Genetic improvement of switchgrass (Panicum virgatum) as a dedicated bioenergy feedstock crop is necessary to reduce delivered feedstock cost.  There are many components that factor into feedstock cost, including biomass yield/acre, costs associated with fertilizer and chemical applications, as well as harvesting and transport.  The goals of the joint Noble Foundation-Ceres switchgrass breeding program are not only targeted toward biomass yield and crop inputs, but also directed at improving the composition and conversion process efficiencies of harvested biomass.  This breeding improvement program is based on knowledge of the genetics of the species and the use of molecular markers to follow the genes determining useful traits. We have therefore sequenced clones in full length cDNA libraries made from a variety of tissues produced under diverse growth conditions to understand the complexity of the switchgrass transcriptome, as well as sequence variability in specific genes.  The sequences are also explored as potential resources for molecular marker development. This talk will focus on the allelic diversity of different groups of genes and the utility of these sequences as molecular markers to accelerate progress in a breeding program.