Contents - Faperta

168 Biotechnological Approaches for Pest Management and Ecological Sustainability
to the original RFLP probes. Nonetheless, this approach is extremely useful for studying
the relationship between various species. When these markers are linked to some specifi c
traits, they can be easily integrated into plant breeding programs for marker-assisted selection
of the trait of interest (Yencho, Cohen, and Byrne, 2000).
Expressed Sequence Tags
The expressed sequence tags (ESTs) are obtained by partial sequencing of random cDNA
clones (Powell et al., 1996; Karp et al., 1997). Once generated, they are useful in cloning
specifi c genes of interest and synteny mapping of functional genes in related organisms.
The ESTs are useful for full genome sequencing and mapping programs to identify active
genes and, thus, help in identifi cation of diagnostic markers. An EST that appears to be unique
can be used to isolate new genes. Development of EST markers is dependent on extensive
sequence data on regions of the genome, which are expressed. However, once developed,
they provide high quality consistent results because they are limited to expressed regions
of the genome, and the markers themselves are directly associated with functional genes.
Single Strand Conformation Polymorphisms
The single strand conformation polymorphisms (SSCPs) are a powerful and rapid technique
for gene analysis, particularly for detection of point mutations and DNA polymorphism
(Srivastava and Narula, 2004). The SSCPs can identify heterozygosity of DNA fragments of
the same molecular weight and can detect changes of a few nucleotide bases as the mobility
of the single-stranded DNA changes with change in its GC content due to conformational
change. To overcome problems of reannealing and complex banding patterns, an improved
technique called asymmetric-PCR SSCP has been developed wherein the denaturation
step has been eliminated and a large-sized sample can be loaded for gel electrophoresis,
making it a potential tool for high throughput analysis (Sunnucks et al., 2000). It is not well
developed for use in plants, although its application in discriminating progenies can be
exploited, once suitable primers are designed for agronomically important traits.
Microsatellites
Microsatellites are multilocus probes creating complex banding patterns, are non-species
specifi c, occur ubiquitously, and belong to the repetitive DNA family (Karp et al., 1997;
Cook et al., 2004). Fingerprints generated by the probes are known as oligonucleotide
fi ngerprints. The methodology has been derived from RFLP, and specifi c fragments are
visualized by hybridization with a labeled micro- or minisatellite probe. Microsatellite
primers generate high levels of polymorphism and detect patterns of codominant inheritance
in populations of segregating progeny. Using microsatellites, some instances of
semicodominance have been identifi ed for Russian wheat aphid, Diuraphis noxia (Kurdj.),
resistance (X.M. Liu et al., 2001). Microsatellite markers have been found to be useful in
many crops for identifi cation of insect resistance genes (Yencho, Cohen, and Byrne, 2000;
X.M. Liu et al., 2001; Miller, Altinkut, and Lapitan, 2001; X.M. Liu, Smith, and Gill, 2002;
Malik et al., 2003; Cook et al., 2004; Zhu et al., 2004).
Simple Sequence Repeats
The simple sequence repeats (SSRs) are tandem arrays of 2 to 5 base repeat units (particularly
dinucleotide repeats) that are widely distributed in eukaryotic DNA (Powell et al.,