Utilizing phenotypic markers in seeds or plants to allow qualitative detection of a proprietary trait in the harvest, to allow a quantitative calculation of the amount of the trait, and to facilitate the calculation and collection of fees for the trait. The phenotypic markers of the seeds can be the seed coat color, and said seeds can be homozygous or heterozygous for the phenotypic difference of seed coat color. Commercial cultivars of seeds with the phenotypic difference of seed color may be grown to include several different seed colors. Trait fees may be assessed on all grain with the proprietary trait, whether the grain was produced from purchased seed or from seed saved from a previous harvest.