Maize is an important staple crop for many countries. Culture dictates maize use, processing, and incorporation into foods. The crop has a rich history of domestication and improvement. With its relative ease of genetic manipulation, maize is considered a model crop for plant genetic experimentation. Recent biotechnological advances, as well as the completed B73 reference genome sequence, have expedited maize improvement. One such profound advance that has greatly increased profitability of maize is the use of transgenes. Despite the many benefits, transgenic plants are problematic when they contaminate transgene-free maize. Maintaining the purity of transgene-free maize is crucial, but often difficult when in close proximity to transgenic fields. Past literature suggests the use of the Ga1 gametophytic cross-incompatibility system to control pollen flow and minimize contamination of transgene-free maize. Yet, information about how the gametophytic cross-incompatibility system functions at the molecular level is still lacking. Our research sought to assemble BACs containing the Ga1-m locus to better understand sequence variation with the B73 reference genome that may be causative of the male function in the Ga1 gametophytic cross-incompatibility system.