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Title

Mining and characterization of EST derived microsatellites in Curcuma longa L

 

Authors

Raj Kumar Joshi, Ananya Kuanar, Sujata Mohanty, Enketeswara Subudhi, Sanghamitra Nayak*

 

Affiliation

Centre of Biotechnology, School of Pharmaceutical Sciences, Siksha O Anusandhan University, Bhubaneswar-751003, India;

 

E-mail*

sanghamitran@yahoo.com; *Corresponding author

 

Phone

 

09437061976

Article Type

 

Hypothesis

 

Date

 

Received August 20, 2010; accepted August 26, 2010; published September 20, 2010

 

Abstract

 

Turmeric (Curcuma longa L.) (Family: Zingiberaceae) is a perennial rhizomatous herbaceous plant often used as a spice since time immemorial. Turmeric plants are also widely known for its medicinal applications. Recently EST-derived SSRs (Simple sequence repeats) are a free by-product of the currently
expanding EST (Expressed Sequence Tag) databases. SSRs have been widely applied as molecular markers in genetic studies. Development of high throughput method for detection of SSRs has given a new dimension in their use as molecular markers. A software tool SciRoKo was used to mine class I SSR in Curcuma EST database comprising 12953 sequences. A total of 568 non-redundant SSR loci were detected with an average of one SSR per 14.73 Kb of EST. Furthermore, trinucleotide was found to be the most abundant repeat type among 16-nucleotide repeat types. It accounted for 41.19% of the total, followed by the mononucleotide (20.07%) and hexanucleotide repeats (15.14%). Among all the repeat motifs, (A/T)n accounted for the highest proportion followed by (AGG)n. These detected SSRs can be greatly used for designing primers that can be used as markers for constructing saturated genetic maps and conducting comparative genomic studies in different Curcuma species.

 

Keywords

 

Curcuma longa, Expresses sequence tags, short sequence repeats, SciRoKo.

 

Citation

 

Joshi et al. Bioinformation 5(3): 128-131 (2010)

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.