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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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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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Genome-wide Association Studies-GWAS01:11

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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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Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also...
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DNA Microarrays

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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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Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
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Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism

Shichen Wang1, Debbie Wong, Kerrie Forrest

  • 1Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.

Plant Biotechnology Journal
|March 21, 2014
PubMed
Summary

Researchers developed a 90K SNP genotyping array for polyploid wheat, enabling accurate genetic variation analysis and haplotype mapping. This tool aids in understanding wheat diversity and trait genetics.

Keywords:
genetic diversitygenotypinghigh-density mappolyploid wheatsingle nucleotide polymorphismwheat iSelect array

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Area of Science:

  • Genomics
  • Plant Science
  • Agricultural Science

Background:

  • High-density genotyping arrays are crucial for analyzing genetic diversity and marker-trait associations.
  • Polyploid wheat presents unique challenges for genetic analysis due to its complex genome structure.

Purpose of the Study:

  • To develop and validate a high-density genotyping array for polyploid wheat.
  • To characterize genetic variation and infer haplotype structure in wheat populations.
  • To establish a resource for diversity studies and trait genetics in wheat.

Main Methods:

  • Development of a 90K gene-associated SNP genotyping array.
  • Application of density-based spatial clustering algorithms for high-throughput genotype calling in polyploid wheat.
  • Genetic mapping of SNPs using eight mapping populations.

Main Results:

  • The 90K SNP array successfully characterized genetic variation in allohexaploid and allotetraploid wheat.
  • Model-free clustering algorithms provided accurate genotype calling, even with low-intensity signals indicating sequence divergence or gene deletions.
  • 46,977 SNPs were genetically mapped, revealing detailed haplotype structures.
  • The array identified presence-absence variation (PAV) in wheat populations.

Conclusions:

  • The developed wheat 90K SNP array and clustering algorithms are effective for analyzing genetic variation and haplotype structure in polyploid wheat.
  • This resource facilitates detailed diversity studies and the investigation of genetic underpinnings for traits in wheat.
  • The methods are robust for handling complex datasets, including those with sequence divergence and PAV.