Maize is genetically and phenotypically diverse. In populations containing only a small proportion of the variation present in the entirety of maize, progress based on phenotypic selection is being realized. This is exemplified by consistent gains in hybrid yields ,  and through progress in long-term selection experiments, such as the Illinois long-term selection study for grain oil and protein content , selection for prolificacy , and selection for seed size , . Phenotypic diversity in maize for yield, composition, and morphological traits has also been documented in multiple diversity panels , , , and in analysis of structured populations such as the nested association mapping (NAM) population, which represents diverse maize types , , , , . Understanding the genetic factors that underlie this extensive phenotypic diversity and allow for continual improvement in populations is essential for efficient manipulation of maize to meet the demands of the increasing human population and the need to adapt to global climate changes.