Association Genetics of Traits Underlying Secondary Cell Wall Chemistry and Ultrastructure in Populus trichocarpa

Populus trichocarpa has an extensive latitudinal range along the west coast of North America, existing in large natural populations. The species has significant ecological importance, and has recently been identified as an importance feedstock for bioenergy applications. An association genetics approach was employed to identify the allelic variation underlying essential biofuel and biomass traits that could be used to accelerate domestication of P. trichocarpa. Twenty individuals, representing provenances along a latitudinal gradient, were selected for Illumina mRNA resequencing, and alignment of transcripts to the Nisqually-1 reference was used to identify over 500,000 SNPs. These SNPs, combined with a larger SNP set generated by whole genome resequencing was employed to generate an Illumina Infinium bead array for genotyping 38,000 SNPs in ~3,700 candidate genes. 643 trees, grown in common gardens, were subject to extensive cell wall phenotyping, and shown to display substantial variation in cell wall chemistry, fiber traits, and biomass characteristics.  Using a unified mixed linear model 95 significant associations with 15 cell wall traits were identified, explaining between 5.4%-23.3% of the variation to the associated SNPs. Several industrially important cell wall traits, such as lignin S:G ratio, had SNPs explaining a large percentage of the variation (5.8%). In addition, a single gene was identified that appears to significantly impact 8 key traits, suggesting a major pleiotropic effect.  This research project has identified several candidate gene alleles underlying the variation in cell wall traits, and are prospects for marker assisted breeding and selection of biofuels traits in Poplar.