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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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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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Infinium Assay for Large-scale SNP Genotyping Applications
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Development, validation and genetic analysis of a large soybean SNP genotyping array.

Yun-Gyeong Lee1, Namhee Jeong, Ji Hong Kim

  • 1Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea; Department of Bioinformatics, University of Science and Technology, Daejeon, 305-806, Korea.

The Plant Journal : for Cell and Molecular Biology
|February 3, 2015
PubMed
Summary

A new Axiom SoyaSNP array, utilizing over 180,000 single nucleotide polymorphism (SNP) markers, enhances soybean (Glycine max) genetic analysis. This tool aids in utilizing wild soybean (Glycine soja) for improved crop breeding and understanding soybean diversity.

Keywords:
Glycine maxSNP arraygenome-wide association studygenotypinghybridunanchored scaffoldvalidation

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Area of Science:

  • Plant genetics
  • Crop science
  • Genomics

Background:

  • Cultivated soybean (Glycine max) exhibits limited genetic diversity, potentially due to underutilization of wild soybean (Glycine soja) resources.
  • Single nucleotide polymorphism (SNP) genotyping arrays offer a powerful approach for analyzing genetic diversity and identifying adaptive genes.

Purpose of the Study:

  • To develop and validate a high-density SNP array for comprehensive soybean genetic analysis.
  • To facilitate high-density genetic mapping and genome-wide association studies in soybean germplasm.

Main Methods:

  • Selection of 180,961 SNPs from extensive genome re-sequencing data of 47 soybean accessions.
  • Creation of the Axiom SoyaSNP array and validation using 222 diverse soybean lines.
  • Phylogenetic and allele frequency analyses to identify natural hybrids and assign unanchored scaffolds.

Main Results:

  • The Axiom SoyaSNP array contains 170,223 high-quality genotyping markers.
  • Identified intermediate soybean accessions as natural hybrids between cultivated and wild types.
  • Successfully assigned over 90 unanchored scaffolds to chromosomes and confirmed SNP distribution in gene-rich regions.

Conclusions:

  • The Axiom SoyaSNP array is a valuable tool for soybean genetic diversity analysis, linkage mapping, and genome-wide association studies.
  • This array can significantly advance soybean breeding by enabling detailed genetic analyses and the identification of important adaptive genes.