SSR Statistics

CicArMiSatDB is freely available online athttp://cicarmisatdb.icrisat.org.

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ICRISAT is a member of the CGIAR Consortium.

Financial support from CGIAR Generation Challenge Programme(GCP) and Department of Science and Technology, Govt. of Indiaunder the framework of Australia-India Strategic Research Fund(AISRF) is gratefully acknowledged. This work has been undertakenas part of the CGIAR Research Program on Grain Legumes.

CicArMiSatDB: A Chickpea microsatellite Database

Availability and requirements

Abstract

Acknowledgements

Summary

Dadakhalandar Doddamani, Mohan A.V.S.K Katta, Aamir W. Khan, Gaurav Agarwal, Trushar Shah and Rajeev K. Varshney*

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India*Address for correspondence: r.k.varshney@cgiar.org

Components Features

Overview of CicArMiSatDBA. Distribution of SSRs classified according to the motif repeats show the abundance of di and tri-nucleotide motifs

B. SSRs have been classified into simple and compound SSRs, Compound SSRs constitute the majority of SSRs in chickpea.

C. SSRs classified by their occurrence in genic and non genic features show predominance of SSRs in non-genic regions.

Interface for CicArMisatDB

Chickpea (Cicer arietinum) is a widely grown legume crop in tropical, sub-tropical and temperate regions.Molecular breeding approaches seem to be essential for enhancing crop productivity in chickpea. Until recently, limitednumbers of molecular markers were available in the case of chickpea for use in molecular breeding. However, the recentadvances in genomics facilitated the development of large scale markers especially SSRs (simple sequence repeats), themarkers of choice in any breeding program. Availability of genome sequence very recently opens new avenues foraccelerating molecular breeding approaches for chickpea improvement. In order to assist genetic studies and breedingapplications, we have developed a user friendly relational database named the Chickpea Microsatellite Database(CicArMiSatDB http://cicarmisatdb.icrisat.org ). This database provides detailed information on SSRs along with their featuresin the genome. SSRs have been classified and made accessible through an easy-to-use web interface. This database isexpected to help chickpea community in particular and legume community in general, to select SSRs of particular type or froma specific region in the genome to advance both basic genomics research as well as applied aspects of crop improvement.

CicArMiSatDB contains chickpea SSRs (48,298), genomic features and validated SSRs (1,300)

The database is designed by integrating software components such as:

PostgresSQL (v9.2.4) to store the data in tables;

Apache web server (v2.22) to access the data using web interface with the help of PHP (v5.4) and

jQuery (v2.0) library was used to ease the implementation of a user friendly interface

Simple search: Motif type,location, Motif of interest, Genicor non-genic

Advanced search: combinationof multiple options

BLAST: Finds homolog region to a query sequence and provides nearest genic and non-genic SSR information.

GBrowse: Visualization of SSRs along with the other genomic features.

CicArMiSatDB is a comprehensive SSR database with auser-friendly web interface to mine and filter the chickpeaSSR markers

Advanced tools (webBLAST and GBrowse) embedded in thisdatabase would help to query and visualize chickpea genomefeatures

The database is made openly accessible to the researchcommunity