Abstract: This invention provides methods for more efficiently breeding novel species, subspecies or varieties of plants possessing desirable traits derived from other species, subspecies or varieties. In particular, the invention provides reagents and methods for quantitatively determining the genetic contribution from each parent in the progeny of a genetic cross between parental plants of different species, subspecies or varieties. The invention also provides methods for isolating hybrid and backcross progeny plants with a desired trait or combination of traits having inherited the minimum amount of DNA from the trait donor plant. Nucleic acid probes specific for species, subspecies and varieties of plants are also provided.