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OJBTM
In Silico mining
of single nucleotide polymorphisms
in expressed sequence tags dataset of Allium cepa L.
Radhika V1,
Reddy DCL, Bhardwaj A,
Aswath C2
Division
of Biotechnology,
Indian Institute of Horticultural Research, Hessaraghatta
Lake, Bangalore , India
ABSTRACT
Radhika V, Reddy DCL, Bhardwaj A, Aswath
C, In Silico mining of single nucleotide
polymorphisms in
expressed sequence tags dataset of Allium cepa L., Online J Bioinformatics, 12(1):18-33,
2011.
Single
nucleotide
polymorphisms (SNPs) are abundant in
plant genomes and
are thus used frequently in genetic analysis and crop breeding
programs. Potential SNPs
from expressed sequence tags
(ESTs) of Allium cepa were mined
for a total of 232 potential SNPs
identified from 20,157 ESTs from NCBI. The
SNPs occurred on an average frequency
of 1 per 57 bp in the EST sequences. The
ratio of
transitions to transversions was 1.7: 1,
and 65 of
the 232 SNP sites were cut by different restriction enzymes. Primers
could be
designed for 227 SNPs and
used for onion breeding
programs after validation in wet lab.
Keywords: Cap3, contig,
SNPDigger, transition, transversion