ARS | Publication request: A Novel Microsatellite Array in Flowering Dogwood (Cornus florida) with Device HAD-GT12

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 17, 2007
Publication Date: January 17, 2007
Citation: Wang, X., Trigiano, R.N., Windham, M., Rinehart, T.A., Spiers, J.M. 2007. A novel microsatellite array in flowering dogwood (cornus florida) with device had-gt12. Plant and Animal Genome Conference.

Technical Abstract: Microsatellites assays were performed traditionally on either high resolution MetaPhor agarose or polyacryamide gels. Gel electrophoresis methods are simple and relatively inexpensive to conduct, however they are difficult to accurately score allele sizes. Recently, capillary electrophoresis has been widely adopted for SSR assays. Capillary electrophoresis with fluorescent labeling is relatively expensive compare to gel electrophoresis. However, an alternative device 'HAD-GT12™, made by eGene, Inc. CA, USA, combines the advantages offered by gel and capillary electrophoresis and works well and effectively to assay SSRs. This instrument runs PCR products directly without labeling, and not only provides the same allele peak profile as capillary electrophoresis, but also fits the data to a clear gel profile similar to that provided by agarose or acrylamide gels. Genomic DNA from twelve flowering dogwood (C. florida) accessions were amplified with one SSR primer set and the products separated with HAD-GT12™, 3%MetaPhor® agarose and 10% acrylamide gel, respectively. Another PCR with fluorescent labeling forward primer was run on the CEQ 8000. The HAD-GT12™ device produced a gel image and allele sizes; whereas the MetaPhor® agarose or acrylamide gel only generate gel images and the allele sizes were estimated manually. These three methods cost about the same to complete. The CEQ 8000 can calculate allele sizes, but does not provide a gel image. Furthermore, the CEQ8000 cost ten times more than HAD-GT12™. The new HAD-GT12™ device will be more powerful for large-scale SSR assays, such as SSR linkage map construction, population genotyping and breeding parent analyses.