Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages
Assembly of a training population (TP) is an important component of effective genomic selection‐based breeding programs. In this study, we examined the power of diverse germplasm assembled from two cassava (Manihot esculenta Crantz) breeding programs in Tanzania at different breeding stages to predi...
| Autores principales: | , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2019
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/107742 |
| _version_ | 1855524445101228032 |
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| author | Somo, M. Kulembeka, H. Mtunda, K. Mrema, E. Salum, K. Wolfe, M.D. Rabbi, Ismail Y. Egesi, Chiedozie N. Kawuki, R.S. Ozimati, A. Lozano, R. Jannink, Jean-Luc |
| author_browse | Egesi, Chiedozie N. Jannink, Jean-Luc Kawuki, R.S. Kulembeka, H. Lozano, R. Mrema, E. Mtunda, K. Ozimati, A. Rabbi, Ismail Y. Salum, K. Somo, M. Wolfe, M.D. |
| author_facet | Somo, M. Kulembeka, H. Mtunda, K. Mrema, E. Salum, K. Wolfe, M.D. Rabbi, Ismail Y. Egesi, Chiedozie N. Kawuki, R.S. Ozimati, A. Lozano, R. Jannink, Jean-Luc |
| author_sort | Somo, M. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Assembly of a training population (TP) is an important component of effective genomic selection‐based breeding programs. In this study, we examined the power of diverse germplasm assembled from two cassava (Manihot esculenta Crantz) breeding programs in Tanzania at different breeding stages to predict traits and discover quantitative trait loci (QTL). This is the first genomic selection and genome‐wide association study (GWAS) on Tanzanian cassava data. We detected QTL associated with cassava mosaic disease (CMD) resistance on chromosomes 12 and 16; QTL conferring resistance to cassava brown streak disease (CBSD) on chromosomes 9 and 11; and QTL on chromosomes 2, 3, 8, and 10 associated with resistance to CBSD for root necrosis. We detected a QTL on chromosome 4 and two QTL on chromosome 12 conferring dual resistance to CMD and CBSD. The use of clones in the same stage to construct TPs provided higher trait prediction accuracy than TPs with a mixture of clones from multiple breeding stages. Moreover, clones in the early breeding stage provided more reliable trait prediction accuracy and are better candidates for constructing a TP. Although larger TP sizes have been associated with improved accuracy, in this study, adding clones from Kibaha to those from Ukiriguru and vice versa did not improve the prediction accuracy of either population. Including the Ugandan TP in either population did not improve trait prediction accuracy. This study applied genomic prediction to understand the implications of constructing TP from clones at different breeding stages pooled from different locations on trait accuracy. |
| format | Journal Article |
| id | CGSpace107742 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1077422025-11-11T10:16:16Z Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages Somo, M. Kulembeka, H. Mtunda, K. Mrema, E. Salum, K. Wolfe, M.D. Rabbi, Ismail Y. Egesi, Chiedozie N. Kawuki, R.S. Ozimati, A. Lozano, R. Jannink, Jean-Luc cassava plant breeding genotypes african cassava mosaic virus quantitative trait loci tanzania uganda east africa Assembly of a training population (TP) is an important component of effective genomic selection‐based breeding programs. In this study, we examined the power of diverse germplasm assembled from two cassava (Manihot esculenta Crantz) breeding programs in Tanzania at different breeding stages to predict traits and discover quantitative trait loci (QTL). This is the first genomic selection and genome‐wide association study (GWAS) on Tanzanian cassava data. We detected QTL associated with cassava mosaic disease (CMD) resistance on chromosomes 12 and 16; QTL conferring resistance to cassava brown streak disease (CBSD) on chromosomes 9 and 11; and QTL on chromosomes 2, 3, 8, and 10 associated with resistance to CBSD for root necrosis. We detected a QTL on chromosome 4 and two QTL on chromosome 12 conferring dual resistance to CMD and CBSD. The use of clones in the same stage to construct TPs provided higher trait prediction accuracy than TPs with a mixture of clones from multiple breeding stages. Moreover, clones in the early breeding stage provided more reliable trait prediction accuracy and are better candidates for constructing a TP. Although larger TP sizes have been associated with improved accuracy, in this study, adding clones from Kibaha to those from Ukiriguru and vice versa did not improve the prediction accuracy of either population. Including the Ugandan TP in either population did not improve trait prediction accuracy. This study applied genomic prediction to understand the implications of constructing TP from clones at different breeding stages pooled from different locations on trait accuracy. 2019-12-11 2020-03-13T10:10:12Z 2020-03-13T10:10:12Z Journal Article https://hdl.handle.net/10568/107742 en Open Access application/pdf Wiley Somo, M., Kulembeka, H., Mtunda, K., Mrema, E., Salum, K., Wolfe, M.D., ... & Jannink, J. (2020). Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages. Crop Science, 60, 896–913. |
| spellingShingle | cassava plant breeding genotypes african cassava mosaic virus quantitative trait loci tanzania uganda east africa Somo, M. Kulembeka, H. Mtunda, K. Mrema, E. Salum, K. Wolfe, M.D. Rabbi, Ismail Y. Egesi, Chiedozie N. Kawuki, R.S. Ozimati, A. Lozano, R. Jannink, Jean-Luc Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages |
| title | Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages |
| title_full | Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages |
| title_fullStr | Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages |
| title_full_unstemmed | Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages |
| title_short | Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages |
| title_sort | genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages |
| topic | cassava plant breeding genotypes african cassava mosaic virus quantitative trait loci tanzania uganda east africa |
| url | https://hdl.handle.net/10568/107742 |
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