These authors contributed equally to this work.
Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms
Version of Record online: 26 JUL 2013
© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust
Volume 200, Issue 3, pages 710–726, November 2013
How to Cite
Porth, I., Klapšte, J., Skyba, O., Hannemann, J., McKown, A. D., Guy, R. D., DiFazio, S. P., Muchero, W., Ranjan, P., Tuskan, G. A., Friedmann, M. C., Ehlting, J., Cronk, Q. C. B., El-Kassaby, Y. A., Douglas, C. J. and Mansfield, S. D. (2013), Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms. New Phytologist, 200: 710–726. doi: 10.1111/nph.12422
- Issue online: 11 OCT 2013
- Version of Record online: 26 JUL 2013
- Manuscript Accepted: 18 JUN 2013
- Manuscript Received: 30 MAR 2013
- the Genome British Columbia Applied Genomics Innovation Program. Grant Number: 103BIO
- the Genome Canada Large-Scale Applied Research Project. Grant Number: 168BIO
- Office of Biological and Environmental Research in the DOE Office of Science
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|nph12422-sup-0001-FigS1.pdf||application/PDF||168K||Fig. S1 Geographical distribution of original sampling locations (drainages) along with levels of population structure (Geneland) in P. trichocarpa.|
|nph12422-sup-0002-FigS2.pdf||application/PDF||83330K||Fig. S2 Details of association data for each trait in P. trichocarpa.|
Fig. S3 Extent of LD between the top 20 SNPs in the simple model for galactose in P. trichocarpa.
Fig. S4 Theoretical power of association analysis as a function of LD (r2) between an SNP marker and a QTL explaining 0.5, 2, or 5% of the total phenotypic variance in a population of variable sizes.
Fig. S5 CRLK42 gene structure, linkage of genotyped SNPs and genetic effects of three SNPs associated with MFA1 in P. trichocarpa.
Fig. S6 Boxplot diagrams depicting the genetic effects of all SNPs located within transcription factors with significant associations with relative mannose and alpha cellulose content (percentage variation in extract-free dry wood) in P. trichocarpa.
|nph12422-sup-0004-FigS7.pdf||application/PDF||4530K||Fig. S7 Boxplot diagrams depicting the genetic effects of SNPs significantly associated with relative holocellulose, alpha cellulose, and hemicellulose content in P. trichocarpa.|
Fig. S8 ARA-5 (RabGTPase) gene structure, linkage of genotyped SNPs and genetic effects of two SNPs associated with relative holocellulose content in P. trichocarpa.
Fig. S9 Structure of the epsin N-terminal homology (ENTH) domain-containing protein gene (POPTR_0018s13970), linkage of genotyped SNPs and genetic effects of four SNPs associated with relative alpha cellulose content in P. trichocarpa.
Fig. S10 Boxplot diagrams depicting the genetic effects of SNPs significantly associated with relative glucose, xylose, mannose, and arabinose content in P. trichocarpa.
Fig. S11 Boxplot diagrams depicting the genetic effects of SNPs significantly associated with relative insoluble lignin, soluble lignin, total lignin, and syringyl lignin content in P. trichocarpa.
Fig. S12 ATMPK20 gene structure, linkage of genotyped SNPs, and genetic effects of three SNPs associated with relative insoluble lignin content in P. trichocarpa.
Fig. S13 Boxplot diagram depicting the genetic effect of an SNP detected in AUD1 with a significant association with soluble lignin content in P. trichocarpa.
|nph12422-sup-0008-FigS14.pdf||application/PDF||6633K||Fig. S14 Boxplot diagrams depicting the genetic effects of SNPs significantly associated with average wood density, % cell wall crystallinity, fiber length, MFA1, and MFA2 in P. trichocarpa.|
Fig. S15 Manhattan plot showing genome-wide SNP–trait associations for fiber length in P. trichocarpa.
Fig. S16 PRR1 gene structure, linkage of genotyped SNPs, and genetic effects of three SNPs associated with average wood density in P. trichocarpa.
Fig. S17 ANAC073 gene structure, linkage of genotyped SNPs and genetic effects of two SNPs associated with cell wall crystallinity in P. trichocarpa.
Fig. S18 Unrooted maximum likelihood phylogenetic tree of the FLA gene family.
|nph12422-sup-0010-TableS1.csv||CSV document||75K||Table S1 Information about the accessions and provenances and the phenotyping of the Populus trichocarpa association mapping population used in the study|
|nph12422-sup-0011-TableS2.csv||CSV document||1K||Table S2 Bayesian information criterion (BIC) table for comparing the simple model (i.e. no correction for population or familial structure), the K model (i.e. correction for familial structure only), the PCA-TOP10 model (i.e. a PCA-based model that uses the first 10 PCs) and the PCA-BIC model (i.e. a PCA-based model that selects PCs via BIC)|
|nph12422-sup-0012-TableS3.csv||CSV document||36K||Table S3 Comprehensive summary of 141 SNP associations within 105 individual genes with trait associations at α ≤ 0.05 in P. trichocarpa, testing 17 wood chemistry and ultrastructure traits and c. 3500 broad-based candidate genes|
|nph12422-sup-0013-TableS4.docx||Word document||23K||Table S4 SNP–trait associations with more than one SNP per P. trichocarpa gene|
|nph12422-sup-0014-TableS5.docx||Word document||16K||Table S5 SNP–trait associations in genes encoding transcription factors for P. trichocarpa|
|nph12422-sup-0015-TableS6.docx||Word document||15K||Table S6 SNP–trait associations in genes involved in cell wall metabolism for P. trichocarpa|
|nph12422-sup-0016-TableS7.docx||Word document||24K||Table S7 SNP–trait associations in genes included based on expression for P. trichocarpa|
|nph12422-sup-0017-TableS8.doc||Word document||50K||Table S8 Sequences of the FLA gene family used to build its phylogeny as displayed in Fig. S18|