Microsatellites or simple sequence repeats based on repeating units of 2-4 bp are the DNA markers of choice in mammalian systems, and are becoming more important in plant systems. The advantages for their usability as molecular markers are that they are codominant and as a PCR-based technique amenable to automatization. Most importantly, microsatellites markers are a multiallelic system that detects a much higher level of DNA polymorphism that any other marker system. Cultivated tomato is well known for its low level of DNA polymorphism. Because of this, highly polymorphic markers are required for mapping and genome analysis within Solanum lycopersicum.
Microsatellites, also known as simple sequence repeats (SSRs) or simple tandem repeats (STRs), have extensively been exploited as molecular markers for diverse applications including genome characterization and mapping. Recently, their role in gene regulation and genome evolution has also been discussed widely.
We have developed TOMSatdb (Tomato Microsatellite database), a web based relational database of microsatellites present in the whole genome sequence. TomSatdb allows microsatellite search using multiple parameters like microsatellite type simple and compound, repeat type (mono- to hexa-nucleotide), copy number, microsatellite length, pattern of the repeat motif itself and the location of the marker on the chromosome. Microsatellites can be retrieved by specifying the chromosome number (or numbers). The database also searches the specified number of markers in a provided location range on a particular chromosome. The nucleotide sequences of the particular marker are also provided to facilitate primer designing for PCR amplification of any desired microsatellite.
TomSatdb is available at http://webapp.cabgrid.res.in/tomsatdb/
Citation:
Mir A Iquebal, Sarika, Vasu Arora, Nidhi Verma, Anil Rai and Dinesh Kumar (2013). First whole genome based microsatellite DNA marker database of tomato for mapping and variety identification. BMC Plant Biology 2013, 13:197.
(Published online on 4 December 2013; http://www.biomedcentral.com/1471-2229/13/197/abstract) (Thompson Impact Factor=4.35)
