Recent advances in next-generation sequencing technologies have provided cost effective platforms for direct detection of high-quality single nucleotide polymorphisms (SNP) markers for genotyping of mapping populations [15-17]. The maize genome sequence and resources such as HapMap greatly assist mapping strategies based on high-throughput genotyping by the identifying genes and polymorphisms that may reside between intervening markers [18-21]. Genotyping-by-sequencing (GBS) [22] is a popular new method for affordably acquiring dense genome wide marker data for large sample size populations and has been successfully utilized for genetic studies in a variety of species [23-26].