Next Generation Sequencing of the Salix purpurea L. Genome and Transcriptome: Tools for the Genetic Improvement of Willow Biomass Crops

Development of genomic selection methods will greatly accelerate the genetic improvement of shrub willows and poplars to attain improved biomass yield, stress tolerance, disease and pest resistance, nutrient and water use efficiency, and optimum biomass composition for conversion to biofuels and bioenergy.  The release and continued analysis of the Populus trichocarpa genome has provided a wealth of information for the elucidation of the genetic basis for variation in key traits important for biomass production and carbon sequestration in woody plants.  As closely related and only recently diverged members of the family Salicaceae, Salix and Populus gene sequences, microsyntenic gene arrangements, and genome structure relationships are highly similar overall, based on current data. Yet there are major phenotypic differences between Salix purpurea and P. trichocarpa, including stem number, crown form, shoot meristem and floral bud phenology, pollination systems, leaf developmental patterns and tolerance to polyploidization. To investigate the molecular basis for variation in those traits, we have used next-generation sequencing data to generate an initial de novo assembly of the S. purpurea genome.  Eight RNA samples from flowers, leaves, roots, and stems were also sequenced and used to assemble the S. purpurea transcriptome. Comparative analysis of the S. purpurea and P. trichocarpa genomes will be discussed, as will the development of high-throughput genotyping-by-sequencing markers for genome assembly, trait mapping, and genomic selection approaches in willow breeding programs.