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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,...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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.
GWAS does not require the identification of the target gene involved in...

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Related Experiment Video

Updated: May 11, 2026

Development of Targeting Induced Local Lesions IN Genomes (TILLING) Populations in Small Grain Crops by Ethyl Methanesulfonate Mutagenesis
08:36

Development of Targeting Induced Local Lesions IN Genomes (TILLING) Populations in Small Grain Crops by Ethyl Methanesulfonate Mutagenesis

Published on: July 16, 2019

Sequence-based SNP genotyping in durum wheat.

Remco M P van Poecke1, Marco Maccaferri, Jifeng Tang

  • 1Keygene N.V., Wageningen, The Netherlands.

Plant Biotechnology Journal
|May 4, 2013
PubMed
Summary

Sequence-based genotyping (SBG) efficiently discovers high-quality single nucleotide polymorphism (SNP) markers for complex plant genomes. This method aids in saturating genetic maps and advancing marker-assisted selection in durum wheat breeding.

Keywords:
PstI/TaqITriticum durum Desf.genome complexity reductionhigh-density mappingillumina sequencingrecombinant inbred lines

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Last Updated: May 11, 2026

Development of Targeting Induced Local Lesions IN Genomes (TILLING) Populations in Small Grain Crops by Ethyl Methanesulfonate Mutagenesis
08:36

Development of Targeting Induced Local Lesions IN Genomes (TILLING) Populations in Small Grain Crops by Ethyl Methanesulfonate Mutagenesis

Published on: July 16, 2019

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13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Area of Science:

  • Plant genetics and breeding
  • Genomics
  • Molecular biology

Background:

  • Marker development for marker-assisted selection relies on next-generation sequencing (NGS).
  • Complex and repetitive genomes in crops like durum wheat pose challenges for marker discovery.

Purpose of the Study:

  • To apply sequence-based genotyping (SBG) for de novo single nucleotide polymorphism (SNP) marker discovery and genotyping in durum wheat.
  • To assess the efficiency and quality of SBG for complex genome analysis and genetic map saturation.

Main Methods:

  • Coupling AFLP®-based complexity reduction with NGS for sequence-based genotyping (SBG).
  • Identifying and genotyping SNPs in a biparental durum wheat population and recombinant inbred lines (RILs).
  • Integrating newly discovered SNP markers into a pre-existing framework genetic map.

Main Results:

  • 9983 putative SNPs were identified, with 2606 markers used for mapping.
  • 91% of usable markers integrated into the existing map, increasing map size by 23% and achieving a marker density of 0.8 cM/marker.
  • SBG markers filled gaps in the framework map, with 63 bins containing only SBG markers.

Conclusions:

  • SBG is a valuable tool for efficient, high-throughput, and high-quality marker discovery and genotyping in complex genomes.
  • The methodology enables significant genetic map saturation and integration of novel markers.
  • SBG facilitates advancements in marker-assisted selection for crop improvement programs.