SSR markers are:
Simple sequence repeats or microsatellites consist of tandem repeats of 1-6 bp motifs such as ATATAT or CAG repeats, abundant and evenly distributed across eukaryotic genomes. Variation in repeat number creates high polymorphism due to slippage during DNA replication by DNA polymerase. Primers flanking repeat amplify locus via PCR, and alleles differ in fragment length detectable by gel electrophoresis or capillary sequencing with fluorescent labels. Because both alleles at locus amplify and can be visualized simultaneously, SSR distinguishes homozygous from heterozygous state: single band for homozygote, two bands of different sizes for heterozygote, fulfilling codominant inheritance pattern following Mendelian segregation ratios 1:2:1 in F2. High reproducibility, locus specificity, and multiallelism make SSRs preferred for genetic diversity, fingerprinting, and linkage mapping. Automated fluorescent labeling enables high throughput genotyping across large breeding populations and germplasm collections efficiently. SSR mutation rate around 10 to minus 3 per generation generates high allelic diversity useful for population genetics, linkage disequilibrium studies, and cultivar fingerprinting for intellectual property rights; multiplex PCR with fluorescent dyes allows simultaneous amplification of many SSR loci increasing efficiency and cost effectiveness for large programs.
Ref: Tautz D. Hypervariability of microsatellites; McCouch et al. 1997 Microsatellite markers in rice – co-dominant nature