determination of genetic diversity between eggplant and its wild ...

such as centromeric areas (Nunome et al. 2003b). For the generation of SSR markers
sequence data are needed (Jones et al. 1997, Nunome et al. 2003b and Varshney et al.
2005). These data are obtained in two ways. One way is by constructing a genomic
library and screening using SSR probes (Jones et al. 1997 and Nunome et al. 2003a).
The other way is based on sequence data supported by publicly available databases
which comprises gene sequences and cDNA libraries (Nunome et al. 2003a, Nunome et
al. 2003b and Varshney et al. 2005). ESTs (Expressed sequence tags) are included in the
second way of accessing microsatellite-related sequence data (Rudd 2003 and Varshney
et al. 2005). From all the resulting sequences, specific primers for SSRs can then be
designed (Figure 1.4.). However, difference in the data type that is used classifies SSRs
as genomic or genic SSRs (Rudd 2003 and Varshney et al. 2005). SSRs designed by
using EST library data are one of the basic type of genic SSRs. Comparison of these
SSRs in terms of their advantages and disadvantages was described in the studies of
Rudd and Varshney et al. (Rudd 2003 and Varshney et al. 2005). Due to being a part of
conserved regions of the genome, SSR primers designed from EST sequences, are
expected to be suitable to apply to other related species (Varshney et al. 2005). This
makes genic SSRs favored in comparison to genomic SSRs. SSRs identified by
genomic library construction and search can be products of transcribed or non-
transcribed regions (Varshney et al. 2005 and Nunome et al. 2003b). This feature while
providing a high rate of polymorphism makes genomic SSRs less transferable among
species (Varshney et al. 2005). One result of these interpretations is a disadvantage of
genic SSRs such that less polymorphism is observed for genic SSRs (Varshney et al.
2005). Another disadvantage is related with the amount of sequence data which is
publicly available as mentioned above. For example, eggplant was reported in SOL
Genomics Network (http://sgn.cornell.edu) as having 3,181 ESTs in total (Mueller et al.
2005). That number was the lowest number within other species mentioned in the same
study: tomato, potato, pepper and petunia (Mueller et al. 2005). However, sequencing
studies continue with the continual addition of new data.
The production of ESTs is a sequencing event and can be directed from each end
of cDNAs or from both ends (Rudd 2003). As a result, several ESTs are produced
(Rudd 2003). These ESTs are then clustered to form contigs which include several
sequence products that overlap and are included in the same region (Rudd 2003 and
Krane and Raymer 2003). If these contigs include many members, then they are called a
multi-member sequence assembly (Figure 1.5.). If a cluster includes small portions of a
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