Crop improvement through pre-breeding utilizes elite lines, germplasm and species of compatible gene pools, but crossing and characterizing the derivatives between incompatible species, especially distant genera or species, is realized to introduce de novo variations that are heritable, stable and especially economically contributing. This is a novel approach to introduce large-scale de novo variations in crops that can be applied to widening of the genetic base. It helps to introduce heritable and agronomical variations that can be evolved in a short time for use in trait specific breeding programmes. In crosses between incompatible species many times F 1 are delusive appearing like maternal parent. But large variations in F 2 are observed due to genetic changes that include partial or complete elimination of the genome from the paternal parent, reshuffling of the maternal genome leading to several changes that are translated to phenotype. Genome, transcriptome and epigenetic reprogramming is responsible for the above genetic changes. Crossing two distant species can be used as an additional tool in plant breeding.