Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices
Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land, and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms...
| Autores principales: | , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2021
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| Acceso en línea: | https://hdl.handle.net/10568/117969 |
| _version_ | 1855531877110120448 |
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| author | Wolfe, M. Chan, A.W. Kulakow, Peter A. Rabbi, I.Y. Jannink, Jean-Luc |
| author_browse | Chan, A.W. Jannink, Jean-Luc Kulakow, Peter A. Rabbi, I.Y. Wolfe, M. |
| author_facet | Wolfe, M. Chan, A.W. Kulakow, Peter A. Rabbi, I.Y. Jannink, Jean-Luc |
| author_sort | Wolfe, M. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land, and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects, and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances, and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses was accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal the new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance). |
| format | Journal Article |
| id | CGSpace117969 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1179692025-11-11T10:37:13Z Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices Wolfe, M. Chan, A.W. Kulakow, Peter A. Rabbi, I.Y. Jannink, Jean-Luc genomics marker-assisted selection cassava forecasting genetic covariance Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land, and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects, and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances, and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses was accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal the new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance). 2021-11-05 2022-02-04T13:18:12Z 2022-02-04T13:18:12Z Journal Article https://hdl.handle.net/10568/117969 en Open Access application/pdf Oxford University Press Wolfe, M., Chan, A.W., Kulakow, P., Rabbi, I.Y. & Jannink, J. (2021). Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices. Genetics, 219(3), 1-14. |
| spellingShingle | genomics marker-assisted selection cassava forecasting genetic covariance Wolfe, M. Chan, A.W. Kulakow, Peter A. Rabbi, I.Y. Jannink, Jean-Luc Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices |
| title | Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices |
| title_full | Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices |
| title_fullStr | Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices |
| title_full_unstemmed | Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices |
| title_short | Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices |
| title_sort | genomic mating in outbred species predicting cross usefulness with additive and total genetic covariance matrices |
| topic | genomics marker-assisted selection cassava forecasting genetic covariance |
| url | https://hdl.handle.net/10568/117969 |
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