Table of Contents
International Journal of Plant Genomics
Volume 2012, Article ID 831460, 15 pages
http://dx.doi.org/10.1155/2012/831460
Review Article

SNP Discovery through Next-Generation Sequencing and Its Applications

1Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
2Department of Applied Genomics, Vineland Research and Innovation Centre, Vineland Station, ON, Canada L0R 2E0
3Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB, Canada R3T 2M9

Received 3 August 2012; Accepted 8 October 2012

Academic Editor: Roberto Tuberosa

Copyright © 2012 Santosh Kumar et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.