Development of amplified fragment length polymorphism markers for Spartina alterniflora

Spartina alterniflora Loisel. plants have been transported across great distances for use in wetland restoration and creation projects. However, little information exists on the geographic genetic structure of S. alterniflora, such as the relatedness of populations within a region and the genetic similarity of imported populations to native populations. A high-resolution tool for assessing genetic similarity and diversity of S. alterniflora populations would be an important step toward understanding these relationships. We optimized a bead beater extraction and amplified fragment length polymorphism (AFLP) protocol for S. alterniflora and evaluated its usefulness in distinguishing plants from adjacent marshes in addition to marshes planted with imported stock. Two primer sets were used in AFLP analysis of four to five plants from each of seven populations. These primer sets generated 372 scoreable loci, of which 235 were polymorphic. High genetic diversity was observed in all populations studied, with nucleotide diversities ranging from 0.0363 to 0.0651. Results from analysis of molecular variance (AMOVA) in this exploratory analysis indicated that intrapopulation genetic diversity was high (59.8% of total variation). The contribution of regional differences was weak. Geographical distances between planting stock origin and native marshes did not correlate with genetic diversity. This study demonstrated the procedure could be used to rapidly and reproducibly generate high-resolution genetic profiles of individual plants. The data produced with this method will be used to further our understanding of the structure of S. alterniflora communities and their function in salt marshes.