Ritwika Das

Microsatellite or SSR markers are codominant DNA markers useful for various biological studies. Polymerase slippage during DNA replication, or slipped strand mispairing, is the main cause of variation in the number of repeat units, resulting in length polymorphism in SSR markers. The present scenario warrants the need of bulk marker mining from the whole genome or from the specific location of the chromosome along with their primer generation. In vitro polymorphism discovery has limitation of both time and cost, hence warranting in silico approaches. PolyMorphPredict is developed using Perl (64 bit, version 5), R (version 3.0) and Java (version 7) and launched at Apache. The user interface is built using Javascript and HTML and integrates MISA and Primer3 for SSR marker mining and primer generation, respectively. In-house PERL scripts were developed for string/ pattern matching to detect polymorphic markers. It consists of major modules like SSR Mining, Primer Generation and Polymorphism Detection. This server at present includes two whole genome sequence, viz., sugarbeet and rice. It detects polymorphic markers, in case both self-designed primers and external primers are provided along with the graphical visualization developed in R software. It is freely available for scientific community at http://webtom.cabgrid.res.in/polypoly/. Revalidation of webserver based e-PCR was done using re-sequencing data of 4 Indian rice varieties (i.e., Co-36, Dubraj, Co-39 and Cauvery) of 3K genome project, IRRI, Philippines and was found in concordance which increases reliability of the developed webserver. PolyMorphPredict is a user friendly, cost effective and time saving web-based tool. It has applications in DUS test for variety identification and management, MAS/GAS, QTL and gene mapping, germplasm improvement, traceability of product/produce, tracing hybridization and introgression events, differentiation of edible derived varieties/ initial varieties, marker development for screening the mapping-based population for the genes involved in several key traits, identification and differentiation of fungi, parentage testing in animals and fish, breed signature of animal and fish and genome finishing.