If it is a new variety of plant that you have found in a screening, you need to establish the trait by back-crossing. In the past you'd have to map the gene responsible for the trait, by crossing to wild type strain, and if no genetic maps are available it would be nearly impossible to isolate the gene...Nowadays you can do next generation sequencing and try to identify the causal mutation by sequence comparisons and specific functional experiments with the encoded candidate gene products.

Also, if a specific gene (and its sequence) is very conserved across different species, you can even design primers from the known sequences of other species to fish out the candidate gene from the species of your interest.