Development and Characterization of Genomic SSR Markers for Switchgrass.

Switchgrass, Panicum virgatum L., has been used for conservation and warm-season pasture purposes in the USA since the 1940s. Since 1991 it has become a promising dedicated bioenergy crop.  Objectives of this study were to develop and characterize genomic simple sequence repeat (SSR) markers for  genetic mapping, germplasm analysis, cultivar identification, and marker-assisted selection. Four microsatellite-enriched libraries, including core sequences CA-, GA-, ACC- and CAG- libraries have been constructed using genomic DNA of  "SL93 7x15", a switchgrass genotype selected in Oklahoma State University (OSU) southern lowland breeding population. Characterization of SSR loci and primer evaluation are ongoing. Seven hundrad fifty eight clones from the CA- enriched library were sequenced at OSU Core Facility, consequently a total of 781 SSR sequences were identified. Predominant motif of the SSR sequences was the expected type - CA/TG. It was observed that 65.2% SSR sequences had a perfect repeat structure while 34.8% had a compound repeats. From the SSR containg sequences, 658 primer pairs were designed by using SSR Locator V.1 software, with 115 SSR-contained clones (15.1%) being identified as redundancy. Of the 543 unique SSR primer combinations, 318 pairs (58.6%) amplified strong bands with expected fragment size ranging from 140 to 350 bp, in SL93 7x15 and/or "NL94 16x13", a northern lowland genotype. Based on these primary results, we expect to develop 1000 or more unique genomic SSR primer pairs from a total of 3072 clones (768 clones from each of the four libraries). In addition, polymorphism of genomic SSR markers to be developed will be investigated among four cultivars of switchgrass, including two upland cultivars such as "Dacotah" and "Blackwell", and two lowland cultivars as “Kanlow” and “Alamo”.