Geoscience Reference
In-Depth Information
as well. SSR contains around 10-50 copies of motifs from 1
to 5 base pairs that may occur in perfect tandem repetition, as
imperfect (interrupted) repeats or together with another repeat
type. These repeated motifs are flanked by unique or single
copy sequences, which give a base clutch for specific amplifica-
tion via PCR. Primers that are complementary to the unique
sequences in those flanking regions can be designed to amplify
single copy products. The other marker systems that have been
developed during this period include restriction landmark
genome scanning, cleaved amplified polymorphic sequence
(CAPS), degenerate oligonucleotide primer PCR, SSCP, mul-
tiple arbitrary amplicon profiling and sequence characterised
amplified region (SCAR). The usage of these marker systems
was not realised as new SSRs.
New-generation molecular markers
Recent advances in
molecular biology have opened the opportunity of utilising vari-
ous types of molecular tools to identify and use genomic varia-
tion improvement of various organisms. Information concerning
the basis of these techniques and their applications involve the
technology spill over of several genome projects. The last 10
years have witnessed the origin of an array of molecular mark-
ers with high-throughput performance coupled with shift from
manual mode of detection to complete automation. Inter simple
sequence repeats (ISSRs), selective amplification of microsat-
ellite polymorphic loci, SNPs, amplified fragment-length poly-
morphism (AFLP), selective restriction fragment amplification,
allele-specific associated primers, cleavage fragment-length
polymorphism, inverse sequence-tagged repeats, directed
amplification of mini satellite DNA-PCR, sequence-specific
amplified polymorphism, retrotransposon-based insertional
polymorphism, inter-retrotransposon amplified polymorphism,
retrotransposon-microsatellite amplified polymorphism, methyl-
ation-sensitive amplification polymorphism, miniature inverted-
repeat transposable element (MITE), three endonuclease AFLP,
inter-MITE polymorphisms sequence-related amplified poly-
morphism, and so on are the markers of recent origin with great
potential in understanding the variation at the DNA level.
Genetic differences observed by DNA markers can be visu-
alised by using a vertical and horizontal gel electrophoresis or
staining by means of ethidium bromide, silver nitrate, detection
with radioactive or colorimetric probes. DNA markers showing
differences between individuals of the same or different species
(polymorphic markers) are generally more useful than mark-
ers that do not discriminate between genotypes (monomorphic
