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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Published on: June 23, 2012

Rapid SNP discovery and genetic mapping using sequenced RAD markers.

Nathan A Baird1, Paul D Etter, Tressa S Atwood

  • 1Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America.

Plos One
|October 15, 2008
PubMed
Summary

Restriction-site associated DNA (RAD) sequencing offers a simple, cost-effective method for high-density single nucleotide polymorphism (SNP) discovery and genotyping in large populations, enabling efficient genetic mapping.

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Area of Science:

  • Genetics
  • Genomics
  • Molecular Biology

Background:

  • Genetic mapping relies on single nucleotide polymorphism (SNP) discovery and genotyping.
  • Existing methods often lack the capacity for high-density SNP analysis in large populations.
  • A simple, inexpensive platform is needed for broad applicability.

Purpose of the Study:

  • To describe a novel method for high-density SNP discovery and genotyping using RAD sequencing.
  • To demonstrate the utility of RAD sequencing for genetic mapping in model organisms.
  • To showcase the adaptability of RAD sequencing for various genetic studies.

Main Methods:

  • Sequencing of restriction-site associated DNA (RAD) tags.
  • Development of a barcoding system for sample multiplexing.
  • Application of RAD sequencing for trait mapping in model organisms (e.g., threespine stickleback, Neurospora crassa).

Main Results:

  • Identification of over 13,000 SNPs.
  • Successful mapping of three traits in two model organisms.
  • Fine mapping of lateral plate armor loss and pelvic structure reduction in threespine stickleback.
  • Mapping of an induced mutation in Neurospora crassa.

Conclusions:

  • RAD sequencing provides an integrated platform for SNP discovery and genotyping.
  • The approach is cost-effective and adaptable for high-density genetic mapping.
  • This method holds wide applicability across diverse organisms for genetic research.