These authors contributed equally to this work.
Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa
Version of Record online: 22 APR 2014
© 2014 The Authors. New Phytologist © 2014 New Phytologist Trust
Volume 203, Issue 2, pages 535–553, July 2014
How to Cite
McKown, A. D., Klápště, J., Guy, R. D., Geraldes, A., Porth, I., Hannemann, J., Friedmann, M., Muchero, W., Tuskan, G. A., Ehlting, J., Cronk, Q. C. B., El-Kassaby, Y. A., Mansfield, S. D. and Douglas, C. J. (2014), Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. New Phytologist, 203: 535–553. doi: 10.1111/nph.12815
- Issue online: 19 JUN 2014
- Version of Record online: 22 APR 2014
- Manuscript Accepted: 14 MAR 2014
- Manuscript Received: 7 NOV 2013
- Genome British Columbia Applied Genomics Innovation Program. Grant Number: 103BIO
- Genome Canada Large-Scale Applied Research Project. Grant Number: 168BIO
- e BioEnergy Science Center
- US Department of Energy Bioenergy Research Facility. Grant Number: DE–AC05–00OR22725
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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 P < 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.xlsx||application/msexcel||19K||Table 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|
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 P < 1.7 × 10−6
Table S7 Comparison of Gene Ontology (GO) terms (categorized as function or process) assigned to genes uncovered through SNP discovery (P < 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)