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PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and

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  • 1Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.

Frontiers in Plant Science
|January 29, 2019
PubMed
Summary

We developed PolyMorphPredict, a user-friendly tool for rapid in silico microsatellite polymorphism discovery. This accelerates genetic diversity studies, variety identification, and marker-assisted selection in plants and animals.

Keywords:
DUSgenic region microsatellitemarkerspolymorphismweb server

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Microsatellites are polymorphic DNA sequences crucial for genetic studies.
  • Traditional methods for microsatellite discovery have limitations, including bias and inefficiency.
  • Existing computational tools lack comprehensive features for microsatellite analysis.

Purpose of the Study:

  • To develop an integrated and user-friendly computational tool for efficient in silico mining of microsatellite loci and primer design.
  • To enable polymorphism discovery and assess microsatellite transferability across species.
  • To facilitate the utilization of previously generated genetic data through evaluation of published primers.

Main Methods:

  • Development of the PolyMorphPredict tool using Perl, R, and Java.
  • Implementation of in silico microsatellite mining from genome/transcriptome data.
  • Integration of electronic PCR (e-PCR) for polymorphism discovery and primer evaluation.
  • Cross-species transferability assessment of microsatellite loci.

Main Results:

  • PolyMorphPredict successfully mines microsatellite loci and computes primers for any species.
  • The tool performs e-PCR for polymorphism discovery and evaluates primer transferability.
  • Validation using five species and 21 genotypes demonstrated the tool's effectiveness.
  • In silico and in vitro PCR experiments in rice confirmed polymorphism predictability.

Conclusions:

  • PolyMorphPredict significantly accelerates in silico microsatellite polymorphism discovery.
  • The tool supports diverse applications including genetic diversity estimation, variety identification, population structure analysis, and marker-assisted selection.
  • It enhances the efficient utilization of genomic data in plant and animal research.