Transgenic Panicum virgatum L. silencing (KD) or over-expressing (OE) specific genes or a small RNA (GAUT4-KD, miRNA156-OE, MYB4-OE, COMT-KD and FPGS-KD) were grown in the field and aerial tissue analyzed for biofuel production traits. Clones representing independent transgenic lines were established and senesced tissue sampled after year one and two growth cycles. Biomass was analyzed for wall sugars, recalcitrance to enzymatic digestibility, and biofuel production using separate hydrolysis and fermentation (SHF). No correlation was found between plant carbohydrate content and biofuel production pointing to overriding structural and compositional elements that influence recalcitrance. Biomass yields were greater for all lines in the second year as plants establish in the field and standard amounts of biomass analyzed from each line had more glucan, xylan and less ethanol (g/g basis) in the second versus the first year samples, pointing to a broad increase in tissue recalcitrance after regrowth from the perennial root. However, biomass from second year growth of transgenics targeted for wall modification, GAUT4-KD, MYB4-OE, COMT-KD and FPGS-KD, had increased carbohydrate and ethanol yields (up to 12 and 21%, respectively) compared with control samples. The parental plant lines were found to have a significant impact on recalcitrance which can be exploited in future strategies. This summarizes progress toward generating next-generation bio-feedstocks with improved properties for microbial and enzymatic deconstruction, while providing a comprehensive quantitative analysis for the bioconversion of multiple plant lines in five transgenic strategies.