Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery

Genome-wide variant detection within a species is the primary initial step towards linking genotypic variation and phenotypes. The conversion of these genetic variants (the most prevalent of these being single-nucleotide polymorphisms or SNPs) into genetic markers is particularly important in agronomically valuable crop species to allow for cost-effective marker-assisted selection strategies, whole-genome fingerprinting, association studies, map-based gene cloning and population-based analyses. Towards these goals, an increasing number of large-scale genetic variant discovery initiatives are being undertaken in conjunction with next-generation sequencing platforms, allowing for drastically quicker and cheaper variant discovery, and leading towards a far more comprehensive view of the genome or transcriptome. This review will summarize the current status of these initiatives and will discuss the expanding role of next-generation sequencing technologies in facilitating crop improvement.