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. 2021 Sep 27;11(10):jkab253.
doi: 10.1093/g3journal/jkab253.

Single-step genomic BLUP enables joint analysis of disconnected breeding programs: an example with Eucalyptus globulus Labill

Andrew N Callister  1 , Ben P Bradshaw  2 , Stephen Elms  3 , Ross A W Gillies  3 , Joanna M Sasse  4 , Jeremy T Brawner  5
Affiliations

Single-step genomic BLUP enables joint analysis of disconnected breeding programs: an example with Eucalyptus globulus Labill

Andrew N Callister et al. G3 (Bethesda). .

Abstract

Single-step GBLUP (HBLUP) efficiently combines genomic, pedigree, and phenotypic information for holistic genetic analyses of disjunct breeding populations. We combined data from two independent multigenerational Eucalyptus globulus breeding populations to provide direct comparisons across the programs and indirect predictions in environments where pedigreed families had not been evaluated. Despite few known pedigree connections between the programs, genomic relationships provided the connectivity required to create a unified relationship matrix, H, which was used to compare pedigree-based and HBLUP models. Stem volume data from 48 sites spread across three regions of southern Australia and wood quality data across 20 sites provided comparisons of model accuracy. Genotyping proved valuable for correcting pedigree errors and HBLUP more precisely defines relationships within and among populations, with relationships among the genotyped individuals used to connect the pedigrees of the two programs. Cryptic relationships among the native range populations provided evidence of population structure and evidence of the origin of landrace populations. HBLUP across programs improved the prediction accuracy of parents and genotyped individuals and enabled breeding value predictions to be directly compared and inferred in regions where little to no testing has been undertaken. The impact of incorporating genetic groups in the estimation of H will further align traditional genetic evaluation pipelines with approaches that incorporate marker-derived relationships into prediction models.

Keywords: HBLUP; MPP; Multiparental Populations; Myrtaceae; breeding value accuracy; forest tree breeding; genomic relationship matrix; genomic selection.

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Figures

Figure 1
Figure 1
Locations of the 48 trials used for this study with (A) reference map of Australia, (B) 6 trials in Gippsland, (C) 14 trials in the Green Triangle, and (D) 28 trials in Western Australia. EG1 trials represented as blue symbols, EG2 trials as green symbols.
Figure 2
Figure 2
Density distribution of realized relationship coefficients within the G matrix of the EG1 program (blue bars) and EG2 program (pink bars) for relationships with expected coefficient of (A) zero, (B) 0.062, (C) 0.125, (D) 0.25, and (E) 0.5.
Figure 3
Figure 3
Frequency of relationship coefficients between programs in the joint G matrix. Inset provides detail for 428 relationships with r > 0.2
Figure 4
Figure 4
Mean breeding value accuracy for different classes of individuals estimated by ABLUP models with and without fixed race effects, within-program HBLUP, and joint HBLUP for (A) EG1 individuals in WA, (B) EG2 individuals in WA, (C) EG1 individuals in GT, (D) EG2 individuals in GT, (E) EG1 individuals in GIPPS, and (F) EG2 individuals in GIPPS. Error bars are standard errors of means.
See this image and copyright information in PMC

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