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(O'Donnell et al.
1998
), and IGS (intergenic spacer region) (Yli-Mattila and Gag-
kaeva
2010
). However, it has been seen that all these sequences do not equally work
well with all species (Nayaka et al.
2011
). Further, the proteins such as histone H3,
calmodulin, and Tri101 are also used for distinction of species besides (Mule et al.
2005
). In short, it is difficult to distinguish and identify
Fusarium
sp. accurately
based on old traditional methods because of their morphological similarity and ge-
netic variation. Hence, for the accurate identification and characterization of species
DNA-based tools are required. In this direction, SSRs (single sequence repeats) of
the EST databases shall provide a way forward in identification and characteriza-
tion of
Fusarium
sp. These sequences are ubiquitously transcribed which are co-
dominant and locus-specific, and also are highly polymorphic, often multi-allelic
and finally SSRs are transferrable among species within genera (Power et al.
1996
;
Morgante et al.
2002
; Varshney et al.
2005a
,
b
). Various EST-SSR markers devel-
oped from EST databases are used for genotyping in several species of flowering
plants (Varshney et al.
2005a
) and these have been developed in many plant species
like rice (Temnykh et al.
2001
) wheat (Eujayl et al.
2002
) rye (Hackauf and Wehling
2002
) Cotton (Han et al.
2006
) Grape (Cordeiro et al.
2001
). These EST-SSR mark-
ers are gene-tagged associated with the expressed gene and are also linked with al-
leles of quantitative and qualitative trait locus (QTLs) (Torben et al.
2007
). So far,
many genomes have been sequenced and thus to the comparative genomics has
become an important discipline which helps to extend the information from one
species (model) to another unrelated species or between related species having a
much complex genome (Gale and Davos
1998
). The EST-SSR markers in related
species show high level of transferability in comparison to anonymous DNA mark-
ers because they are more conserved and thus these markers are useful for com-
parative genomics, comparative mapping and evolutionary studies across species
(Cordeiro et al.
2001
; Thiel et al.
2003
; Eujayl et al.
2004
; Scott et al.
2000
; Saha
et al.
2004
). However, the degree of polymorphism may be limited due to conserved
nature of EST-SSRs (Torben et al.
2007
) as the transferability across species of the
SSR loci within genus is reported above 50 % (Thiel et al.
2003
; Eujayl et al.
2004
;
Peakall et al.
1998
; Gaitán-Solís et al.
2002
; Dirlewanger et al.
2002
) and the trans-
ferability across genera of SSRs loci is reported to be poor (Thiel et al.
2003
; Peak-
all et al.
1998
; White and Powell
1997
; Roa et al.
2000
). Amongst the molecular
markers the SSRs are widely used for molecular mapping, selection, assessment of
genetic diversity, protection of varieties and thus helping to link genotypic and phe-
notypic variation (Powell et al.
1996
; Gupta and Varshney
2000
; Varshney et al.
2005a
). The SSRs are comprised of tandemly repeated sequences having mono-,
di-, tri-, tetra-, penta-, or hexa- nucleotide units (Ellegren
2004
) found in coding and
non-coding regions in prokaryotic and eukaryotic DNA.
The presence of various characteristics within SSRs such as relative abundance,
multi-allelic nature, simple detection, high reproducibility, co-dominant inheritance,
multi-allelic nature, and extensive genome coverage make them the ideal molecular
markers (Powell et al.
1996
). However, the SSRs are known to experience high rate
of mutations (reversible length-altering) by replication slippage (transient disso-
ciation of replicating DNA) and unequal crossing over (misaligned reassociation),
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