SSRs or 'microsatellites'

Simple sequence repeats (SSRs) are clusters of 2-5 nucleotides that are repeated after one another for 10-100 times. These non-coding repeats are present at vast numbers throughout eukaryotic genomes. SSRs consist of dinucleotides, like (CA)n, trinucleotides, like (CAG)n, and tetranucleotides, like (CATG)n, etc. The symbol n represents the number of repeats within a SSR. Polymorphism exists when n has a different value between homologous alleles.

Consider two small pieces of homologous chromosomes with 'caca repeats' (CA)14 and (CA)16. In one homologue, the sequence CA is repeated fourteen times (n=14) and in the other sixteen times (n=16):

CGGCTTTCGCACACACACACACACACACACACACACATTCGGCTCAGCT
GCCGAAAGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAGCCGAGTCGA

CGGCTTTCGCACACACACACACACACACACACACACACACATTCGGCTCAGCT
GCCGAAAGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAGCCGAGTCGA

The development of SSR markers starts with the creation of a small genomic library. The genomic library is screened for SSRs using a number of repetitive sequence oligonucleotide (random) probes, to identify desired DNA fragments. The SSRs and their unique flanking regions are then sequenced. Primers are chosen that match the flanking DNA sequence of the SSRs, followed by PCR amplification, after which the DNA is run through a gel. After treatment with ethidium bromide, bands are visible. If the bands are different in size, the amplified fragments ('amplicons') are polymorphic, due to a different number of copies of the repeated sequence.

SSR markers are codominant. In a given population, usually a large number of alleles are detected, because of the large variation in n. SSR markers can be used to analyze closely-related populations within a species, and sometimes even among related species, because of the presence of identical conserved sequences flanking the SSR. Be aware that differences in size between alleles, may favor the amplification of one allele above the other.

Summary

→    SSR markers are codominant and usually detect many alleles

→    SSR markers are highly reproducible

→    SSR markers developed for one species can often also be used in other related species

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