Jointed goatgrass (JGG) is a noxious weed in winter wheat fields. A proposed method of cotrolling JGG is to use herbicide resistant wheat. However, wheat and JGG can hybridize in the field and the hybrid could serve as a bridge for gene migration between the two species. The two species share the D-genome and recombination between the D genomes of the two species has been demonstrated indicating that putting transgene on D-genome would allow for gene migration. One proposed method to minimize the risk of gene migration was to put gene on unshared genomes (A or B) of wheat. To test this hypothesis, glyphosate resistant wheat lines carrying resistance on either A, B or D-genome were hybridized with JGG. Prior to the initial backcross with JGG, the F₁ hybrids were sprayed with glyphosate to confirm for herbicide resistance. The BC₁ population produced was then divided into sprayed and unsprayed sub-populations. Both sub-populations were similar for their gene transmission rates. Higher than expected gene transmission rate (>50%) was observed in both BC₁ sub-populations regardless of the transgene genome location. The BC₂ generations obtained from sprayed and unsprayed populations were further analyzed for gene transmission rates. Unlike BC₁ populations, in BC₂ generation the gene transmission rates in the sprayed populations were different from the unsprayed populations. The results showed higher than expected gene transmission rate for the A (100%) and B (96%) genomes in the BC₂ populations derived from sprayed BC₁. In contrast, in the unsprayed BC₂ generation the gene transmission rate for the A (48%) and B (50%) genomes was normal. Results from BC₁ and BC₂ generations suggest that spraying with glyphosate leads to gametophytic and/or sporophytic selection resulting in higher than expected gene retention rates. The implication of this for gene migration from wheat to JGG will be discussed.