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Single Nucleotide Polymorphisms-SNPs

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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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Related Experiment Video

Updated: Jun 13, 2026

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

How many SNPs are enough?

Peter E Smouse¹

¹Department of Ecology, Evolution & Natural Resources, Rutgers University, New Brunswick, NJ 08901-8551, USA. smouse@aesop.rutgers.edu

Molecular Ecology

|May 12, 2010

Summary

This summary is machine-generated.

Researchers used single nucleotide polymorphism (SNP) markers to assess genetic relatedness and inbreeding in zebra finches. While SNP panels improve accuracy, individual inbreeding estimates remain limited, though relatedness measures bracket pedigree expectations well.

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Area of Science:

Population Genetics
Quantitative Genetics
Behavioral Ecology

Background:

Historically, allozyme analysis aimed to measure individual inbreeding and pairwise genetic relatedness using polymorphic loci.
Mendel's Laws indicate numerous independently segregating loci are necessary for accurate genetic assessments.

Purpose of the Study:

To evaluate the accuracy of single nucleotide polymorphism (SNP) panels for assessing heterozygosity and pairwise relatedness in a zebra finch breeding colony.
To compare the effectiveness of SNP panels versus microsatellite markers for estimating genetic parameters.

Main Methods:

Utilized a 771-marker SNP panel to analyze heterozygosity and pairwise relatedness in zebra finches.
Compared SNP data with theoretical expectations derived from a detailed pedigree.
Assessed the impact of increasing SNP numbers on accuracy.
Compared SNP panel results with a 20-locus microsatellite panel.

Main Results:

Adding SNPs to a microsatellite panel enhanced accuracy, but adding microsatellites to a 125-SNP panel yielded minimal improvement.
Estimating individual inbreeding levels using genetic markers showed limited accuracy.
Average pairwise relatedness measures closely matched pedigree relationships, but individual pair variances remained substantial.

Conclusions:

SNP panels are valuable for assessing genetic relatedness, but individual inbreeding estimation accuracy is constrained.
A large number of SNP markers is more beneficial than adding microsatellites to an existing SNP panel.
Genetic marker panels effectively bracket average relatedness but have limitations in resolving individual pair variances.