Potato is heterozygous, a characteristic that contributes to its extreme genetic diversity and has probably been a key factor in its survival. This heterozygosity is reflected by the fact that random DNA markers are highly polymorphic among breeding lines, and such DNA polymorphism is not matched by any other major crop. Potato's heterozygosity is attributed to self-incompatibility and has most likely been enhanced by millions of years of asexual propagation by tubers.

Selection based on maximum heterozygosity, rather than additive genetic variance, is critical in potato breeding, especially for quantitative traits. Many single gene traits, such as disease resistance, occur at corresponding loci as Rr and Rrrr allelic conditions in diploid and tetraploid potato species, respectively. The heterozygosity and tetrasomic inheritance makes genetic analysis impossible for most agronomically important traits. Thus, the genetics of a majority of the breeding traits in potato are either poorly understood or not established at all.