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United States Department of Agriculture

Agricultural Research Service

Title: A Method to Increase Efficiency in Developing Genomic Maps by Exploiting Ssr Markers from Other Taxons

item Kamps, Terry

Submitted to: Plant Animal and Microbe Genomes Conference
Publication Type: Abstract Only
Publication Acceptance Date: October 30, 2001
Publication Date: January 12, 2002

Technical Abstract: Microsatellites, simple sequence repeats (SSRs), are an increasingly important resource for obtaining highly informative molecular markers needed by both plant and animal researchers for genomic map construction. The labor intensive and costly processes involved in developing these markers have hindered widespread application to species outside those having major economic and scientific impact. An alternative to creating customized SSR marker sets is to exploit existing PCR primer sequences that amplify characterized SSR-containing loci of other species. Low percentages of genetically informative markers, however, have been reported in earlier attempts to transfer plant SSR-type markers to non-source species. This research was aimed at developing a generalized cross-taxa protocol to enhance PCR-based marker transferability by determining an optimized PCR strategy amenable to high throughput technology. Genomic DNA from the non- source Tripsacum species was tested for amplification and polymorphism characteristics with SSR primer sources derived from its evolutionarily flanking relatives, Sorghum bicolor and maize. Four 'touchdown' PCR programs ending in final annealing temperatures 0, 5, 10 and 15øC below the source species recommendations revealed that the 5øC reduction best augmented Tripsacum DNA amplification success with both primer collections. Specifically, amplification percentages resulting from 60 maize and 32 sorghum derived primers were improved from 33% to 82% and 41% to 87%, respectively. Importantly, the increased amplification success also raised detection of potentially informative loci with the maize designed primers from 12% to 42%, and 25% to 52% with the sorghum originated primers. Polymorph transmission data with these markers will also be presented.

Last Modified: 4/22/2015
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