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Figure 2. Results of population structure analyses using a Bayesian approach implemented by STRUCTURE (A) and PCA (Principal coordinate analysis) (B). Colors define three Genetic Group: Group 1 in blue (Eastern and Western Otways races and the Chilean provenance of the Uruguayan trials), Group 2 in red (Strzelecki Ranges race and E. globulus spp. pseudoglobulus (Naudin ex Maiden), and Group 3 in yellow (Furneaux North-eastern and South-eastern Tasmania races, Chilean provenance of the Argentinean trial and Portuguese land race provenances). doi:10.1371/journal.pone.0081267.g002

Figure 2 Results of population structure analyses using a Bayesian approach implemented by STRUCTURE (A) and PCA (Principal coordinate analysis) (B). Colors define three Genetic Group: Group 1 in blue (Eastern and Western Otways races and the Chilean provenance of the Uruguayan trials), Group 2 in red (Strzelecki Ranges race and E. globulus spp. pseudoglobulus (Naudin ex Maiden), and Group 3 in yellow (Furneaux North-eastern and South-eastern Tasmania races, Chilean provenance of the Argentinean trial and Portuguese land race provenances). doi:10.1371/journal.pone.0081267.g002

Related Figures (9)

Figure 1. Reference genetic map position of 1,909 DArT markers assayed in the association study. Map position from Hudson et al. (2012). doi:10.1371/journal.pone.0081267.g001
Figure 1. Reference genetic map position of 1,909 DArT markers assayed in the association study. Map position from Hudson et al. (2012). doi:10.1371/journal.pone.0081267.g001
Table 2. Mean squared differences (MSD) between observed and expected p-values for the six association genetics models applied in the study. The selected models are highlighted in bold (see text for models’ and traits’ abbreviations) doi:10.1371/journal.pone.0081267.t002
Table 2. Mean squared differences (MSD) between observed and expected p-values for the six association genetics models applied in the study. The selected models are highlighted in bold (see text for models’ and traits’ abbreviations) doi:10.1371/journal.pone.0081267.t002
Figure 3. Heat map of the pair-wise relationship coefficients among the 303 £. g/obulus trees produced from the SPAGeDi progr showing the three Genetic Groups: Genetic Group 1, 2 and 3 from right to left. The heat scale represents pair-wise relationship coefficie! for all pairs of individual trees. Values greater than 0.5 are not shown and account for only 0.08% of the distribution. doi:10.1371/journal.pone.0081267.g003
Figure 3. Heat map of the pair-wise relationship coefficients among the 303 £. g/obulus trees produced from the SPAGeDi progr showing the three Genetic Groups: Genetic Group 1, 2 and 3 from right to left. The heat scale represents pair-wise relationship coefficie! for all pairs of individual trees. Values greater than 0.5 are not shown and account for only 0.08% of the distribution. doi:10.1371/journal.pone.0081267.g003
Figure 4. Plots of the observed vs. expected p-values for the six association genetics models studied for all traits. See text for models’ and traits’ abbreviation. doi:10.1371/journal.pone.0081267.g004
Figure 4. Plots of the observed vs. expected p-values for the six association genetics models studied for all traits. See text for models’ and traits’ abbreviation. doi:10.1371/journal.pone.0081267.g004
Figure 5. Association mapping results from the different linear models indicating the number of significant (p-value<0.05) DArT markers associated with growth and wood properties traits. 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. doi:10.1371/iournal none.0081267.q005
Figure 5. Association mapping results from the different linear models indicating the number of significant (p-value<0.05) DArT markers associated with growth and wood properties traits. 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. doi:10.1371/iournal none.0081267.q005
In bold, the number of significant marker-trait associations detected in the selected models by trait combination (see text for models’ and traits’ abbreviations). doi:10.1371/journal.pone.0081267.t003 Table 3. Association mapping results from the different linear models indicating the number (and percentage) of significant markers found associated with growth and wood property traits after correction for multiple testing (FDR p-value<0.05).
In bold, the number of significant marker-trait associations detected in the selected models by trait combination (see text for models’ and traits’ abbreviations). doi:10.1371/journal.pone.0081267.t003 Table 3. Association mapping results from the different linear models indicating the number (and percentage) of significant markers found associated with growth and wood property traits after correction for multiple testing (FDR p-value<0.05).
Shown are p-values after correction for multiple testing (FDR p-value<0.05, Q-value) and estimates of percent phenotypic variance putatively explained (R*). Highlighted in bold, the best trait by model combinations reportec based on the degree of deviation from the uniform distribution and estimates of the mean square differences (MSD) between the observed and expected p-values (see text for models’ and traits’ abbreviations). doi:10.1371/journal.pone.0081 267.004 Table 4. Significant DArT marker-trait associations for DBH and S:G ratio retained for the six models.
Shown are p-values after correction for multiple testing (FDR p-value<0.05, Q-value) and estimates of percent phenotypic variance putatively explained (R*). Highlighted in bold, the best trait by model combinations reportec based on the degree of deviation from the uniform distribution and estimates of the mean square differences (MSD) between the observed and expected p-values (see text for models’ and traits’ abbreviations). doi:10.1371/journal.pone.0081 267.004 Table 4. Significant DArT marker-trait associations for DBH and S:G ratio retained for the six models.
Table 5. Genomic position of the DArT marker-trait associations detected and putative underlying genes found by a simple BLASTX search in the Eucalyptus grandis reference genome version 1.1 (available in Phytozone) (see text for traits’ abbreviations). NOTE: ° Burrows-Wheeler Alignment position of DArT marker probe to the Eucalyptus grandis reference genome as described in [42]. °Eucalyptus grandis genome chromosome scaffold to which DArT marker probe had best alignment score as described in [42]; scaffold numbered over 11 correspond to still unanchored sequence scaffolds. “P, biological process; F, molecular function; C, cellular component. 4EC number, enzyme classification number. n.a. sequence not available for DArT marker probe. doi:10.1371/journal.pone.0081267.t005
Table 5. Genomic position of the DArT marker-trait associations detected and putative underlying genes found by a simple BLASTX search in the Eucalyptus grandis reference genome version 1.1 (available in Phytozone) (see text for traits’ abbreviations). NOTE: ° Burrows-Wheeler Alignment position of DArT marker probe to the Eucalyptus grandis reference genome as described in [42]. °Eucalyptus grandis genome chromosome scaffold to which DArT marker probe had best alignment score as described in [42]; scaffold numbered over 11 correspond to still unanchored sequence scaffolds. “P, biological process; F, molecular function; C, cellular component. 4EC number, enzyme classification number. n.a. sequence not available for DArT marker probe. doi:10.1371/journal.pone.0081267.t005
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