Multi-environment Genomic Selection in Rice Elite Breeding Lines
Assessing the performance of elite lines in target environments is essential for breeding programs to select the most relevant genotypes. One of the main complexities in this task resides in accounting for the genotype by environment interactions. Genomic prediction models that integrate information...
| Autores principales: | , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/163985 |
| _version_ | 1855520143122104320 |
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| author | Nguyen, Van Hieu Morantte, Rose Imee Zhella Lopena, Vitaliano Verdeprado, Holden Murori, Rosemary Ndayiragije, Alexis Katiyar, Sanjay Kumar Islam, Md. Rafiqul Juma, Roselyne Uside Flandez-Galvez, Hayde Glaszmann, Jean-Christophe Cobb, Joshua N. Bartholomé, Jérôme |
| author_browse | Bartholomé, Jérôme Cobb, Joshua N. Flandez-Galvez, Hayde Glaszmann, Jean-Christophe Islam, Md. Rafiqul Juma, Roselyne Uside Katiyar, Sanjay Kumar Lopena, Vitaliano Morantte, Rose Imee Zhella Murori, Rosemary Ndayiragije, Alexis Nguyen, Van Hieu Verdeprado, Holden |
| author_facet | Nguyen, Van Hieu Morantte, Rose Imee Zhella Lopena, Vitaliano Verdeprado, Holden Murori, Rosemary Ndayiragije, Alexis Katiyar, Sanjay Kumar Islam, Md. Rafiqul Juma, Roselyne Uside Flandez-Galvez, Hayde Glaszmann, Jean-Christophe Cobb, Joshua N. Bartholomé, Jérôme |
| author_sort | Nguyen, Van Hieu |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Assessing the performance of elite lines in target environments is essential for breeding programs to select the most relevant genotypes. One of the main complexities in this task resides in accounting for the genotype by environment interactions. Genomic prediction models that integrate information from multi-environment trials and environmental covariates can be efficient tools in this context. The objective of this study was to assess the predictive ability of different genomic prediction models to optimize the use of multi-environment information. We used 111 elite breeding lines representing the diversity of the international rice research institute breeding program for irrigated ecosystems. The lines were evaluated for three traits (days to flowering, plant height, and grain yield) in 15 environments in Asia and Africa and genotyped with 882 SNP markers. We evaluated the efficiency of genomic prediction to predict untested environments using seven multi-environment models and three cross-validation scenarios. Results The elite lines were found to belong to the indica group and more specifically the indica-1B subgroup which gathered improved material originating from the Green Revolution. Phenotypic correlations between environments were high for days to flowering and plant height (33% and 54% of pairwise correlation greater than 0.5) but low for grain yield (lower than 0.2 in most cases). Clustering analyses based on environmental covariates separated Asia’s and Africa's environments into different clusters or subclusters. The predictive abilities ranged from 0.06 to 0.79 for days to flowering, 0.25–0.88 for plant height, and − 0.29–0.62 for grain yield. We found that models integrating genotype-by-environment interaction effects did not perform significantly better than models integrating only main effects (genotypes and environment or environmental covariates). The different cross-validation scenarios showed that, in most cases, the use of all available environments gave better results than a subset. Conclusion Multi-environment genomic prediction models with main effects were sufficient for accurate phenotypic prediction of elite lines in targeted environments. These results will help refine the testing strategy to update the genomic prediction models to improve predictive ability. |
| format | Journal Article |
| id | CGSpace163985 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1639852025-05-14T10:23:58Z Multi-environment Genomic Selection in Rice Elite Breeding Lines Nguyen, Van Hieu Morantte, Rose Imee Zhella Lopena, Vitaliano Verdeprado, Holden Murori, Rosemary Ndayiragije, Alexis Katiyar, Sanjay Kumar Islam, Md. Rafiqul Juma, Roselyne Uside Flandez-Galvez, Hayde Glaszmann, Jean-Christophe Cobb, Joshua N. Bartholomé, Jérôme agronomy crop science plant science soil science Assessing the performance of elite lines in target environments is essential for breeding programs to select the most relevant genotypes. One of the main complexities in this task resides in accounting for the genotype by environment interactions. Genomic prediction models that integrate information from multi-environment trials and environmental covariates can be efficient tools in this context. The objective of this study was to assess the predictive ability of different genomic prediction models to optimize the use of multi-environment information. We used 111 elite breeding lines representing the diversity of the international rice research institute breeding program for irrigated ecosystems. The lines were evaluated for three traits (days to flowering, plant height, and grain yield) in 15 environments in Asia and Africa and genotyped with 882 SNP markers. We evaluated the efficiency of genomic prediction to predict untested environments using seven multi-environment models and three cross-validation scenarios. Results The elite lines were found to belong to the indica group and more specifically the indica-1B subgroup which gathered improved material originating from the Green Revolution. Phenotypic correlations between environments were high for days to flowering and plant height (33% and 54% of pairwise correlation greater than 0.5) but low for grain yield (lower than 0.2 in most cases). Clustering analyses based on environmental covariates separated Asia’s and Africa's environments into different clusters or subclusters. The predictive abilities ranged from 0.06 to 0.79 for days to flowering, 0.25–0.88 for plant height, and − 0.29–0.62 for grain yield. We found that models integrating genotype-by-environment interaction effects did not perform significantly better than models integrating only main effects (genotypes and environment or environmental covariates). The different cross-validation scenarios showed that, in most cases, the use of all available environments gave better results than a subset. Conclusion Multi-environment genomic prediction models with main effects were sufficient for accurate phenotypic prediction of elite lines in targeted environments. These results will help refine the testing strategy to update the genomic prediction models to improve predictive ability. 2023-12 2024-12-19T12:53:18Z 2024-12-19T12:53:18Z Journal Article https://hdl.handle.net/10568/163985 en Open Access Springer Nguyen, V. H., Morantte, R. I. Z., Lopena, V., Verdeprado, H., Murori, R., Ndayiragije, A., Katiyar, S. K., Islam, M. R., Juma, R. U., Flandez-Galvez, H., Glaszmann, J.-C., Cobb, J. N., & Bartholomé, J. (2023). Multi-environment Genomic Selection in Rice Elite Breeding Lines. Rice, 16(1). https://doi.org/10.1186/s12284-023-00623-6 |
| spellingShingle | agronomy crop science plant science soil science Nguyen, Van Hieu Morantte, Rose Imee Zhella Lopena, Vitaliano Verdeprado, Holden Murori, Rosemary Ndayiragije, Alexis Katiyar, Sanjay Kumar Islam, Md. Rafiqul Juma, Roselyne Uside Flandez-Galvez, Hayde Glaszmann, Jean-Christophe Cobb, Joshua N. Bartholomé, Jérôme Multi-environment Genomic Selection in Rice Elite Breeding Lines |
| title | Multi-environment Genomic Selection in Rice Elite Breeding Lines |
| title_full | Multi-environment Genomic Selection in Rice Elite Breeding Lines |
| title_fullStr | Multi-environment Genomic Selection in Rice Elite Breeding Lines |
| title_full_unstemmed | Multi-environment Genomic Selection in Rice Elite Breeding Lines |
| title_short | Multi-environment Genomic Selection in Rice Elite Breeding Lines |
| title_sort | multi environment genomic selection in rice elite breeding lines |
| topic | agronomy crop science plant science soil science |
| url | https://hdl.handle.net/10568/163985 |
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