Sequencing of the first complete genome was accomplished over 20 years ago (Fleischmann, 1995), and since then the number of sequenced genomes has grown rapidly to include thousands of species (NCBI Genome Browser, 2016), including many crops of economic importance (Morrell, 2012). With so many sequences available, comparative genomics has emerged as a logical and powerful tool for finding changes at the DNA level that underlie a given species’ unique characteristics (Touchman, 2010). With the advent of cost-effective high-throughput sequencing technology, it is now more feasible than ever to generate complete re-sequencing data sets for entire populations, and the future of crop genomics and molecular breeding will soon transition from the use of selected markers to focus on comparisons of entire individual genomes both within and across species (Morrell, 2012).