Minisatellites (VNTRs) and Microsatellites (SSRs)

Genetic Engineering and Biotechnology 2.  Restriction Maps and Molecular Genetic Maps
Restriction mapping
Restriction cleavage and gel electrophoresis
Construction of a restriction map
Use of partial digests, end labeling and hybridization in restriction mapping
Restriction fragment length polymorphisms (RFLPs) as markers for genetic maps
Linkage and recombination between molecular and phenotypic markers
Random amplified polymorphic DNA (RAPDs) using PCR 
Minisatellites (VNTRs) and Microsatellites (SSRs)
Chromosome Walking and Characterization of Chromosome Segments
Reverse Genetics and Chromosome Jumping (or Hopping) Libraries
Minisatellites (VNTRs) and Microsatellites (SSRs)
It has also been recently emphasized that polyallelic markers will be very useful for mapping both the simple Mendelian traits as well as polygenic traits in segregating populations. The most widespread of these polyallelic markers are minisatellites or the variable number of tandem repeat (VNTR) loci, which are uncovered by locus specific probes and exhibit highly polyallelic fragment length variation. An interesting and common example of VNTRs involves the number of tandem repeat loci associated with rRNA genes in rDNA concentrated at nucleolar organizing regions (NORs) of specific chromosomes of an organism. Like rRNA genes, most VNTR loci are concentrated in proterminal regions of chromosomes, and thus may not be able to provide the desired density of markers. This problem has largely been overcome in microsatellite or SSR loci.

Microsatellites or simple sequence repeats (SSRs) represent variation in the repeat number of sequences, 1-6 bp long (VNTRs can be as long as 1 kbp), such as (AC)n or (AAC)n, etc. Being smaller in size, SSRs are more common and amenable to PCR analysis (Fig. 40.10), Recently, more then 300 loci representing microsatellites, were mapped each in human and mouse genomes. Similar effort are also being made in several crop plants.

Generation and visualization of simple sequence repeat (SSR) length polymorphism.
Fig. 40.10 Generation and visualization of simple sequence repeat (SSR) length polymorphism.