SNP Discovery through Next-Generation Sequencing and Its Applications
By Santosh Kumar, Travis W. Banks, S. Cloutier. International Journal of Plant Genomics, 2012
332 citations recorded by the source corpus.
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.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/44634335a360607f7f61b70075c9faf4b9d57652
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Citations in the corpus
- Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping (2014, background): “Efforts have been made to develop SNP markers through various approaches, such as chip hybridization or targeting-specific genomic regions [1].”
- Avoiding damage and achieving cold tolerance in rice plants (2013, background): “According to Kumar et al. (2012), the connection of three interlaced research areas is needed to effectively accelerate the development of improved cultivars with enhanced stress tolerance: next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic ”
- Applications of next-generation sequencing to the study of biological invasions (2015, background): “Such high-density arrays (Ramos et al., 2009; Kumar et al., 2012), for example, Illumina’s Infinium assay, can accurately genotype any number of SNPs (up to a million in one assay) across many individuals (Adler et al.”