Plant genome design method defines DNA markers M1 to M5, for target region, DNA marker M2 is defined at an end on an upstream side of a target region, or upstream thereof, DNA marker M1 is defined upstream of the DNA marker M2, DNA marker M4 is defined at an end on a downstream side of the target region, or downstream thereof, DNA marker M5 is defined downstream of the DNA marker M4, and DNA marker M3 is defined in the target region; and designs a genome so that a substitution region, containing the target region, in a chromosome of the original cultivar to be substituted with a chromosome fragment derived from the foreign cultivar has an end on an upstream side between DNA marker M1 and DNA marker M2, and an end on a downstream side of the substitution region between DNA marker M4 and DNA marker M5.
