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Whole wheat products provide critical nutrients for human health, though differences in wheat flavor are not well understood. Using the house mouse as a model system, flavor was examined using a two-choice feeding system and the Student’s <i>t</i> statistic. To eliminate the confounding effect of processing, whole grain was used. The Student’s <i>t</i> statistic used previously identified “Yummy” and “yucky” check varieties. The study took the Student’s<i> t</i> statistic beyond a theoretical measure of flavor preference to use as a phenotype in genetic mapping study. The Clark’s Cream x NY6432 RIL population was created in the early 1990s and has been mapped extensively. Both varieties are white wheats; Clark’s Cream has a hard kernel texture and NY6432 has a soft kernel texture. The “Yummy” and “yucky” check varieties were soft white and hard white wheats, respectively. A new genetic linkage map was created for this population. Marker-trait association was performed using the Student’s<i> t</i> phenotype from each check. Twenty-two significant associations were found among the two check comparisons. Because mice prefer soft kernel texture over hard, the effect of both the Puroindoline haplotype and the phenotypic expression of kernel texture were used as covariates in further marker-trait association analyses. Twenty-eight markers exhibited significant associations with the Student’s <i>t</i> in the two covariate analyses, with an additional five having significant associations in both the Puroindoline covariate and kernel texture covariate. These five markers show that there is a definitive genetic basis for flavor preference beyond kernel texture. These markers open the door for closer examination of specific genetic regions where the “Yummy” and “yucky” genes are likely to reside. Identifying the flavor genes will allow the development of varieties with more palatability for whole-wheat products.