Genetic Linkage Maps: Strategies, Resources and Achievements - Genetics, Genomics and Breeding of Crop Plants - page 93

3.3.5 SSR
SSR (simple sequence repeat), also known as microsatellite or STR (short
tandem repeats), is a class of DNA sequence stretches characterized by highly
repeated di-, tri-, tetra-, or penta-nucleotide motifs (e.g., CACACACA...,
CATCATCAT..., ACGTACGTACGT..., or TAAAATAAAATAAAA) and spread
throughout the genomes. SSR polymorphisms are assayed by specifically
amplifying a small DNA fragment that contains the repeats via PCR and
then by sizing the amplified fragments on agarose, polyacrylamide gel, or
capillary electrophoresis. The number of repeats varies among genotypes
under investigation and results in a length variation of the amplified
fragments. Being highly polymorphic, highly abundant, co-dominant
inheritance, analytically simple and readily transferable, makes SSR the
marker of choice over many other markers for genomic studies.
Abundant interspersed repetitive DNA elements in different eukaryotes
were observed from the limited amount of DNA sequence information in the
early 1980s (Miesfeld et al. 1981; Hamada and Kakunaga 1982). Weber and
May (1989) first realized that this class of sequence represents a vast new
pool of potential genetic markers to be used to fill the gaps in the existing
human genetic map and to improve map resolution. The use of STR in
human genome mapping turned out to be a great success. Gyapay et al.
(1994) mapped 2,066 (AC) n STR markers to the human genetic linkage map
and Dib et al. (1996) added 5,264 (AC/TG) n STR markers to the map.
SSR polymorphism was first reported in crop plants in soybean (Akkaya
et al. 1992). Since then SSR markers have been developed in a number of
crop species such as rice (Morgante and Olivieri 1993; Wu and Tanksley
1993), barley (Becker and Heun 1995), corn (Senior and Heun 1993) and
tomato (Broun and Tanksley 1996). SSR markers rapidly displaced RFLP
markers not only in plant genome mapping but also in other applied areas
such as genotype identification and variety protection (Smith and Helentjaris
1996), seed purity evaluation and germplasm conservation (Brown and
Kresovich 1996), germplasm diversity studies (Xiao et al. 1996), quantitative
trait loci (QTL) analysis (Blair and McCouch 1997), pedigree analysis and
marker-assisted breeding (Ayres et al. 1997), and as anchor points in
screening of large insert libraries for positional gene cloning.
Since sequence information is needed for designing specific primer pairs
for individual SSR markers, the initial development of SSR started with a
laborious and costly approach of screening genomic libraries by hybridizing
with SSR probes and sequencing the hybridized positive clones. The SSR-
enrichment procedure of using biotin-labeled SSR-containing probes in
combination with magnetic beads coated with streptavidin or a nitrate filter
(Edwards et al. 1996) in small-insert libraries considerably improved the
efficiency of isolating SSR sequences from the genome and hence reduced