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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,...

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Novel Sequence Discovery by Subtractive Genomics
09:40

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Published on: January 25, 2019

SNP discovery by high-throughput sequencing in soybean.

Xiaolei Wu1, Chengwei Ren, Trupti Joshi

  • 1Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA.

BMC Genomics
|August 13, 2010
PubMed
Summary

This study efficiently identifies numerous single nucleotide polymorphisms (SNPs) for quantitative trait loci (QTL) fine mapping using massively parallel sequencing. The approach enhances marker density in targeted genomic regions for complex trait gene discovery.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Plant Breeding

Background:

  • Massively parallel genotyping technologies enable quantitative trait loci (QTL) fine mapping and map-based cloning of complex trait genes.
  • High-density genetic markers are crucial for fine-mapping and map-based cloning of economically important genes.
  • Single nucleotide polymorphisms (SNPs) are abundant genetic variations vital for QTL mapping studies.

Purpose of the Study:

  • To cost-effectively identify SNP markers for fine-mapping QTL regions.
  • To test the validation rate of SNPs predicted from low-depth Solexa sequencing reads.
  • To evaluate a pooled DNA fragment reduced representation library for SNP discovery in complex genomes like soybean.

Main Methods:

  • Utilized Illumina/Solexa high-throughput sequencing technology.
  • Employed a reduced representation DNA library approach.
  • Applied SNP detection methods to short sequence reads.

Main Results:

  • Identified 39,022 putative SNPs from two parental lines using a reduced representation library.
  • Achieved validation rates of 72% (low stringency) and 85% (high stringency) for putative SNPs.
  • Validated 164 SNP markers to increase marker density in a target QTL region to one marker per 42 K bp.

Conclusions:

  • Demonstrated a rapid SNP identification method for QTL fine mapping using massively parallel sequencing and genome complexity reduction.
  • This SNP discovery approach is efficient for targeting multiple QTL regions within a single genetic population.
  • The method is applicable to SNP discovery in other crop species.