Biofuels derived from plant biomass present a promising avenue to address the negative aspects of fossil-fuel dependence. The sustainability of biofuel production relies in part on the efficient degradation of lignocellulosic feedstocks. In order to capitalize on the potential of lignocellulosic biofuels, the genes underlying natural genetic variation for conversion efficiency must be determined. We have developed a robust and high-throughput assay to measure feedstock quality using the anaerobic bacterium Clostridium phytofermentans. We have measured biomass accumulation phenotypes and utilized this assay to perform quantitative trait locus (QTL) mapping and a genome-wide association study (GWAS) in the model grass species Brachypodium distachyon. We detected four biomass accumulation QTLs and one bioconversion QTL, BIOFUEL1 (BFL1). We additionally found four significant total biomass accumulation marker-trait associations (MTAs) and two bioconversion MTAs within our GWAS. We developed near-isogenic lines and confirmed the effect of the BFL1 QTL and provide evidence that Bradi2g01480, a glucosyltransferase belonging to CaZY family 61 is the current best candidate for underling this QTL. Additionally, we have performed whole-genome resequencing on a total of 42 B. distachyon accessions at an average coverage of 72x to accelerate candidate gene discovery. These accessions will join the growing genetic resources for B. distachyon, enabling even more robust association studies in the future. The discovery of genomic regions significantly associated with biomass accumulation and conversion phenotypes should enable more rapid gene discovery. Only by uncovering the genes regulating these biofuel-related phenotypes can there be efficient and targeted development of improved, dedicated biofuel feedstocks.