Bayesian divergence-based approach for genomic multitrait ordinal selection
Effective genomic selection for ordinal traits, such as disease resistance scores, is a persistent challenge in plant breeding due to the discrete, ordered nature of these phenotypes. This study presents a novel Bayesian divergence-based framework for multitrait ordinal selection, implemented in the...
| Autores principales: | , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2025
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/179091 |
| _version_ | 1855532613641437184 |
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| author | Villar-Hernández, Bartolo de Jesús Singh, Pawan Kumar Lozano, Nerida Vitale, Paolo Gerard, Guillermo Sebastián Breseghello, Flavio Dreisigacker, Susanne Crossa, Jose |
| author_browse | Breseghello, Flavio Crossa, Jose Dreisigacker, Susanne Gerard, Guillermo Sebastián Lozano, Nerida Singh, Pawan Kumar Villar-Hernández, Bartolo de Jesús Vitale, Paolo |
| author_facet | Villar-Hernández, Bartolo de Jesús Singh, Pawan Kumar Lozano, Nerida Vitale, Paolo Gerard, Guillermo Sebastián Breseghello, Flavio Dreisigacker, Susanne Crossa, Jose |
| author_sort | Villar-Hernández, Bartolo de Jesús |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Effective genomic selection for ordinal traits, such as disease resistance scores, is a persistent challenge in plant breeding due to the discrete, ordered nature of these phenotypes. This study presents a novel Bayesian divergence-based framework for multitrait ordinal selection, implemented in the extended Multitrait Parental Selection R package (MPS-R). By leveraging decision-theoretic loss functions, including the Kullback–Leibler (KL) divergence, Bhattacharyya distance, and Hellinger distance, our approach quantifies the distance between candidate distributions and breeder-defined target distributions. Through extensive simulations under 6 scenarios combining different genetic correlation structures and heritability levels, we demonstrate the comparative performance of each loss function. KL divergence consistently yielded superior genetic gains, especially in moderate heritability settings. Additionally, random sampling validation using real wheat disease resistance data confirmed the utility of these methods in practical breeding contexts. The MPS-R package implements this methodology through user-friendly functions tailored for ordinal trait selection in breeding applications. Our results demonstrate that this toolset provides a flexible, robust, and biologically grounded framework to enhance selection efficiency in breeding programs targeting complex, multitrait ordinal phenotypes. A couple of limitations employed by the simulation scheme used on the study are also discussed. |
| format | Journal Article |
| id | CGSpace179091 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1790912025-12-20T02:11:38Z Bayesian divergence-based approach for genomic multitrait ordinal selection Villar-Hernández, Bartolo de Jesús Singh, Pawan Kumar Lozano, Nerida Vitale, Paolo Gerard, Guillermo Sebastián Breseghello, Flavio Dreisigacker, Susanne Crossa, Jose bayesian theory marker-assisted selection wheat breeding genomics forecasting Effective genomic selection for ordinal traits, such as disease resistance scores, is a persistent challenge in plant breeding due to the discrete, ordered nature of these phenotypes. This study presents a novel Bayesian divergence-based framework for multitrait ordinal selection, implemented in the extended Multitrait Parental Selection R package (MPS-R). By leveraging decision-theoretic loss functions, including the Kullback–Leibler (KL) divergence, Bhattacharyya distance, and Hellinger distance, our approach quantifies the distance between candidate distributions and breeder-defined target distributions. Through extensive simulations under 6 scenarios combining different genetic correlation structures and heritability levels, we demonstrate the comparative performance of each loss function. KL divergence consistently yielded superior genetic gains, especially in moderate heritability settings. Additionally, random sampling validation using real wheat disease resistance data confirmed the utility of these methods in practical breeding contexts. The MPS-R package implements this methodology through user-friendly functions tailored for ordinal trait selection in breeding applications. Our results demonstrate that this toolset provides a flexible, robust, and biologically grounded framework to enhance selection efficiency in breeding programs targeting complex, multitrait ordinal phenotypes. A couple of limitations employed by the simulation scheme used on the study are also discussed. 2025-10 2025-12-19T21:36:53Z 2025-12-19T21:36:53Z Journal Article https://hdl.handle.net/10568/179091 en Open Access application/pdf Oxford University Press Villar-Hernández, B.d.J., Singh, P., Lozano-Ramírez, N., Vitale, P., Gerard, G., Breseghello, F., Dreisigacker, S., & Crossa, J. (2025). Bayesian divergence-based approach for genomic multitrait ordinal selection. G3: Genes Genomes Genetics, 15(10). https://doi.org/10.1093/g3journal/jkaf183 |
| spellingShingle | bayesian theory marker-assisted selection wheat breeding genomics forecasting Villar-Hernández, Bartolo de Jesús Singh, Pawan Kumar Lozano, Nerida Vitale, Paolo Gerard, Guillermo Sebastián Breseghello, Flavio Dreisigacker, Susanne Crossa, Jose Bayesian divergence-based approach for genomic multitrait ordinal selection |
| title | Bayesian divergence-based approach for genomic multitrait ordinal selection |
| title_full | Bayesian divergence-based approach for genomic multitrait ordinal selection |
| title_fullStr | Bayesian divergence-based approach for genomic multitrait ordinal selection |
| title_full_unstemmed | Bayesian divergence-based approach for genomic multitrait ordinal selection |
| title_short | Bayesian divergence-based approach for genomic multitrait ordinal selection |
| title_sort | bayesian divergence based approach for genomic multitrait ordinal selection |
| topic | bayesian theory marker-assisted selection wheat breeding genomics forecasting |
| url | https://hdl.handle.net/10568/179091 |
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