Title

Identification of single nucleotide polymorphism in ginger using expressed sequence tags

Authors

Arumugam Chandrasekar¹, Aikkal Riju¹, Kandiyl Sithara³, Sahadevan Anoop² and Santhosh J Eapen^1,*

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.