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Related Concept Videos

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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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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Development and Evaluation of a Barley 50k iSelect SNP Array.

Micha M Bayer1, Paulo Rapazote-Flores1, Martin Ganal2

  • 1The James Hutton Institute, Dundee, United Kingdom.

Frontiers in Plant Science
|November 2, 2017
PubMed
Summary

A new 50k Illumina Infinium iSelect genotyping array for barley was developed using exome capture data. This cost-effective array provides accurate SNP positions for genetic mapping and backward compatibility with existing platforms.

Keywords:
SNPbarleyexome capturegenotyping chipiSelect

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Area of Science:

  • Plant genetics and genomics
  • Agricultural science
  • Bioinformatics

Background:

  • High-throughput genotyping arrays offer a cost-effective alternative to sequencing for genetic studies.
  • Barley (Hordeum vulgare) is a globally significant cereal crop requiring advanced genotyping tools.
  • Existing genotyping arrays have limitations in marker density and scope.

Purpose of the Study:

  • To develop a novel, high-density 50k Illumina Infinium iSelect genotyping array for barley.
  • To leverage exome capture data and a pseudomolecule assembly for accurate marker placement and annotation.
  • To ensure backward compatibility with existing barley genotyping platforms.

Main Methods:

  • Designed a 50k Illumina Infinium iSelect array using SNPs from European barley exome capture data mapped to the barley pseudomolecule.
  • Included markers from a previous 9k iSelect array for continuity.
  • Validated SNP accuracy by comparing new array genotypes with legacy datasets and tested utility in a segregating population.

Main Results:

  • The 50k array features 49,267 SNP markers, with 44,040 functional assays, including 6,251 from the 9k array.
  • SNP validation showed high agreement rates (98.1% for 9k SNPs, 93.9% for exome capture SNPs).
  • Genetic mapping of a segregating population successfully placed over 14,000 SNPs, correlating closely with physical positions.

Conclusions:

  • The new 50k barley genotyping array is a valuable tool for genetic research and breeding.
  • Accurate SNP placement and high call rates facilitate robust genetic mapping.
  • Site-specific adjustment of cluster files is recommended for optimal genotype scoring with this array.