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genes) called 'loci' (singular 'locus') and are broadly differenti-
ated into three categories (Collard et al. 2005):
1. Morphological markers: Morphological markers are usu-
ally visually characterised phenotypic characters, such as
flower colour, seed shape, growth habits or pigmentation.
2. Biochemical markers: Biochemical markers, also known
as 'Isozyme' markers, are allelic variants of enzymes,
which express differences in enzymes that are detected
by electrophoresis and specific staining.
3. DNA (or molecular) markers: Reveal sites of variation at
the DNA level.
The major disadvantages of morphological and biochemi-
cal markers are that they may be limited in number and are
influenced by environmental factors or the developmental stage
of the plant (Winter and Kahl 1995). However, despite these
limitations, morphological and biochemical markers have been
extremely useful to plant breeders (Eagles et al. 2001; Weeden
et al. 1993). In contrast to the instability of morphological and
biochemical markers to different environmental conditions,
molecular markers are stable and are more in number.
DNA markers are the most widely used type of markers due
to their abundance in the genome. They arise from different
classes of DNA mutations, such as substitution mutations (point
mutations), rearrangements (insertions or deletions) or errors in
replication of tandemly repeated DNA (Paterson 1996). These
markers are selectively neutral because they are usually located
in noncoding regions of DNA. Unlike morphological and bio-
chemical markers, DNA markers are basically unlimited in
number and are not affected by environmental factors and/or
the developmental stage of the plant (Winter and Kahl 1995).
Apart from the use of DNA markers in the construction of link-
age maps, they have numerous applications in plant breeding,
such as assessing the level of genetic diversity within germplasm
and cultivar identity (Collard et al. 2005). A list of commonly
used molecular markers and their properties are summarised in
Table 17.1. On the basis of advancement in molecular markers
used, these markers can be categorised into first-, second- and
new-generation molecular markers.
Molecular
markers
First-generation molecular markers The concept of util-
ising variations at the DNA level as genetic markers initi-
ated with restriction fragment-length polymorphism (RFLP).
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