Targeted development of informative microsatellite (SSR) markers.
We describe a novel approach, selectively amplified microsatellite (SAM) analysis, for the targeted development of informative simple sequence repeat (SSR) markers. A modified selectively amplified microsatellite polymorphic loci assay is used to generate multi-locus SSR fingerprints that provide a source of polymorphic DNA markers (SAMs) for use in genetic studies. These polymorphisms capture the repeat length variation associated with SSRs and allow their chromosomal location to be determined prior to the expense of isolating and characterising individual loci. SAMs can then be converted to locus-specific SSR markers with the design and synthesis of a single primer specific to the conserved region flanking the repeat. This approach offers a cost-efficient and rapid method for developing SSR markers for predetermined chromosomal locations and of potential informativeness. The high recovery rate of useful SSR markers makes this strategy a valuable tool for population and genetic mapping studies. The utility of SAM analysis was demonstrated by the development of SSR markers in bread wheat.
Hayden
M J
MJ
Plant Breeding Institute, University of Sydney, PMB 11, Camden, NSW 2570, Australia and Quality Wheat CRC, Locked Bag 1345, PO North Ryde, NSW 2113, Australia. matthewh@camden.usyd.edu.au
Sharp
P J
PJ
D000483:Alleles; D002874:Chromosome Mapping; D017124:Conserved Sequence / Q000235:genetics; D016172:DNA Fingerprinting / Q000379:methods; D017931:DNA Primers / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics*; D018745:Genome, Plant; D018895:Microsatellite Repeats / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic / Q000235:genetics*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D013489:Suppression, Genetic; D013698:Templates, Genetic; D014908:Triticum / Q000235:genetics*
D017931:DNA Primers; D018744:DNA, Plant; D005819:Genetic Markers