Genetic parameters for growth, wood density and pulp yield in Eucalyptus globulus

Genetic variation and co-variation among the key pulpwood selection traits for Eucalyptus globulus were estimated for a range of sites in Portugal, with the aim of improving genetic parameters used to predict breeding values and correlated response to selection. The trials comprised clonally replicated full-sib families (eight trials) and unrelated clones (17 trials), and exhibited varying levels of pedigree connectivity. The traits studied were stem diameter at breast height, Pilodyn penetration (an indirect measure of wood basic density) and near infrared reflectance predicted pulp yield. Univariate and multivariate linear mixed models were fitted within and across sites, and estimates of additive genetic, total genetic, environmental and phenotypic variances and covariances were obtained. All traits studied exhibited significant levels of additive genetic variation. The average estimated within-site narrowsense heritability was 0.19±0.03 for diameter and 0.29± 0.03 for Pilodyn penetration, and the pooled estimate for predicted pulp yield was 0.42±0.14. When they could be tested, dominance and epistatic effects were generally not statistically significant, although broad-sense heritability estimates were slightly higher than narrow-sense heritability estimates. Averaged across trials, positive additive (0.64±0.08), total genetic (0.58±0.04), environmental (0.38±0.03) and phenotypic (0.43±0.02) correlation estimates were consistently obtained between diameter and Pilodyn penetration. This data argues for at least some form of pleiotropic relationship between these two traits and that selection for fast growth will adversely affect wood density in this population. Estimates of the across-site genetic correlations for diameter and Pilodyn penetration were high, indicating that the genotype by environment interaction is low across the range of sites tested. This result supports the use of single aggregated selection criteria for growth and wood density across planting environments in Portugal, as opposed to having to select for performance in different environment

Genetic parameters and comparison between native and local landraces of Eucalyptus globulus Labill. ssp. globulus growing in the central highlands of Colombia

International audienceAimsThe objective of this study was to compare the merit of the Colombian landrace relative to the various Australian native races of Eucalyptus globulus Labill. ssp. globulus and study the genetic control of key traits such as growth, wood density, and leaf phase change in the unique conditions of the Colombian highlands.MethodsThe genetic study was based on open-pollinated families from native Australian and Colombian landrace origin, tested across four trials spanning two generations of breeding. A multisite mixed linear model with genetic groups was fitted to the data to estimate race merit and the variance and covariances between traits, ages, and sites.ResultsRace effects for growth were small and only significant at the older site. In contrast, races differ significantly for height to phase change and density. The Colombian landrace and South and NE Tasmania races changed leaf type at a higher tree height. King Island and Recherche Bay had low density values, whereas the Colombian landrace had the highest. Heritability was moderate for growth traits (between 0.09 and 0.40), high for height to phase change (between 0.42 and 0.69), and moderate for wood density (0.28). The genetic correlation between growth and height to phase change was in general positive, but variable across sites. There was no correlation between growth and density. Despite large differences in growth between trials, pairwise genetic correlations suggest that genotype-by-site interaction is negligible. However, there was a poor correspondence between first-generation (ex-native stands) and second-generation families (ex-multi-provenance progeny trial). This suggests that breeding value estimates based on native open-pollinated material are unreliable.ConclusionResults confirm negligible race differences for growth, but not for wood density. Future breeding efforts should include the various genetic backgrounds including the Colombian landrace which constitutes a very important source, especially because of its high density. Despite a low Genotype by Environment interaction, the poor genetic correspondence between the first- and second-generation trials indicates that selections for growth should be based on information coming mainly from the advanced-generation trials

A case study of Eucalyptus globulus fingerprinting for breeding

• Introduction Tree genetic improvement programs usually lack, in general, pedigree information. Since molecular markers can be used to estimate the level of genetic similarity between individuals, we genotyped a sample of a Portuguese Eucalyptus globulus breeding population—a reference population of 125 individuals—with 16 microsatellites (SSR). • Materials and methods Using genotypes from the reference population, we developed a simulation approach to recurrently generate (105 replicates) virtual offspring with different relatedness: selfed, half-sib, full-sib and unrelated individuals. Four commonly used pairwise similarity coefficients were tested on these groups of simulated offspring. Significant deficits in heterozygosity were found for some markers in the reference population, likely due to the presence of null alleles. Therefore, the impact of null alleles in the relatedness estimates was also studied. We conservatively assumed that all homozygotes in the reference population were carriers of null alleles. • Results All estimators were unbiased, but one of them was better adjusted to our data set, even when null alleles were considered. The estimator’s accuracy and precision were validated with individuals of known pedigree obtained from controlled crosses made with the same reference population’s parents. Additionally, a clustering algorithm based on the estimator of choice was constructed, in order to infer the relatedness among 24 E. globulus elite individuals. We detected four putatively related elite individuals’ pairs (six pairs considering the presence of null alleles). • Conclusions This work demonstrates that in the absence of pedigree information, our approach could be useful to identify relatives and minimize consanguinity in breeding populations

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

Plots of the observed vs. expected <i>p-values</i> for the six association genetics models studied for all traits.

<p>See text for models' and traits' abbreviation.</p

Genomic position of the DArT marker-trait associations detected and putative underlying genes found by a simple BLASTX search in the <i>Eucalyptus grandis</i> reference genome version 1.1 (available in Phytozone) (see text for traits' abbreviations).

<p><b>NOTE</b>: <i>^a</i> Burrows-Wheeler Alignment position of DArT marker probe to the <i>Eucalyptus grandis</i> reference genome as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081267#pone.0081267-Petroli1" target="_blank">[42]</a>.</p><p><i>^b</i><i>Eucalyptus grandis</i> genome chromosome scaffold to which DArT marker probe had best alignment score as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081267#pone.0081267-Petroli1" target="_blank">[42]</a>; scaffold numbered over 11 correspond to still unanchored sequence scaffolds.</p><p><i>^c</i>P, biological process; F, molecular function; C, cellular component.</p><p><i>^d</i>EC number, enzyme classification number.</p><p>n.a. sequence not available for DArT marker probe.</p

Association mapping results from the different linear models indicating the number of significant (<i>p</i>-value≤0.05) DArT markers associated with growth and wood properties traits.

<p>In each bar, the gray and black areas represent the number of significant DArT markers from the specific model (i.e., GLM, Q, P, K, Q+K and P+K) and overlapping between the specific model and GLM, respectively. See text for models' and traits' abbreviation.</p

Description of progeny trials in the different sites, numbers of individuals phenotyped and genotyped and phenotypic trait means (see text for traits' abbreviations).

a<p>Number of provenances (number of open-pollinated families) in the trial.</p>b<p>Number of provenances (number of open-pollinated families) sampled in the association population.</p>c<p>Ages at measurements of diameter at breast height and Pilodyn penetration and wood properties.</p>d<p>Number of trees measured for wood properties (WP) and genotyped for the association study.</p

Heat map of the pair-wise relationship coefficients among the 303 <i>E. globulus</i> trees produced from the SPAGeDi program showing the three Genetic Groups: Genetic Group 1, 2 and 3 from right to left.

<p>The heat scale represents pair-wise relationship coefficients for all pairs of individual trees. Values greater than 0.5 are not shown and account for only 0.08% of the distribution.</p