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nph12815-sup-0001-FigS1-S5.docxWord document4060K

Fig. S1 Compiled Q–Q plots for all phenology traits indicating five structure model choices (simple, P, Q, K, P + K, Q + K).

Fig. S2 Compiled Q–Q plots for all biomass traits indicating five structure model choices (simple, P, Q, K, P + K, Q + K).

Fig. S3 Compiled Q–Q plots for all ecophysiology traits indicating five structure model choices (simple, P, Q, K, P + K, Q + K).

Fig. S4 Proportion of the phenotypic variance explained by significant SNP–trait associations (cumulative R2) for each trait within each trait category at < 1.7 × 10−6.

Fig. S5 Proportion of the phenotypic variance explained by significant SNP–trait associations (cumulative R2) vs broad-sense heritability values (H2) of phenotypic traits.

nph12815-sup-0002-TableS1a.xlsxapplication/msexcel19KTable S1 (a) Phenotypic trait data in Populus trichocarpa used for genome-wide association study; (b) genotypic SNP data Populus trichocarpa used for genome-wide association study
nph12815-sup-0003-TableS1b.csvCSV document39133K 
nph12815-sup-0004-TableS2-S10.xlsxapplication/msexcel1531K

Table S2 Bayesian Information Criterion (BIC) indicating log likelihood values for model selection in genome-wide association study

Table S3 Comparison of significant genes and SNPs from genome-wide association study by chromosome

Table S4 Annotations of SNPs uncovered from ‘Nisqually-1’ genome Populus trichocarpa v2.2 to v3.0

Table S5 Full details of SNP–trait associations using genome-wide association studies indicating population structure correction model, associated P-values, significance (α), marker R2, closest Arabidopsis homolog and putative gene function/annotation

Table S6 Pairwise linkage disequilibrium (LD) r2 values between all SNP markers significant at < 1.7 × 10−6

Table S7 Comparison of Gene Ontology (GO) terms (categorized as function or process) assigned to genes uncovered through SNP discovery (< 1.7 × 10−6) and genes on the array

Table S8 Candidate genes/SNPs with multiple associations to traits and average phenotypic value associated with each allelic variant

Table S9 Pairwise linkage disequilibrium (LD) r2 values between SNP markers of different genes with effects across multiple trait categories

Table S10 Genetic trait correlations among biomass, ecophysiology, and phenology traits indicating Pearson's Product-Moment Correlation coefficients (r)