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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology.

Rebekah E Oliver1, Gerard R Lazo, Joseph D Lutz

  • 1USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, ID, USA.

BMC Genomics
|January 29, 2011
PubMed
Summary
This summary is machine-generated.

This study developed a fast and efficient bioinformatics pipeline for discovering and genotyping single nucleotide polymorphism (SNP) markers in oat (Avena sativa). This method aids genomic research in complex polyploid species.

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Area of Science:

  • Genomics
  • Plant Breeding
  • Bioinformatics

Background:

  • Oat genome complexity and limited sequence data hinder genetic marker discovery.
  • Developing efficient methods for single nucleotide polymorphism (SNP) discovery and genotyping is crucial for oat genomics.

Purpose of the Study:

  • To generate expressed sequence tag (EST) data for oat.
  • To develop a bioinformatics pipeline for SNP discovery in oat.
  • To establish a rapid, cost-effective genotyping method for complex polyploid genomes.

Main Methods:

  • Assembled ~127,000 contigs from ~1 million Roche 454 sequence reads.
  • Filtered contigs using a novel bioinformatics pipeline to identify 96 in silico SNPs.
  • Validated SNP polymorphism and utility using high-resolution melting (HRM) analysis and genetic diversity assessment in 34 oat genotypes.

Main Results:

  • Identified 52 polymorphic SNPs from 96 candidates, with 48 segregating as single Mendelian loci.
  • 44 validated SNPs were mapped to the existing oat linkage map.
  • HRM analysis revealed complex polymorphisms and multiple alleles in oat germplasm pools, confirming marker utility for genetic diversity studies.

Conclusions:

  • The developed high-throughput SNP discovery pipeline is effective for oat genomics.
  • High-resolution melting (HRM) analysis provides a simple and informative platform for SNP genotyping.
  • These techniques offer a model for SNP discovery and genotyping in other complex genomes.