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    SNP Discovery through Next-Generation Sequencing and Its Applications

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    IJPG.2012.831460.xml (6.715Kb)
    IJPG.2012.831460.pdf (1.718Mb)
    Date
    2012-11-22
    Author
    Kumar, Santosh
    Banks, Travis W.
    Cloutier, Sylvie
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    Abstract
    The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference.
    URI
    http://dx.doi.org/10.1155/2012/831460
    http://hdl.handle.net/1993/30505
    Collections
    • Faculty of Agricultural and Food Sciences Scholarly Works [97]
    • University of Manitoba Scholarship [1981]

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