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

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 multi-generational 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 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.

Accounting for population structure in genomic predictions of Eucalyptus globulus

“…This study used a subset of the E. globulus phenotype data analyzed by Callister et al (2021) . Full-sib family data for 13 progeny tests in the “Green Triangle” region of Australia were provided by 2 separate multigenerational commercial tree improvement programs, EG1 (Australian Bluegum Plantations) and EG2 (HVP Plantations) ( Fig.…”

“…The authors suggested that true average relationships within races were probably substantially larger than those estimated in H and that accommodating ancestral race effects in HBLUP should be prioritized. The goals for the present study extend from this recent work ( Callister et al 2021 ) using a subset of their data. Our goals were to (1) fit models including MF and examine relationships corresponding to race, landrace, and plus tree (infusion) populations and (2) use the LR approach ( Legarra and Reverter 2018 ) to evaluate goodness of fit for genetic models with and without genomic relationship information, with genetic groups excluded or incorporated as UPGs, or as MFs.…”

“…McRae et al 2004 ; Brawner et al 2010 ; Callister et al 2011 ; Klápště et al 2019 ), typically as unknown parent groups (UPGs) that were developed to account for missing parents in livestock populations ( Quaas 1988 ; Westell et al 1988 ). This approach treats provenances as fixed effects, and it results in more conservative estimates of heritability relative to treating founders as unrelated individuals ( Callister et al 2021 ).…”

“…Although there have been a number of studies applying this “HBLUP” approach to forest tree populations (e.g. Ratcliffe et al 2017 ; Klápště et al 2018 ; Thavamanikumar et al 2020 ; Ukrainetz and Mansfield 2020 ; Callister et al 2021 ; Jurcic et al 2021 ), none have yet considered multiple base populations such as provenances.…”

“… Callister et al (2021) used HBLUP to conduct a joint analysis of 2 disconnected E. globulus breeding populations that were linked using marker-derived pedigree. Relationships within the resulting H matrix tended to be significantly positive among population founders from the same population, while across-race relationships among founders ranged from significantly positive to significantly negative.…”