Prairie cordgrass (Spartina pectinata Bosc ex Link) is an indigenous, perennial grass of North America that is being developed into a cellulosic biomass crop suitable for biofuel production. Limited research has been performed into the breeding of prairie cordgrass; this research details an initial investigation into the development of a breeding program for this species. Genomic libraries enriched for four simple sequence repeat (SSR) motifs were developed, 25 clones from each library were sequenced, identifying 70？SSR regions, and primers were developed for these regions, 35 of which were amplified under standard PCR conditions. These SSR markers were used to validate the crossing methodology of prairie cordgrass and it was found that crosses between two plants occurred without the need for emasculation. The successful cross between two clones of prairie cordgrass indicates that this species is not self-incompatible. The results from this research will be used to instigate the production of a molecular map of prairie cordgrass which can be used to incorporate marker-assisted selection (MAS) protocols into a breeding program to improve this species for cellulosic biomass production. 1. Introduction Recent world issues associated with fuel consumption and supply have turned attention towards biofuel production, especially cellulosic biofuel. Perennial grasses provide an optimal source of cellulosic biomass due to their high yield potential. Prairie cordgrass (Spartina pectinata Bosc ex Link) is a perennial indigenous grass of North America and can be found as a native from Texas to near the Arctic Circle [1]. Ongoing studies on prairie cordgrass in comparison with switchgrass (Panicum virgatum L.) indicate that prairie cordgrass could produce more biomass than switchgrass [2]. Furthermore, results from the comparison of prairie cordgrass and switchgrass performed by Boe and Lee in 2007 [2] indicated that prairie cordgrass has a wider environmental amplitude and is adapted to poorly drained wet areas which can have high salinity and be poorly aerated, regions not suitable for the production of conventional crops such as maize (Zea mays) [2, 3]. These results are indicative of the potential of prairie cordgrass as a source of biomass for cellulosic biofuel production. A research program at South Dakota State University (SDSU) is underway to develop native prairie cordgrass into a viable cellulosic biomass crop. The development of a new crop species requires a multidisciplinary approach; examining and validating each step before commercialization can
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