Molecular Tools

• Application of molecular methods can identify the genetic causes and/or consequences of changes in the demography of populations.
• It is possible to generate hundreds of characters for a population study using molecular techniques. Determination of plant populations exhibiting maximum genetic diversity can allow selection for replanting programmes designed to maintain levels of polymorphism.
• Screening of genetic diversity within and among populations of plants may be carried out using amplified fragment length polymorphisms (AFLPs).

AFLPs exhibit a higher number of polymorphisms when compared with many other molecular methods because of the greater number of loci sampled in a single assay

An AFLP band is assumed to correspond to a single locus. The presence of the band represents the dominant genotype while an absence represents the homozygous recessive genotype and it is assumed that there are 2 alleles at each locus.

Specimens of Arthropodium cirratumare shown (above) growing in cultivation An example of an AFLP gel is shown (right). Samples are from populations of A. cirratum  Bands represent loci and may provide genetic information, including F-statistics and geneflow estimates

The AFLP method involves the digestion of genomic DNA with 2 restriction endonucleases.
The resulting fragments are ligated to specific single stranded oligonucleotide adapters.
They are then amplified by PCR with primers containing selective nucleotides homologous to the adapters, with 1-3 base pair extensions at the 3' end.
DNA fragments complimentary to the extensions are amplified selectively and visualised on polyacrylamide gels using silver staining (see figure above).