Geoscience Reference
In-Depth Information
markers) of same or different species. Polymorphic markers can
also be described as co-dominant or dominant. This description
is based on whether markers can differentiate between homo-
zygotes and heterozygotes. Co-dominant markers indicate dif-
ferences in the size of DNA whereas dominant markers are
either present or absent. In the strictest sense, different forms
of a DNA marker (e.g. different sized bands on gels) are called
marker 'alleles'. Co-dominant markers may have many differ-
ent alleles whereas a dominant marker has only two alleles.
It is beyond the scope of this chapter to discuss the technical
method of how DNA markers are generated.
This section provides a brief classification of these molecu-
lar markers on the basis of its functions. Molecular markers can
be classified into two major groups: (1) based on DNA/DNA
hybridisation (e.g. RFLP) and (2) based on PCR amplification
of genomic DNA fragments (RAPD, ISSR, SSR, SCAR, AFLP,
SNP, CAPS, etc.).
1
.
Hybridisation-based molecular markers.
RFLP markers
are the most widely used hybridisation-based molecular
markers in humans and plant genome analysis. These
markers were first used in 1975 to identify DNA sequence
polymorphisms for genetic mapping of a temperature-
sensitive mutation of adeno-virus serotypes (Grodzicker
et al. 1975). It was then utilised for human genome map-
ping (Botstein et al. 1980), and later adopted for plant
genomes (Helentjaris et al. 1986; Weber and Helentjaris
1989). The technique is based on restriction enzymes that
reveal a pattern of difference between DNA fragment
sizes in individual organisms. Although two individu-
als of the same species have almost identical genomes,
they will always differ at a few nucleotides due to one or
more of the following causes: point mutation, insertion/
deletion, translocation, inversion and duplication. Some
of the differences in DNA sequences at the restriction
sites can result in the gain, loss or relocation of a restric-
tion site. Hence, digestion of DNA with restriction
enzymes results in fragments whose number and size can
vary among individuals, populations and species. The
brief steps involved in RFLP molecular marker assay are
as follows (Semagn et al. 2006):
a. Digestion of the DNA with one or more restriction
enzyme(s)
b.
Separation of the restriction fragments in agarose gel
