Analysis of diversity among accessions of Amorpha fruticosa L. and Desmanthus illinoensis (Michx.) MacMillan

False indigo (Amorpha fruticosa L.) and Illinois bundleflower [Desmanthus illinoensis (Michx.) MacMillan] are leguminous species native to North America with potential to diversify and enhance the sustainability of agriculture. False indigo is a shrub that could be used for summer livestock forage, biomass energy, reclamation of degraded environments, or as N-rich green manure. Illinois bundleflower can improve the quality and productivity of warm-season grass pastures and is a potential high-protein perennial grain. Research to develop these crops will depend on knowledge of available accessions. My objectives were to evaluate the diversity among accessions of false indigo and Illinois bundleflower in three locations and to evaluate the genetic diversity within and between Illinois bundleflower accessions with AFLP molecular markers.; All 47 traits measured on false indigo were influenced by accession in at least one location (P < 0.05). Leaf concentration of false indigo forage was high, averaging 660 g kg−1 at one location in August. Forage quality of false indigo leaves was high, with average crude protein, acid detergent fiber, and neutral detergent fiber concentrations in July of 205, 226, and 235 g kg−1, respectively. The most productive false indigo accessions have potential to produce high leaf and biomass yields under a single annual cutting management.; All 58 traits measured on Illinois bundleflower were influenced by accession (P < 0.05) in at least one location. Forage harvested in August had average crude protein, acid detergent fiber, and neutral detergent fiber concentrations of 150, 393, and 436 g kg−1, respectively. At one location, the highest seed-yielding accession produced 1.7 Mg seed ha−1. Southern accessions had the greatest forage and seed potential, were later maturing, but lacked persistence in the northern USA.; Evaluation of diversity in 50 Illinois bundleflower accessions with 159 polymorphic AFLP markers showed that 83% of the molecular variance was found between two major types of Illinois bundleflower. The less common of the types contained greater genetic diversity and consisted of accessions from the south-central USA. To expedite the AFLP analysis, Peakmatcher software was developed. Peakmatcher reduces the time required for gel scoring to 9 to 11% of the time required for manual scoring.