Simple-Sequence Length Polymorphisms SSLPs Short tandemly repeated DNA sequences that are present in variable copy numbers at a given locus. Scattered throughout genome. Different people may have different numbers of these repeats at different loci (think of different copy numbers as alleles). Microsatellite Markers: Tandem repeats of a 2 bp sequence such as CA. Minisatellite Markers (aka Variable Number Tandem Repeats): Tandem repeating units of bp.

Using microsatellites as molecular markers Use PCR primers that are complementary to single copy sequences flanking microsatellites to amplify microsatellite-containing region. Depending on number of microsatellite repeats, will get different lengths PCR products (many different possible alleles, not just two)

VNTRs can be used to generate DNA fingerprints Since some repeated sequences are present at multiple places in genome, a single probe can detect multiple VNTRs on one genomic Southern blot. DNA fingerprint = set of VNTR fragments from an individual’s genome. 3 separate VNTR loci

Advantages of SSLPs compared to RFLPs 1.Unlike RFLPs, both microsatellites and minisatellites usually have > 2 alleles. By having more allele possibilities, each allele can be used as a more specific tag. 2.In a population, heterozygosity for a particular RFLP may be low, whereas heterozygosity for SSLP alleles tends to be higher. Need RFLP or SSLP differences in order to be useful for mapping (or DNA fingerprinting). Can detect SSLPs by PCR, therefore, need very little DNA for diagnostic tests. Because a single minisatellite probe can detect multiple VNTRs, can simultaneously examine multiple VNTR loci at a time.

Linkage map of human X chromosome SSLPs mapped to many locations throughout genome

Fluorescent In Situ Hybridization (FISH) Used for low resolution mapping i.e., determining approximate locations of genes or other DNA sequences in genome.

Can use RFLP or SSLP tests to determine genotype of individual even before phenotype (e.g., disease) is observed. Ethical concerns: What if disease-causing allele can be detected, but no treatment is available? Who gets the information?

Prenatal diagnosis for genetic diseases Extract DNA from cells & use for RFLP or SSLP analysis.