Molecular markers are widely used in plant genetic research and breeding. Single Nucleotide Polymorphisms (SNPs) are currently the marker of choice due to their large numbers in virtually all populations of individuals. The applications of SNP markers have clearly been demonstrated in human genomics where complete sequencing of the human genome led to the discovery of several million SNPs [1] and technologies to analyze large sets of SNPs (up to 1 million) have been developed. SNPs have been applied in areas as diverse as human forensics [2] and diagnostics [3], aquaculture [4], marker assisted-breeding of dairy cattle [5], crop improvement [6], conservation [7], and resource management in fisheries [8]. Functional genomic studies have capitalized upon SNPs located within regulatory genes, transcripts, and Expressed Sequence Tags (ESTs)

[9, 10]. Until recently large scale SNP discovery in plants was limited to maize, Arabidopsis, and rice [11-15]. Genetic applications such as linkage mapping, population structure, association studies, map-based cloning, marker-assisted plant breeding, and functional genomics continue to be enabled by access to large collections of SNPs. Arabidopsis thaliana was the first plant genome sequenced [16] followed soon after by rice [17, 18]. In the year 2011 alone, the number of plant genomes sequenced doubled as compared to the number sequenced in the previous decade, resulting in currently, 31 and counting, publicly released sequenced plant genomes (https://www.phytozome.net/). With the ever increasing throughput of next-generation sequencing (NGS), de novo and reference-based SNP discovery and application are now feasible for numerous plant species.