Optimizing QTL introgression via stochastic simulations: an example of the IRRI rice breeding program
A key limitation in the ability of breeding programs to leverage benefits of major-gene marker-assisted selection is the availability of those genes in appropriate elite germplasm. In this context, our study compared three strategies to develop new recipients for QTL introgression (Background recove...
| Autores principales: | , |
|---|---|
| Formato: | Preprint |
| Lenguaje: | Inglés |
| Publicado: |
Research Square Platform LLC
2022
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/126653 |
| _version_ | 1855533131099013120 |
|---|---|
| author | Platten, John Damien Fritsche-Neto, Roberto |
| author_browse | Fritsche-Neto, Roberto Platten, John Damien |
| author_facet | Platten, John Damien Fritsche-Neto, Roberto |
| author_sort | Platten, John Damien |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | A key limitation in the ability of breeding programs to leverage benefits of major-gene marker-assisted selection
is the availability of those genes in appropriate elite germplasm. In this context, our study compared three
strategies to develop new recipients for QTL introgression (Background recovery (BG), Selective sweep (SS),
and Breeding values (BV)) in a short-term breeding program (over five breeding cycles). Furthermore, we
evaluated two different numbers of recipients (10 and 20) in the introgression process and how they influence
the population performance and the QTL fixation over cycles. Finally, we used rice as a model of a self-
pollinated crop and implemented stochastic simulations. Each strategy was simulated and replicated 40 times.
Regardless of the selection strategy used, the QTL introgression resulted in substantial penalties in yield
performance. However, introducing fewer new parents to the augmentation process minimized this effect.
Conversely, the time required to achieve fixation of target QTLs showed substantial differences, with selection
for BV during augmentation out-performing other methods. Overall, the BV_10 strategy (10 parents selected
based on genomic estimated breeding values) displayed the best trade-off between reduced penalty from
introducing new QTLs with a reasonable speed at which those QTLs can achieve fixation over subsequent
breeding cycles. |
| format | Preprint |
| id | CGSpace126653 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Research Square Platform LLC |
| publisherStr | Research Square Platform LLC |
| record_format | dspace |
| spelling | CGSpace1266532025-11-12T04:58:38Z Optimizing QTL introgression via stochastic simulations: an example of the IRRI rice breeding program Platten, John Damien Fritsche-Neto, Roberto breeding genomics selection quality quantitative trait loci simulation models A key limitation in the ability of breeding programs to leverage benefits of major-gene marker-assisted selection is the availability of those genes in appropriate elite germplasm. In this context, our study compared three strategies to develop new recipients for QTL introgression (Background recovery (BG), Selective sweep (SS), and Breeding values (BV)) in a short-term breeding program (over five breeding cycles). Furthermore, we evaluated two different numbers of recipients (10 and 20) in the introgression process and how they influence the population performance and the QTL fixation over cycles. Finally, we used rice as a model of a self- pollinated crop and implemented stochastic simulations. Each strategy was simulated and replicated 40 times. Regardless of the selection strategy used, the QTL introgression resulted in substantial penalties in yield performance. However, introducing fewer new parents to the augmentation process minimized this effect. Conversely, the time required to achieve fixation of target QTLs showed substantial differences, with selection for BV during augmentation out-performing other methods. Overall, the BV_10 strategy (10 parents selected based on genomic estimated breeding values) displayed the best trade-off between reduced penalty from introducing new QTLs with a reasonable speed at which those QTLs can achieve fixation over subsequent breeding cycles. 2022-07-06 2023-01-06T09:22:18Z 2023-01-06T09:22:18Z Preprint https://hdl.handle.net/10568/126653 en Open Access application/pdf Research Square Platform LLC Platten, John Damien and Fritsche-Neto, Roberto. 2022. Optimizing QTL introgression via stochastic simulations: An example of the IRRI rice breeding program. Research Square |
| spellingShingle | breeding genomics selection quality quantitative trait loci simulation models Platten, John Damien Fritsche-Neto, Roberto Optimizing QTL introgression via stochastic simulations: an example of the IRRI rice breeding program |
| title | Optimizing QTL introgression via stochastic simulations: an example of the IRRI rice breeding program |
| title_full | Optimizing QTL introgression via stochastic simulations: an example of the IRRI rice breeding program |
| title_fullStr | Optimizing QTL introgression via stochastic simulations: an example of the IRRI rice breeding program |
| title_full_unstemmed | Optimizing QTL introgression via stochastic simulations: an example of the IRRI rice breeding program |
| title_short | Optimizing QTL introgression via stochastic simulations: an example of the IRRI rice breeding program |
| title_sort | optimizing qtl introgression via stochastic simulations an example of the irri rice breeding program |
| topic | breeding genomics selection quality quantitative trait loci simulation models |
| url | https://hdl.handle.net/10568/126653 |
| work_keys_str_mv | AT plattenjohndamien optimizingqtlintrogressionviastochasticsimulationsanexampleoftheirriricebreedingprogram AT fritschenetoroberto optimizingqtlintrogressionviastochasticsimulationsanexampleoftheirriricebreedingprogram |