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Single Nucleotide Polymorphisms-SNPs01:05

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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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Genotyping of Staphylococcus aureus by Ribosomal Spacer PCR RS-PCR
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SSR genotyping.

Annaliese S Mason1

  • 1School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia, annaliese.mason@uq.edu.au.

Methods in Molecular Biology (Clifton, N.J.)
|November 7, 2014
PubMed
Summary
This summary is machine-generated.

Simple sequence repeat (SSR) genotyping uses polymorphic DNA markers to detect allelic variation in plant populations. These microsatellite markers are widely distributed, easy to use, and crucial for plant genetic research.

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Area of Science:

  • Genetics
  • Molecular Biology
  • Plant Science

Background:

  • Simple Sequence Repeats (SSRs), also known as microsatellites, are repetitive DNA sequences found throughout plant genomes.
  • SSRs are characterized by short repeat units (1-6 bp) and are prone to mutations, leading to high polymorphism.
  • These markers are present in both genic and non-genic regions and can be found in expressed sequence tags (ESTs).

Purpose of the Study:

  • To describe the methodology of SSR genotyping for plant DNA analysis.
  • To highlight the utility of SSRs as molecular markers in plant genetics.

Main Methods:

  • SSR genotyping involves designing primers to amplify SSR sequences from genomic DNA.
  • Polymerase chain reaction (PCR) is used to amplify the SSR repeat regions.
  • Amplified DNA products are visualized, typically using gel electrophoresis.

Main Results:

  • SSR sequences exhibit high levels of polymorphism due to mutations in repeat units.
  • This polymorphism allows for the effective detection of allelic variation within plant populations.
  • SSRs are distributed widely across plant genomes, making them versatile markers.

Conclusions:

  • SSRs are highly favored molecular markers for plant genotyping due to their polymorphism, distribution, and ease of use.
  • These markers have been instrumental in plant genetics for two decades and will remain valuable.
  • SSR genotyping provides a robust method for analyzing genetic diversity in plants.