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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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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: Apr 4, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
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High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster).

C Plomion1,2, J Bartholomé1,2, I Lesur1,3

  • 1BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.

Molecular Ecology Resources
|September 12, 2015
PubMed
Summary

Researchers developed a 9k SNP array for maritime pine, creating the densest genetic map for the species. This tool aids in understanding local adaptation and improving breeding strategies for this vital forest tree.

Keywords:
linkage mappingmaritime pinepopulation geneticssingle nucleotide polymorphism

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Area of Science:

  • Forestry
  • Genetics
  • Ecology

Background:

  • Maritime pine is crucial for Mediterranean ecosystems.
  • Its distribution across diverse environments makes it ideal for studying adaptation to climate change.
  • Genetic variation studies are vital for conservation and breeding.

Purpose of the Study:

  • Develop a high-density genetic map for maritime pine using SNP genotyping.
  • Assess genetic diversity and population structure within French and Portuguese maritime pine gene pools.
  • Identify genetic markers for seed provenance and support breeding strategies.

Main Methods:

  • Developed a 9k Illumina Infinium SNP array for maritime pine.
  • Genotyped individuals from an inbred pedigree, breeding population, and natural populations.
  • Constructed the densest gene-based linkage map using mapped SNPs.
  • Analyzed genetic diversity and population structure using SNP data.

Main Results:

  • A significant proportion of SNPs (24.4%) were mapped, creating the densest gene-based linkage map for maritime pine.
  • French natural and breeding populations showed similar levels of genetic diversity.
  • High genetic differentiation was observed between Portuguese and French gene pools, identifying potential markers for seed certification.

Conclusions:

  • The developed SNP array and linkage map are valuable resources for maritime pine research.
  • Findings support understanding of local adaptation and evolutionary processes.
  • The identified markers can enhance seed provenance control and inform future breeding programs.