasticity predictions. Furthermore, we discussed theoretical backgrounds underlying how intrinsic envirotype-phenotype covariances within the phenotypic records can impact the accuracy of GP. The E-GP is an efficient approach to better use environmental databases to deliver climate-smart solutions, reduce field costs, and anticipate future scenarios. |
| format | Journal Article |
| id | CGSpace164183 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1641832025-05-14T10:24:08Z Enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity in maize Costa-Neto, Germano Crossa, José Fritsche-Neto, Roberto plant science adaptability climate-smart genomic selection selective phenotyping Quantitative genetics states that phenotypic variation is a consequence of the interaction between genetic and environmental factors. Predictive breeding is based on this statement, and because of this, ways of modeling genetic effects are still evolving. At the same time, the same refinement must be used for processing environmental information. Here, we present an “enviromic assembly approach,” which includes using ecophysiology knowledge in shaping environmental relatedness into whole-genome predictions (GP) for plant breeding (referred to as enviromic-aided genomic prediction, E-GP). We propose that the quality of an environment is defined by the core of environmental typologies and their frequencies, which describe different zones of plant adaptation. From this, we derived markers of environmental similarity cost-effectively. Combined with the traditional additive and non-additive effects, this approach may better represent the putative phenotypic variation observed across diverse growing conditions (i.e., phenotypic plasticity). Then, we designed optimized multi-environment trials coupling genetic algorithms, enviromic assembly, and genomic kinships capable of providingin-silicorealization of the genotype-environment combinations that must be phenotyped in the field. As proof of concept, we highlighted two E-GP applications: (1) managing the lack of phenotypic information in training accurate GP models across diverse environments and (2) guiding an early screening for yield plasticity exerting optimized phenotyping efforts. Our approach was tested using two tropical maize sets, two types of enviromics assembly, six experimental network sizes, and two types of optimized training set across environments. We observed that E-GP outperforms benchmark GP in all scenarios, especially when considering smaller training sets. The representativeness of genotype-environment combinations is more critical than the size of multi-environment trials (METs). The conventional genomic best-unbiased prediction (GBLUP) is inefficient in predicting the quality of a yet-to-be-seen environment, while enviromic assembly enabled it by increasing the accuracy of yield plasticity predictions. Furthermore, we discussed theoretical backgrounds underlying how intrinsic envirotype-phenotype covariances within the phenotypic records can impact the accuracy of GP. The E-GP is an efficient approach to better use environmental databases to deliver climate-smart solutions, reduce field costs, and anticipate future scenarios. 2021-10-07 2024-12-19T12:53:35Z 2024-12-19T12:53:35Z Journal Article https://hdl.handle.net/10568/164183 en Open Access Frontiers Media Costa-Neto, Germano; Crossa, Jose and Fritsche-Neto, Roberto. 2021. Enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity in maize. Front. Plant Sci., Volume 12 |
| spellingShingle | plant science adaptability climate-smart genomic selection selective phenotyping Costa-Neto, Germano Crossa, José Fritsche-Neto, Roberto Enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity in maize |
| title | Enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity in maize |
| title_full | Enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity in maize |
| title_fullStr | Enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity in maize |
| title_full_unstemmed | Enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity in maize |
| title_short | Enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity in maize |
| title_sort | enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity in maize |
| topic | plant science adaptability climate-smart genomic selection selective phenotyping |
| url | https://hdl.handle.net/10568/164183 |
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