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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

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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Comparing Copy Number Variations and SNPs02:26

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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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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.
GWAS does not require the identification of the target gene involved in...
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Genotyping by sequencing for SNP marker development in onion.

Joanne A Labate1, Jeffrey C Glaubitz2, Michael J Havey3

  • 1Plant Genetic Resources Unit, United States Department of Agriculture, Agricultural Research Service, 630 W. North St., Geneva, NY 14456, USA.

Genome
|August 28, 2020
PubMed
Summary

Genotyping by sequencing (GBS) successfully identified 284 high-quality single nucleotide polymorphisms (SNPs) in onion, aiding genetic characterization despite its large genome. This method is promising for discovering molecular markers in onion (Allium cepa).

Keywords:
carte génétiquedoubled haploid linesgenetic mapgenotyping by sequencinggermoplasmegermplasmgénotypage par séquençagegénétique des populationslignées haploïdes doubléespolymorphisme mononucléotidiquepopulation geneticssingle nucleotide polymorphism

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Area of Science:

  • Plant genetics
  • Genomics
  • Molecular biology

Background:

  • Onion (Allium cepa) possesses a large nuclear genome (16 gigabases per 1C), complicating molecular marker development.
  • Single nucleotide polymorphisms (SNPs) offer advantages for genetic characterization and marker-aided selection due to codominance and prevalence in elite germplasm.

Purpose of the Study:

  • To identify single nucleotide polymorphisms (SNPs) in onion using genotyping by sequencing (GBS).
  • To develop molecular markers for genetic characterization and marker-aided selection in onion.
  • To assess genetic diversity and inbreeding in USDA National Plant Germplasm System (NPGS) accessions.

Main Methods:

  • Genotyping by sequencing (GBS) was performed on onion plants, including F2 families, doubled haploid (DH) lines, and 94 NPGS accessions.
  • The TASSEL 3.0 Universal Network Enabled Analysis (UNEAK) bioinformatics pipeline was used for SNP calling.
  • A pseudo-reference genome was constructed from F2 and DH plant sequences to genotype all accessions, followed by quality filtering and placement on an existing genetic map.

Main Results:

  • A set of 284 high-quality SNPs was identified and mapped.
  • Onion accessions exhibited moderate genetic diversity (mean He = 0.341) and significant inbreeding (mean F = 0.592).
  • GBS proved effective for SNP discovery in onion, even without a complete reference genome, necessitating custom bioinformatics approaches.

Conclusions:

  • Genotyping by sequencing (GBS) is a viable and promising method for SNP discovery in onion, facilitating the development of molecular markers.
  • The identified SNPs can be utilized for genetic characterization and marker-aided selection in onion breeding programs.
  • The study highlights the need for specialized bioinformatics pipelines to handle SNP discovery in large-genome species like onion.