Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus.

The promise of association genetics to identify genes or genomic regions controlling complex traits has generated a flurry of interest. Such phenotype-genotype associations could be useful to accelerate tree breeding cycles, increase precision and selection intensity for late expressing, low heritability traits. However, the prospects of association genetics in highly heterozygous undomesticated forest trees can be severely impacted by the presence of cryptic population and pedigree structure. To investigate how to better account for this, we compared the GLM and five combinations of the Unified Mixed Model ( UMM ) on data of a low-density genome-wide association study for growth and wood property traits carried out in a Eucalyptus globulus population (n = 303) with 7,680 Diversity Array Technology (DArT) markers. Model comparisons were based on the degree of deviation from the uniform distribution and estimates of the mean square differences between the observed and expected p-values of all significant marker-trait associations detected. Our analysis revealed the presence of population and family structure. There was not a single best model for all traits. Striking differences in detection power and accuracy were observed among the different models especially when population structure was not accounted for. The UMM method was the best and produced superior results when compared to GLM for all traits. Following stringent correction for false discoveries, 18 marker-trait associations were detected, 16 for tree diameter growth and two for lignin monomer composition (S:G ratio), a key wood property trait. The two DArT markers associated with S:G ratio on chromosome 10, physically map within 1 Mbp of the ferulate 5-hydroxylase (F5H) gene, providing a putative independent validation of this marker-trait association. This study details the merit of collectively integrate population structure and relatedness in association analyses in undomesticated, highly heterozygous forest trees, and provides additional insights into the nature of complex quantitative traits in Eucalyptus.

Additive and non-additive genetic parameters from clonally replicated and seedling progenies of Eucalyptus globulus.

The first estimates of the importance of epistatic effects within Eucalyptus globulus were obtained from analysis of clonally replicated full-sib progeny tests grown in Portugal. Parents comprised diverse selections from the Portuguese landrace. Variance components were estimated for 4-year-old diameter growth and pilodyn penetration, an indirect measure of wood density, both key traits in the pulpwood breeding objective. The experimental components of variance were used to estimate heritabilities and proportions of the phenotypic variance due to dominance and epistasis. The additive variance was the only significant genetic component affecting either diameter or pilodyn. Estimates of the additive, dominance and epistatic effects accounted for 8-10%, 0-4% and 0.4% of the phenotypic variance in diameter, and for 11-17%, 0% and 5% of the phenotypic variance in pilodyn, respectively. A comparison of residual coefficients of variation within seedling and cloned progenies indicated that C effects within clones were not a serious source of random variability. Despite the test sites encompassing a diverse range of locations, no important genotype by environment interaction was detected. The results suggested that an improvement strategy combining both recurrent selection for additive genetic merit and clonal testing may be adequate for optimizing genetic gains from this genetic base.