Table 1.
Analysis of variance (ANOVA) testing the effect of clone, year, and clone × year interaction of AUDPC.
Figure 1.
Quantile-quantile plots of expected and observed P values evaluating the type-1 error in a simple model (simple), the top ten principal components (PCA-TOP10), BIC selected PCs (PCA-BIC), the K model (KINSHIP), and the Q model (Q MATRIX) with goodness of fit test using Bayesian Information Criterion for 2009, 2010, and 2011 (top to bottom).
Table 2.
Correlation coefficients of the population structure, latitude, and AUDPC in each year.
Table 3.
SNPs associated with AUDPC in 2009, 2010, and 2011.
Figure 2.
Manhattan plot of the results from association analysis for AUDPC in 2009, 2010, and 2011 (from top to bottom).
The red line represents the P value (P<1.45×10−5, P<1.15×10−5, and P<1.35×10−5 in 2009, 2010, and 2011, respectively) corresponding to permutated P of α = 0.05 as the threshold for multiple testing corrections. SNPs repeated in time are highlighted in green and identified by gene name in black. SNPs within genes showing expression profile changes in response to M. larici-populina are highlighted in green and identified by gene name in red.
Figure 3.
Pairwise linkage disequilibrium plot of FAR-RED IMPAIRED RESPONSE1 and FAR-RED ELONGATED HYPOCOTYL3 with gene structures.
SNPs significant in 2010 are indicated with an asterisk; SNPs significant in 2011 are indicated with a cross. Scaffold_6_ 1402770 in the intergenic region had the highest significance (P = 3.64×10−6) and explained 2.5% (R2 = 0.025) of the phenotypic variance in 2010.
Figure 4.
Pairwise linkage disequilibrium plot of NITRATE TRANSPORTER2.1 and NITRATE TRANSPORTER2.4 with gene structures.
SNPs significant are indicated with an asterisk. Scaffold_9_ 1676227 in the intergenic region had the highest significance (P = 3.52×10−7) and largest effect on AUDPC in 2010 (R2 = 0.034). Scaffold_143_2955 was annotated to Potri.009G008500 in JGI Populus trichocarpa genome v3.