Prepare for a genetic face-off as we unravel the intriguing world of microsatellites in our latest PDF, "SSR vs. ISSR Showdown." Dive into the microscopic realm of Simple Sequence Repeats (SSR) and Inter-Simple Sequence Repeats (ISSR), as we dissect their unique features, applications, and the genetic tales they unveil.

1. Simple
Sequence
Repeats
Microsatellite
markers
Microsatellites are tandem
stretches of mono-, di-, tri- or
tetranucleotide sequence
motifs that frequently
occur as randomly dispersed
repetitive elements in
eukaryotic genome

2. • Genetic markers resulting from variation in length of SSR loci (
tandem repeats of very short motifs ( 1-6 bp) e.g.(GT)n, (CAC)n).
• Microsatellite markers are developed by PCR amplification of genomic
DNA segments recognized by primers complementary to unique
flanking sequences (specific primers 20-25 base ).
• Primer sequence might be identified from:
➢Published sequences
➢or Screening a clone library for repeat units and sequencing the
positive clones

3. Advantages
• Highly abundant and evenly
distributed in the genome
• Highly polymorphic.
• Codominant.
• Rapidly typed and easy to
automate
Disadvantages
• Require knowledge about the
primers sequence.

4. Inter
Simple
Sequence
Repeat

5. • Genomic DNA amplified with a microsatellite complementary primer
[eg: (GACA)4 , (GT)n.. etc)].
• SSR- based primers are usually 15 mers to 20 mers enabling high
stringency amplifications than RAPD.
• Amplified products are resolvable on:
➢ agarose gel using ethidium bromide staining.
➢or polyacrylamide gels by silver staining.

8. • SSR markers are microsatellite
DNA
• contain nucleotide repeats of 1-
6 nucleotides
• recognize heterozygous loci
• amplify tandem repeats
• codominant
• ISSR markers occur between
microsatellite DNA.
• contain nucleotide repeats of
100-300 nucleotides.
• recognize multiple loci.
• amplify random sequences of
the genome.
• dominant