No 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.

Genetic groups have been widely adopted in tree breeding to account for provenance effects within pedigree-derived relationship matrices. However, provenances or genetic groups have not yet been incorporated into single-step genomic BLUP (‘HBLUP’) analyses of tree populations. To quantify the impact of accounting for population structure in Eucalyptus globulus, we used HBLUP to compare breeding value predictions from models excluding base population effects and models including either fixed genetic groups or the marker-derived proxies, also known as metafounders (MF). Full-sib families from two separate breeding populations were evaluated across 13 sites in the ‘Green Triangle’ region of Australia. Gamma matrices (Γ) describing similarities among MF reflected the geographic distribution of populations and the origins of two land races were identified. Diagonal elements of Γ provided population diversity or allelic covariation estimates between 0.24 to 0.56. Genetic group solutions were strongly correlated with MF solutions across models and MF effects influenced the genetic solutions of base population parents. The accuracy, stability, dispersion, and bias of model solutions were compared using the linear regression method. Addition of genomic information increased accuracy from 0.41 to 0.47 and stability from 0.68 to 0.71, while increasing bias slightly. Dispersion was within 0.10 of the ideal value (1.0) for all models. Although inclusion of MF did not strongly affect accuracy or stability and had mixed effects on bias, we nevertheless recommend the incorporation of MF in prediction models to represent the hierarchical genetic population structure of recently domesticated populations.

Improving the efficiency of fertilizer application is paramount to both the sustainability and profitability of forest plantations. Therefore, developing reliable, cost-effective tools to assess tree nutritional status is of great interest. This investigation sought to assess the use of phloem sap derived metabolites as an indicator of nutritional status on a background of seasonal water availability of E. globulus trees grown under field conditions. Phloem is a central conduit for long distance transport and signaling in plants and offers great promise in reflecting plant scale resource limitations. Changes in the abundance of solutes and isotopes in phloem sap are sensitive to environmental cues. With a focus on both water and nutrient availability, we characterize patterns in phloem sugars, amino acids and the abundance of carbon isotopes in phloem sap obtained from E. globulus among different seasons and fertilizer treatments. Phloem derived total amino acid concentration was found to increase with increasing nitrogen (N) supply, however, this response was lost with the concurrent addition of phosphorus (P) and at the highest level of N supply. Significant seasonal variation in all measured parameters was also detected highlighting the need for caution in making quantitative relationships with growth. Broader implications of the interactive effects of both water supply and multi-nutrient additions, and relationships with growth are discussed.