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Related Experiment Videos

Simple sequence repeat marker loci discovery using SSR primer.

Andrew J Robinson1, Christopher G Love, Jacqueline Batley

  • 1Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University, Bundoora 3086, Victoria, Australia.

Bioinformatics (Oxford, England)
|February 14, 2004
PubMed
Summary
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SSR Primer is a new tool that automates the identification of simple sequence repeats (SSRs) and designs PCR primers. This aids plant breeding by streamlining molecular marker development for genome and phenotype mapping.

Area of Science:

  • Genetics
  • Bioinformatics
  • Molecular Biology

Background:

  • Simple sequence repeats (SSRs) are crucial molecular markers.
  • Applications include genome mapping, phenotype mapping, and marker-assisted selection in crop plants.
  • SSR markers are also vital in molecular ecology and diversity studies.

Purpose of the Study:

  • To develop an automated tool for identifying SSRs and designing PCR primers.
  • To create a pipeline integrating SSR identification and primer design for plant breeding programs.
  • To provide a user-friendly, web-based interface for remote access.

Main Methods:

  • Developed a PERL script named SSR Primer.
  • Integrated SPUTNIK (SSR repeat finder) with Primer3 (PCR primer design program).

Related Experiment Videos

  • Utilized a web-based interface for sequence submission and analysis.

    • Main Results:

    • The SSR Primer tool successfully identifies SSR loci within submitted DNA sequences.
    • It automatically designs locus-specific PCR primers for SSR amplification.
    • The integrated pipeline streamlines the process of SSR marker development.

    Conclusions:

    • SSR Primer provides an automated and efficient solution for SSR marker development.
    • This tool supports plant breeding programs by facilitating genome and phenotype mapping.
    • The web-based accessibility enhances its utility for researchers worldwide.