Nixtamalization or alkaline cooking is used to process white food-grade corn into tortillas and tortilla chips. To identify QTLs associated with 6 kernel quality these traits an F2:3 mapping population was created from two commercial white inbreds, SD79 and SD80. F2 individuals were genotyped using 35 SSR marker loci. Significant single effect QTLs and two-way interactions were assembled into multiple locus models for each trait, explaining from 49.7 to 77.8% of the phenotypic variation. Many loci exerted effects solely through interactions. Overall, the genetics underlying each trait exhibited characteristics of classic quantitative traits, they did not involve large single effects, there was extensive evidence of epistasis, transgressive segregation is present for most traits, and both additive and dominant gene action is involved. The distribution of identified QTLs indicates that kernel quality traits appear in clusters throughout the genome most likely the result of pleiotropic effects at these loci.