UBC Faculty Research and Publications

Genomics of adaptation and wood properties in Populus trichocarpa Douglas, Carl Sep 13, 2011

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ORAL PRESENTATION Open AccessGenomics of adaptation and wood propertiesin Populus trichocarpaCarl DouglasFrom IUFRO Tree Biotechnology Conference 2011: From Genomes to Integration and DeliveryArraial d’Ajuda, Bahia, Brazil. 26 June - 2 July 2011Populus trichocarpa (black cottonwood) and P. balsami-fera (balsam poplar) are native to North America wherelarge natural populations exist. P. trichocarpa has anextensive north-south range along the west coast, whileP. balsamifera has a northerly range across the conti-nent from Alaska to the North American east coast.Both species are well suited for highly productive bioe-nergy biomass plantations in north-temperate climates.We are investigating the large reservoirs of natural gen-otypic and phenotypic variation in wild populations ofthese species, with an initial focus on P. trichocarpa, toidentify allelic variation underlying optimal biofuel andbiomass traits that could be used for accelerated domes-tication. We sampled genetic variation in P. trichocarpaby Illumina transcriptome resequencing of 20 indivi-duals from provenances along a latitudinal gradientfrom 60?N to 44?N. This analysis revealed extensivenucleotide, gene expression and alternative splicingpolymorphism in 10,000 xylem-expressed genes. Align-ment of transcript sequences to the P. trichocarpa Nis-qually-1 reference genome was used to identify over500,000 SNPs. These SNPs were combined with a largerSNP set generated by whole genome resequencing ofmultiple P. trichocarpa individuals carried out by the USDOE Bioenergy Sciences Center (BESC) to populate aP. trichocarpa SNP database. Using the Illumina iSelectprocess, we generated an Illumina Infinium bead arrayfor genotyping of 34,000 SNPs that tag 3,700 candidategenes selected for their potential involvement in bio-mass, adaptation, and wood traits. Using this bead arrayin collaboration with BESC, we obtained candidate geneSNP genotypes for over 700 P. trichocarpa individualsgrown in common gardens. This analysis of these datarevealed extensive genotypic polymorphism in the tar-geted gene set. In parallel, we carried out phenotypingof the trees from the wild populations grown in com-mon gardens, quantifying variation in over 85 morpho-logical, growth, physiological, wood chemistry, andwood quality traits. Population genetic analysis of theSNP data, its use for genotype-phenotype associationstudies to identify candidate gene alleles underlying var-iation in traits of interest, and the prospects of using theresults for marker assisted breeding will be discussed.Published: 13 September 2011doi:10.1186/1753-6561-5-S7-O2Cite this article as: Douglas: Genomics of adaptation and woodproperties in Populus trichocarpa. BMC Proceedings 2011 5(Suppl 7):O2.Submit your next manuscript to BioMed Centraland take full advantage of: • Convenient online submission• Thorough peer review• No space constraints or color figure charges• Immediate publication on acceptance• Inclusion in PubMed, CAS, Scopus and Google Scholar• Research which is freely available for redistributionSubmit your manuscript at www.biomedcentral.com/submitCorrespondence: carl.douglas@ubc.caUniversity of British Columbia, USADouglas BMC Proceedings 2011, 5(Suppl 7):O2http://www.biomedcentral.com/1753-6561/5/S7/O2© 2011 Douglas; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative CommonsAttribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction inany medium, provided the original work is properly cited.


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