1-12: First look at Allele-Specific Expression in Populus trichocarpa using Next Generation Sequencing.

Monday, April 29, 2013
Exhibit Hall
Arnaud Capron, Charles Hefer, Hua Bao and Carl Douglas, Department of Botany, University of British Columbia, Vancouver, BC, Canada

Poplar (Populus trichocarpa) has become the model for woody plants, with a complete draft genome published in 2006 and is the center of continuing efforts due to the economic weight of the forestry industry and its varied downstream applications. Recent advances in high-throughput sequencing have allowed the study of whole genomes in many species, including poplar and ongoing efforts are aiming at cataloguing the extent of natural variation in the species. One of the pursued goals being the improvement of plantation species for cellulosic biomass production and extractability.

Here, we took advantage of Next-Generation Sequencing of genomes and transcriptomes of several Populus trichocarpa clones to identify genes showing Allele-Specific Expression (ASE) and its impact, particularly in genes involved in cellulose and lignin biosynthetic pathways, with the idea of unearthing new variants of interest. ASE is one of the less understood aspect of natural variations, looking at the interplay between alleles at the same locus. Several studies have uncovered the previously unknown extent of the ASE phenomenon, at the gene level in Drosophila and maize or at even exon level in human cell culture. A total of 50,000 Single Nucleotide Polymorphisms (SNPs) were detected in a collection of nine accessions, representing between 15% and 35% of the SNPs polled, covering 9,000 genes. A number of genes involved in the control of various wood property traits were discovered to display preferential allele expression. However, the different observed ASE patterns hint at several types of underlying regulation systems to achieve this state.