Univ. of California Riverside Core Instrumentation Facility: Fragment Analysis
CIF offers analysis of microsatellites (also known as simple sequence repeats, SSRs) and amplified fragment length polymorphisms (AFLPs) by sizing under denaturing conditions in our 16-capillary instrument, an Applied Biosystems (ABI) 3100 Genetic Analyzer. We also train in use of ABIs GeneMapper 3.7, software for genotyping and analysis of data from the 3100.
Microsatellites, also known as simple sequence repeats (SSRs),
are perfect or slightly imperfect tandem repeats of a particular k-mer that
occur in all organisms. The repeat unit comprises 1-13 bases; the most common
repeat units in humans are dinucleotides consisting of AC and AT. The important
things about SSRs in genetic studies are their co-dominance, allowing estimation
of allele frequencies, their high degree of length polymorphism and their relatively
high frequency of occurrence, often sufficient to serve as markers, whether
for linkage studies or phylogenetic studies among individuals or populations,
both animals and plants. Typical applications are in conservation biology, demographic
history and as markers for identification of QTLs.
Analysis of amplified fragment length polymorphisms (AFLPs) is a relatively
cheap way to generate hundreds of informative genetic markers. AFLPs combine
aspects of RFLP (restriction fragment length polymorphisms) and RAPD (random
amplified polymorphic DNA) markers in use of restriction of genomic DNA and
(after adaptor ligation) PCR amplification; the result is a highly reproducible
set of fragments, with a high degree of polymorphism, for electrophoretic sizing
at single base resolution and comparitive genotypic analysis, most commonly
between closely related species.
A PowerPoint presentation from a CIF workshop on fragment analysis is available for download here:
Fragment Analysis at UC Riverside