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Single Nucleotide Polymorphisms-SNPs

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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Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

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SNP Mining from Maize 454 EST Sequences.

W Brad Barbazuk¹, Scott Emrich, Patrick S Schnable

¹Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.

|March 2, 2011

Summary

This summary is machine-generated.

This study generated 454 expressed sequence tags (ESTs) from maize shoot apical meristem (SAM) cDNA. The PolyBayes tool was then used to identify single-nucleotide polymorphisms (SNPs) within these maize sequences.

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Published on: July 29, 2019

Area of Science:

Plant genetics and genomics
Bioinformatics and computational biology

Background:

Maize (Zea mays) genetic research relies on identifying variations like single-nucleotide polymorphisms (SNPs).
Shoot apical meristem (SAM) is crucial for plant development and harbors valuable genetic information.

Purpose of the Study:

To establish a protocol for generating and analyzing expressed sequence tags (ESTs) from maize SAM.
To identify single-nucleotide polymorphisms (SNPs) using next-generation sequencing data.

Main Methods:

Sequencing of shoot apical meristem (SAM) cDNA from maize inbred lines using the 454 Life Sciences GS-20 system.
Generation of 454 expressed sequence tags (ESTs).
Application of the PolyBayes computational tool for SNP identification.

Main Results:

Successfully generated 454 ESTs from maize SAM cDNA.
Identified single-nucleotide polymorphisms (SNPs) within the generated ESTs using PolyBayes.
Demonstrated the utility of PolyBayes for SNP discovery in 454 sequence data.

Conclusions:

The developed protocol provides a reliable method for generating maize ESTs.
PolyBayes is an effective tool for identifying SNPs in 454 sequence data, particularly for maize research.
This approach facilitates genetic variation discovery in important crop species.