Linkage maps of many plant species were limited in size until the advent of molecular mapping. The primary difficulty with developing linkage maps was the inability to incorporate many markers into a single stock to be used for genetic analysis. This inability occurred because of the deleterious effects of the expression of all mutant phenotypes in the single stock. Because normal DNA or protein molecules are used to score the genetic material, molecular markers are phenotypically neutral. This is a significant advantage compared to traditional phenotypic markers.