Targeted development of informative microsatellite (SSR) markers

Abstract

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.

Development, characterization, and variability analysis of microsatellites from a commercial cultivar of Musa acuminata

“…Gongjiao, a commercial diploid cultivar in China, using the SAM protocol (Hayden and Sharp 2001b). After recovery, cloning, and sequencing, the fragments were analyzed by the SSRIT software (http://www.gramene.org/gramene/searches/ ssrtool) and were used to design appropriate primers with the Primer3 software (http://www.genome.wi.…”

“…Researchers have developed SSR primers using many methods such as the classical screening of genomic library (Ujino et al 1998), microsatellite enrichment (Huang et al 1999), 5 0 -anchor polymerase chain reaction (PCR) (Fisher et al 1996), sequence-tagged microsatellite profiling (STMP, Hayden and Sharp 2001a), selectively amplified microsatellite (SAM, Hayden and Sharp 2001b) and database blast search (Ramsay et al 2000). SAM is an important method to efficiently develop SSR markers.…”

Characterization of microsatellite markers in cassava based on microsatellite-AFLP technique

“…Traditionally, microsatellite marker development has involved genomic library construction and screening. This is both time-consuming and expensive (Fisher et al, 1996;Hayden and Sharp, 2001), and moreover, the recovery rate of useful microsatellite markers is generally low. In addition, predetermination of the copy number of microsatellite loci is not possible (Hayden and Sharp, 2001).…”

“…This is both time-consuming and expensive (Fisher et al, 1996;Hayden and Sharp, 2001), and moreover, the recovery rate of useful microsatellite markers is generally low. In addition, predetermination of the copy number of microsatellite loci is not possible (Hayden and Sharp, 2001). An alternative approach to overcome these limitations is the microsatellite-based amplified fragment length polymorphism (M-AFLP) technique, a PCR-based approach that combines the concept of AFLP with the microsatellite anchor primer technique (Van Eijk et al, 2001;Yang et al, 2001;Acquadro et al, 2005) through a two-step "primer extension", which offers the rapid development of SSR markers at a lower cost (Van Eijk et al, 2001).…”

A new approach to extending the wheat marker pool by anchored PCR amplification of compound SSRs

“…These approaches have attempted to target the development of SSRs to specific regions of the genome (Cregan et al 1999;Hayden and Sharp 2001b;Li et al 2001), and reduce the cost of marker development by utilising strategies that reduce the number of primers required (Fisher et al 1996;Hayden and Sharp 2001a). An example of the latter approach is anchored PCR, in which microsatellite amplification is achieved with one primer complementary to the flanking sequence, and one that is specific for the repeat motif.…”