Development and Characterization of Microsatellite Markers for Population Genetic Analysis of Coreopsis Species

Microsatellite markers have become a powerful tool for population genetic analyses.  Few such markers have been reported for Coreopsis, a strictly New World genus with centers of diversity in Mexico, the Andes, and eastern North America.  To develop microsatellite markers, genomic DNA of Coreopsis leavenworthii was sheared, and SSR-containing sequences were enriched using the "GA" SSR motif.  Of the 384 clones sequenced, 16 sequences shared similarities with reported plant genes and nine sequences were similar to retrotransposable elements. One hundred and eighty one clones (47%) contained five or more simple sequence repeats. Among the SSR-containing clones, seven were redundant, and 20 did not have sufficient lengths of flanking sequences for primer designing. Based on the remaining SSR-containing sequences, 100 pairs of primers were designed. Sixty six pairs of primers were tested on C. leavenworthii genomic DNA and 61 (92.4%) pairs amplified PCR products. The availability of these SSR markers should facilitate DNA fingerprinting of C. leavenworthii and related species, understanding of their evolution, estimation of their genetic diversity, and in-depth analysis of their genetic relationship at the molecular level.