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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,...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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%...
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: Jun 25, 2026

Phloem Sap Sampling from Brassica napus for 3D-PAGE of Protein and Ribonucleoprotein Complexes
11:23

Phloem Sap Sampling from Brassica napus for 3D-PAGE of Protein and Ribonucleoprotein Complexes

Published on: January 9, 2018

Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing.

Martin Trick1, Yan Long, Jinling Meng

  • 1John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK.

Plant Biotechnology Journal
|February 12, 2009
PubMed
Summary

Researchers identified thousands of single nucleotide polymorphisms (SNPs) in oilseed rape (Brassica napus) using expressed sequence tags (ESTs). Most detected polymorphisms were hemi-SNPs, originating from homoeologous genes, and showed heritability suitable for genetic mapping.

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An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis
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An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis

Published on: January 11, 2017

Related Experiment Videos

Last Updated: Jun 25, 2026

Phloem Sap Sampling from Brassica napus for 3D-PAGE of Protein and Ribonucleoprotein Complexes
11:23

Phloem Sap Sampling from Brassica napus for 3D-PAGE of Protein and Ribonucleoprotein Complexes

Published on: January 9, 2018

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs
08:49

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

Published on: September 16, 2019

An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis
06:31

An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis

Published on: January 11, 2017

Area of Science:

  • Plant genomics
  • Molecular genetics
  • Crop science

Background:

  • Polyploid crops like oilseed rape (Brassica napus) present unique challenges for genetic analysis due to their complex genome structure.
  • Understanding genetic variation is crucial for crop improvement and breeding programs.

Purpose of the Study:

  • To develop and apply computational methods for identifying single nucleotide polymorphisms (SNPs) in oilseed rape using expressed sequence tags (ESTs).
  • To characterize the nature and frequency of SNPs, particularly hemi-SNPs, between two oilseed rape cultivars.
  • To assess the heritability and potential utility of identified SNPs for genetic mapping and association studies.

Main Methods:

  • Generation of approximately 20 million expressed sequence tags (ESTs) per cultivar using the Solexa sequencing system for Tapidor and Ningyou 7 oilseed rape cultivars.
  • Alignment of ESTs to a reference set of Brassica species unigenes to identify sequence variations.
  • Development of computational tools to detect and genotype SNPs in a doubled haploid mapping population derived from the parental lines.

Main Results:

  • Detection of 23,330-41,593 putative SNPs between Tapidor and Ningyou 7, with an estimated polymorphism rate of 0.047%-0.084%.
  • Identification that 87.5-91.2% of detected polymorphisms were hemi-SNPs, arising from homoeologous genes within the polyploid genome.
  • Demonstration of largely expected allele segregation for identified SNPs in a doubled haploid mapping population, indicating heritability.

Conclusions:

  • The study successfully identified a substantial number of SNPs in oilseed rape, providing valuable genetic resources.
  • The high proportion of hemi-SNPs highlights the importance of considering homoeologous gene transcription in polyploid genetic analyses.
  • The identified SNPs are suitable for applications in linkage map construction and association genetics for oilseed rape improvement.