Simple Sequence Repeats (SSR, also referred to as microsatellites)

SSR markers are based short sequences of nucleotides (2-6 units in length) that are repeated in tandem:

Di-nucleotide repeat: CACACACA
Tri-nucleotide repeat: ATGATGATGATG

It is believed that when DNA is being replicated, errors occur in the process and extra sets of these repeated sequences are added to the strand. Over time, these repeated sequences vary in length between one cultivar and another.

Example of allelic variation in SSRs:

Allele A: CACACACA (4 repeats of the CA sequence)
Allele B: CACACACACACA (6 repeats of the CA sequence)

These variations in length are easy to trace in the lab and allow us to track genotypic variation in breeding programs.

SSR Advantages:

• Co-dominant (more informative when dealing with heterozygotes)
• Highly variable (important for species with narrow gene pools)
• Widely used
• Excellent for use in marker assisted selection, fingerprinting and marker assisted backcrossing