Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca
Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and precision of estimated genetic parameters, as well as rankings of selection candidates, using single-step genomic evaluation (HBLUP). In this study, two traits with diverse heritabilities [tree height (HT) and wood density (WD)] were assessed at various levels of family genotyping efforts (0, 25, 50, 75, and 100%) from a population of white spruce (Picea glauca) consisting of 1694 trees from 214 open-pollinated families, representing 43 provenances in Québec, Canada. The results revealed that HBLUP bivariate analysis is effective in reducing the known bias in heritability estimates of open-pollinated populations, as it exposes hidden relatedness, potential pedigree errors, and inbreeding. The addition of genomic information in the analysis considerably improved the accuracy in breeding value estimates by accounting for both Mendelian sampling and historical coancestry that were not captured by the contemporary pedigree alone. Increasing family genotyping efforts were associated with continuous improvement in model fit, precision of genetic parameters, and breeding value accuracy. Yet, improvements were observed even at minimal genotyping effort, indicating that even modest genotyping effort is effective in improving genetic evaluation. The combined utilization of both pedigree and genomic information may be a cost-effective approach to increase the accuracy of breeding values in forest tree breeding programs where shallow pedigrees and large testing populations are the norm.
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2017-03
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Subjects: | Picea Glauca, Genética, Genotipos, Arboles Forestales, Genetics, Genotypes, Forest Trees, |
Online Access: | http://hdl.handle.net/20.500.12123/1495 http://www.g3journal.org/content/ggg/7/3/935.full.pdf https://doi.org/10.1534/g3.116.037895 |
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oai:localhost:20.500.12123-14952024-03-27T18:18:18Z Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca Ratcliffe, Blaise El-Dien, Omnia Gamal Cappa, Eduardo Pablo Porth, Ilga Klapste, Jaroslav El-Kassaby, Yousry A. Chen, Charles Picea Glauca Genética Genotipos Arboles Forestales Genetics Genotypes Forest Trees Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and precision of estimated genetic parameters, as well as rankings of selection candidates, using single-step genomic evaluation (HBLUP). In this study, two traits with diverse heritabilities [tree height (HT) and wood density (WD)] were assessed at various levels of family genotyping efforts (0, 25, 50, 75, and 100%) from a population of white spruce (Picea glauca) consisting of 1694 trees from 214 open-pollinated families, representing 43 provenances in Québec, Canada. The results revealed that HBLUP bivariate analysis is effective in reducing the known bias in heritability estimates of open-pollinated populations, as it exposes hidden relatedness, potential pedigree errors, and inbreeding. The addition of genomic information in the analysis considerably improved the accuracy in breeding value estimates by accounting for both Mendelian sampling and historical coancestry that were not captured by the contemporary pedigree alone. Increasing family genotyping efforts were associated with continuous improvement in model fit, precision of genetic parameters, and breeding value accuracy. Yet, improvements were observed even at minimal genotyping effort, indicating that even modest genotyping effort is effective in improving genetic evaluation. The combined utilization of both pedigree and genomic information may be a cost-effective approach to increase the accuracy of breeding values in forest tree breeding programs where shallow pedigrees and large testing populations are the norm. Inst. de Recursos Biológicos Fil: Rateliffe, Blaise. University of British Columbia, Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá Fil: El-Dien, Omnia Gamal. University of British Columbia, Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá. Alexandria University. Faculty of Pharmacy. Pharmacognosy Department; Egipto Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina Fil: Porth, Ilga. Université Laval Québec. Faculté de Foresterie, de Géographie et Géomatique. Départment des Sciences du Bois et de la Forêt; Canadá Fil: Klapste, Jaroslav. Czech University of Life Sciences Prague. Faculty of Forestry and Wood Sciences. Department of Genetics and Physiology of Forest Trees; República Checa. Scion (New Zealand Forest Research Institute Ltd.); Nueva Zelanda Fil: El-Kassaby, Yousry A. University of British Columbia, Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá Fil: Chen, Charles. Oklahoma State University. Department of Biochemistry and Molecular Biology; Estados Unidos 2017-10-17T14:01:07Z 2017-10-17T14:01:07Z 2017-03 info:eu-repo/semantics/article info:ar-repo/semantics/artículo info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/1495 http://www.g3journal.org/content/ggg/7/3/935.full.pdf 2160-1836 (Online) https://doi.org/10.1534/g3.116.037895 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf G3: Genes, Genomes, Genetics 7 (3) : 935-942 (March 2017) |
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Picea Glauca Genética Genotipos Arboles Forestales Genetics Genotypes Forest Trees Picea Glauca Genética Genotipos Arboles Forestales Genetics Genotypes Forest Trees |
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Picea Glauca Genética Genotipos Arboles Forestales Genetics Genotypes Forest Trees Picea Glauca Genética Genotipos Arboles Forestales Genetics Genotypes Forest Trees Ratcliffe, Blaise El-Dien, Omnia Gamal Cappa, Eduardo Pablo Porth, Ilga Klapste, Jaroslav El-Kassaby, Yousry A. Chen, Charles Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca |
description |
Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and precision of estimated genetic parameters, as well as rankings of selection candidates, using single-step genomic evaluation (HBLUP). In this study, two traits with diverse heritabilities [tree height (HT) and wood density (WD)] were assessed at various levels of family genotyping efforts (0, 25, 50, 75, and 100%) from a population of white spruce (Picea glauca) consisting of 1694 trees from 214 open-pollinated families, representing 43 provenances in Québec, Canada. The results revealed that HBLUP bivariate analysis is effective in reducing the known bias in heritability estimates of open-pollinated populations, as it exposes hidden relatedness, potential pedigree errors, and inbreeding. The addition of genomic information in the analysis considerably improved the accuracy in breeding value estimates by accounting for both Mendelian sampling and historical coancestry that were not captured by the contemporary pedigree alone. Increasing family genotyping efforts were associated with continuous improvement in model fit, precision of genetic parameters, and breeding value accuracy. Yet, improvements were observed even at minimal genotyping effort, indicating that even modest genotyping effort is effective in improving genetic evaluation. The combined utilization of both pedigree and genomic information may be a cost-effective approach to increase the accuracy of breeding values in forest tree breeding programs where shallow pedigrees and large testing populations are the norm. |
format |
info:eu-repo/semantics/article |
topic_facet |
Picea Glauca Genética Genotipos Arboles Forestales Genetics Genotypes Forest Trees |
author |
Ratcliffe, Blaise El-Dien, Omnia Gamal Cappa, Eduardo Pablo Porth, Ilga Klapste, Jaroslav El-Kassaby, Yousry A. Chen, Charles |
author_facet |
Ratcliffe, Blaise El-Dien, Omnia Gamal Cappa, Eduardo Pablo Porth, Ilga Klapste, Jaroslav El-Kassaby, Yousry A. Chen, Charles |
author_sort |
Ratcliffe, Blaise |
title |
Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca |
title_short |
Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca |
title_full |
Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca |
title_fullStr |
Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca |
title_full_unstemmed |
Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca |
title_sort |
single-step blup with varying genotyping effort in open-pollinated picea glauca |
publishDate |
2017-03 |
url |
http://hdl.handle.net/20.500.12123/1495 http://www.g3journal.org/content/ggg/7/3/935.full.pdf https://doi.org/10.1534/g3.116.037895 |
work_keys_str_mv |
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