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Online Journal of Bioinformatics
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Identification of SSR-ESTs
corresponding to alkaloid, phenylpropanoid
and terpenoid biosynthesis in MAP’s
Bioinformatics
& In Silico Biology Division, Central Institute of Medicinal &
Aromatic Plants (CSIR), P.O.
CIMAP, Lucknow-226015 (UP),
ABSTRACT
Tripathi KP, Roy S, Khan F, Shasany
AK, Sharma A, Khanuja SPS., Identification of SSR-ESTs corresponding to alkaloid, phenylpropanoid
and terpenoid biosynthesis in MAP’s,
Online J Bioinformatics, 9 (1): 78-91, 2008.
Simple sequence
repeats (SSRs) are repetitions of nucleotide motifs
of 1 to 5 bases and are currently the markers of choice in many plants and
animals genomes. SSRs are the DNA regions where a few
bases are tandemly repeated. SSRs
have been proven to be the markers of choice in plants genetics research and
for breeding purposes because of their hyper-variability and ease of detection.
However, development of these markers is expensive, labour
intensive and time consuming, if they are being developed from genomic
libraries. In this study, SSRs were mined in silico from
ESTs of medicinal and aromatic plants (MAPs) corresponding to secondary metabolites e.g.
Alkaloids, Phenylpropanoids and Terpenoids.
SSRs are potential candidates for markers, gene
tagging, comparative genomics research and breeding purposes. For this,
comparative genomic study was performed for finding the corresponding genes to
these SSR-ESTs using Arabidopsis thaliana as a model organism. Results revealed
that the SSRs e.g.,
941 trinucleotides, 213 dinucleotides,
157 tetranucleotides and 179 pentanucleotides
were distributed throughout the studied datasets of ESTs
in medicinal plants viz., Coptis japonica, Oryza sativa, Papaver somniferum, Catharanthus roseus, Phaseolus vulgaris, Capsicum annuum, Mentha piperita and Euphorbia tirucalli.
Primers associated with the SSR-ESTs were also
designed successfully. Moreover, functional perspectives of these SSRs suggest that microsatellites
are more than mere repetitive sequences and their role have been attributed to
many biological functions. Because of their abundance and high polymorphism, microsatellites could be widely used to develop genetic
markers for the construction of linkage maps of medicinal crops.
Keywords: ESTs, SSRs, Microsatellites, Primers,
Markers, Secondary metabolites, Alkaloids, Phenylpropanoids,
Terpenoids, Medicinal & Aromatic Plants.
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