Contents - Faperta

170 Biotechnological Approaches for Pest Management and Ecological Sustainability
genomic DNA, which increases their specifi city. These are dominant markers, though occasionally
a few of them exhibit codominance. An unlimited number of primers can be synthesized
for various combinations of di-, tri-, tetra-, and pentanucleotides, with an anchor
made up of a few bases, and can be exploited for a broad range of applications in plant species.
Sequence Characterized Amplified Regions
RAPD-generated polymorphic DNA bands can be sequenced and the information used
to design location specifi c sequence characterized amplifi ed regions (SCARs) (Hernandez,
Martin, and Dorado, 1999). These are similar to STS markers in construction and application.
The presence or absence of the band indicates variation in sequence. They have a
better reproducibility than RAPDs. SCARs are usually dominant markers; however, some
of them can be converted into codominant markers by digesting the PCR products with
restriction enzymes and polymorphism can be deduced by either denaturing gel electrophoresis
or SSCP. SCARs are more informative for genetic mapping than dominant
RAPDs, and can be used for map-based cloning. SCARs also allow comparative mapping
or homology studies among related species, thus making them extremely adaptable. SCARs
have been used to identify and map genes for resistance to rice gall midge, O. oryzae
(Sardesai et al., 2002) and brown planthopper, N. lugens (Renganayaki et al., 2002).
Amplified Fragment Length Polymorphisms
The amplifi ed fragment length polymorphisms (AFLP) markers are based on selective
PCR amplifi cation of restriction enzyme-digested DNA fragments (Vos et al., 1995). The
DNA generated in each amplifi cation contains molecular markers of random origin, but
the process results in a large number of amplifi ed DNA bands from one amplifi cation.
Sample DNA is digested with different restriction enzymes and restriction enzyme adaptors
are then annealed to the restriction products. Restriction digests are then preselected
by PCR amplifi cation with general restriction enzymes attached to unique oligonucleotide
primers and preselected PCR products, and then selectively amplifi ed using specifi c
3≤ oligonucleotide primers. Amplifi ed fragments are denatured and then separated
using polyacrylamide gel electrophoresis, and the gel exposed to radiographic fi lm to
view the AFLP polymorphic banding patterns. The AFLP markers detect many DNA
polymorphisms and have been used successfully to identify and map resistance to brown
planthopper, N. lugens (Sharma et al., 2001) and gall midge, O. oryzae (Sardesai et al., 2002)
in rice; and pod borer, H. armigera resistance in chickpea (Lawlor et al., 1998).
Single Nucleotide Polymorphisms
The vast majority of allelic differences between DNA sequences of individuals are point mutations
due to single nucleotide polymorphisms (SNPs) (Brookes, 1999). As such, there are a
vast number of potential SNP markers in all species. Considerable amounts of sequence data
are required to develop SNP markers. However, their advantage lies in the potential to screen
for allelic differences using methods that do not involve electrophoresis, as in microarrays.
Diversity Array Technology
Diversity array technology (DArT) is a sequence-independent, high-throughput method,
able to detect polymorphism at hundreds of marker loci in a single experiment (Akbari et al.,