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In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB

Sarika1, Vasu Arora1, Mir Asif Iquebal2, Anil Rai1 and Dinesh Kumar13*

Author affiliations

1 Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi, 110012, India

2 Division of Biometrics & Statistical Modelling, Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi, 110012, India

3 Genes & Genetic Resources Molecular Analysis Lab, National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India

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Citation and License

BMC Genomics 2013, 14:43  doi:10.1186/1471-2164-14-43

Published: 19 January 2013

Abstract

Background

Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiation hybrid of buffalo and these reported STR can be used further in final gap plugging and “finishing” expected in de novo genome assembly. QTL and gene mapping needs mining of putative STR from buffalo genome at equal interval on each and every chromosome. Such markers have potential role in improvement of desirable characteristics, such as high milk yields, resistance to diseases, high growth rate. The STR mining from whole genome and development of user friendly database is yet to be done to reap the benefit of whole genome sequence.

Description

By in silico microsatellite mining of whole genome, we have developed first STR database of water buffalo, BuffSatDb (Buffalo MicroSatellite Database (http://cabindb.iasri.res.in/buffsatdb/ webcite) which is a web based relational database of 910529 microsatellite markers, developed using PHP and MySQL database. Microsatellite markers have been generated using MIcroSAtellite tool. It is simple and systematic web based search for customised retrieval of chromosome wise and genome-wide microsatellites. Search has been enabled based on chromosomes, motif type (mono-hexa), repeat motif and repeat kind (simple and composite). The search may be customised by limiting location of STR on chromosome as well as number of markers in that range. This is a novel approach and not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of the selected markers enabling researcher to select markers of choice at desired interval over the chromosome. The unique add-on of degenerate bases further helps in resolving presence of degenerate bases in current buffalo assembly.

Conclusion

Being first buffalo STR database in the world , this would not only pave the way in resolving current assembly problem but shall be of immense use for global community in QTL/gene mapping critically required to increase knowledge in the endeavour to increase buffalo productivity, especially for third world country where rural economy is significantly dependent on buffalo productivity.

Keywords:
de novo; Microsatellites; Primers; Radiation hybrid; Water buffalo