title: Single-Step BLUP with Varying Genotyping Effort in Open-PollinatedPicea glauca.
abstract: 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.
authors.affiliation: Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
authors.forename: Blaise
authors.identifier: 0000-0003-4469-2929
authors.initials: B
authors.lastname: Ratcliffe
authors.affiliation: Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.|Pharmacognosy Department, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt.
authors.forename: Omnia Gamal
authors.identifier: 0000-0002-9112-8522
authors.initials: OG
authors.lastname: El-Dien
authors.affiliation: Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Recursos Biológicos, Las Cabañas y De Los Reseros s/n, 1686 Hurlingham, Buenos Aires, Argentina.
authors.forename: Eduardo P
authors.identifier: 0000-0002-6234-2263
authors.initials: EP
authors.lastname: Cappa
authors.affiliation: Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval Québec, G1V 0A6, Canada.
authors.forename: Ilga
authors.identifier: 0000-0002-9344-6348
authors.initials: I
authors.lastname: Porth
authors.affiliation: Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, 165 21 Praha 6, Czech Republic.|Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua 3046, New Zealand.
authors.forename: Jaroslav
authors.identifier: 0000-0001-5504-3735
authors.initials: J
authors.lastname: Klápště
authors.affiliation: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74078-3035.
authors.forename: Charles
authors.identifier: 0000-0002-2203-0433
authors.initials: C
authors.lastname: Chen
authors.affiliation: Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada y.el-kassaby@ubc.ca.
authors.forename: Yousry A
authors.identifier: 0000-0002-4887-8977
authors.initials: YA
authors.lastname: El-Kassaby
mesh_terms: D001947:Breeding; D005819:Genetic Markers; D060005:Genotyping Techniques / Q000379:methods*; D010375:Pedigree; D028222:Picea / Q000235:genetics*; D054817:Pollination / Q000235:genetics*
chemical_list: D005819:Genetic Markers
keywords: GenPred; HBLUP; Shared Data Resources; bivariate mixed model; genomic selection; single-step BLUP; tree improvement