SSR Marker Help
While microsatellites or simple sequence repeats (SSRs) normally occur in non-coding regions of the genome, they can also occur in either 3' or 5' UTRs of ESTs or even in coding regions (usually triplet repeats). For this reason, the tomato and potato EST sequences contained in SGN were screened for microsatellite sequence motifs in May 2001 using analytical tools developed by Genomics Edge Technologies, Inc; St. Louis, Missouri. The purpose was to identify SSRs that might be useful a polymorphic molecular markers genetic and breeding studies in tomato. The search parameters were for all possible repeat motifs 2 bp to 6 bp with repeat blocks > 20 bp. The search algorithms allowed for imperfect repeats as well as complex repeats.
For those wishing to test SSRs for mapping/polymorphism
studies, it is recommended (based on empirical testing) to start
- dinucleotides > 12 repeats
- trinucleotide > 8 repeats
- tetra to hexonuclotides > 6 repeats