Abstract
Microsatellites are ubiquitously distributed, polymorphic repeat sequence valuable for association, selection, population structure and identification. They can be mined by genomic library, probe hybridization and sequencing of selected clones. Such approach has many limitations like biased hybridization and selection of larger repeats. In silico mining of polymorphic markers using data of various genotypes can be rapid and economical. Available tools lack in some or other aspects like: targeted user defined primer generation, polymorphism discovery using multiple sequence, size and number limits of input sequence, no option for primer generation and e-PCR evaluation, transferability, lack of complete automation and user-friendliness. They also lack the provision to evaluate published primers in e-PCR mode to generate additional allelic data using re-sequenced data of various genotypes for judicious utilization of previously generated data. We developed the tool (PolyMorphPredict) using Perl, R, Java and launched at Apache which is available at http://webtom.cabgrid.res.in/polypred/. It mines microsatellite loci and computes primers from genome/transcriptome data of any species. It can perform e-PCR using published primers for polymorphism discovery and across species transferability of microsatellite loci. Present tool has been evaluated using five species of different genome size having 21 genotypes. Though server is equipped with genomic data of three species for test run with gel simulation, but can be used for any species. Further, polymorphism predictability has been validated using in silico and in vitro PCR of four rice genotypes. This tool can accelerate the in silico microsatellite polymorphism discovery in re-sequencing projects of any species of plant and animal for their diversity estimation along with variety/breed identification, population structure, MAS, QTL and gene discovery, traceability, parentage testing, fungal diagnostics and genome finishing.
Highlights
A good molecular marker has attributes like simplicity, abundance/wide genome coverage, ubiquity, inheritance/codominance, and multi-allelism or polymorphism among genomes with universality of genotyping in terms of reproducibility and amenability for multiplexing in detection (Powell et al, 1996)
We aim to develop the tool having provision for evaluation of published primers on various genotypes with in species and transferability between heterologous species in e-polymerase chain reaction (PCR) mode to generate allelic data for germplasm management and improvement, ecological diversity, population genetics and evolutionary analysis
The Home page consists of a brief description of microsatellite marker, polymorphism and overview of the web server
Summary
A good molecular marker has attributes like simplicity, abundance/wide genome coverage, ubiquity, inheritance/codominance, and multi-allelism or polymorphism among genomes with universality of genotyping in terms of reproducibility and amenability for multiplexing in detection (Powell et al, 1996). Since SSR locus has higher mutation rate it results into change in allelic array length (by addition or deletion of repeat) and making it a preferred hypervariable codominant markers. It can be used in linkage mapping, QTL and gene discovery, population genetics, pedigree/parentage analysis, phylogenetics and evolutionary studies, gene regulation and genetic disorder (Cavagnaro et al, 2010)
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