Record Details

Identification of single nucleotide polymorphism in ginger using expressed sequence tags

DSpice at Indian Institute of Spices Research

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Field Value
 
Creator CHANDRASEKAR, A
RIJU, A
SITHARA, K
ANOOP, S
EAPEN, S J
 
Date 2010-10-30T09:52:03Z
2010-10-30T09:52:03Z
2009
 
Identifier Bioinformation 4(3): 119-122 (2009)
0973-2063
http://hdl.handle.net/123456789/620
 
Description Ginger (Zingiber officinale Rosc) (Family: Zingiberaceae) is a herbaceous perennial, the rhizomes of which are used as a spice. Ginger is a plant which is well known for its medicinal applications. Recently EST-derived SNPs are a free by-product of the currently expanding EST (Expressed
Sequence Tag) databases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion/deletion) has led to a revolution in their use as molecular markers. Available (38139) Ginger EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script AutoSNP version 1.0 which has used 31905 ESTs for detecting SNPs and Indel sites. We found 64026 SNP sites and 7034
indel polymorphisms with frequency of 0.84 SNPs / 100 bp. Among the three tissues from which the EST libraries had been generated, Rhizomes had high frequency of 1.08 SNPs/indels per 100 bp whereas the leaves had lowest frequency of 0.63 per 100 bp and root is showing relative frequency 0.82/100bp. Transitions and transversion ratio is 0.90. In overall detected SNP, transversion is high when compare to transition. These detected SNPs can be used as markers for genetic studies.
 
Format 65200 bytes
application/pdf
 
Language en
 
Subject Zingiber officinale Rosc
Expressed Sequence Tag
In silico
Ginger
SNPs
 
Title Identification of single nucleotide polymorphism in ginger using expressed sequence tags
 
Type Article