BACK TO CONTENTS   |    PDF   |    PREVIOUS   |    NEXT

Title

 

 

 

 

 

Identification of single nucleotide polymorphism in ginger using expressed sequence tags

 

Authors

 

Arumugam Chandrasekar1, Aikkal Riju1, Kandiyl Sithara3, Sahadevan Anoop2 and Santhosh J Eapen1,*

 

Affiliation

 

1Bioinformatics centre, Indian Institute of spice research, P.B.No.1701, Marikunnu P.O, Calicut -673012, Kerala, India; 2 Ottankulam, Athicode (P.O), Palakkad (Dist), Kerala 678554, India; 3Kandiyl House, Makkada (P.O), Kakkodi, Calicut 673617. Kerala, India

 

Email

 

sjeapen@spices.res.in

Article Type

 

Hypothesis

Date

 

Received April 28, 2009; Revised May 10, 2009; Accepted June 08, 2009; Published September 30, 2009

 

Abstract

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.

 

Keywords

Zingiber officinale Rosc, Expressed Sequence Tag, in silico, Ginger, SNPs, Indel

 

Citation

 

Chandrasekar et al., Bioinformation 4(3): 119-122 (2009)

Edited by

 

P. Kangueane

 

ISSN

 

0973-2063

 

Publisher

 

Biomedical Informatics

License

 

 

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.