Stability in transgene inheritance and expression is an important consideration in utilizing transgenic germplasm for the development of commercially viable transgenic crops. In the present study, inheritance of the carotenogenic transgene encoding enzyme phytoene synthase (psy) was studied in rice through PCR analysis in F₂, BC₁F₁ (Swarna X F₁), its reciprocal cross (F₁ X Swarna) and BC₂F₂ populations. Segregation distortion was observed for the transgene in F₂ and BC₁F₁ (Swarna X F₁) populations. However, in the case of reciprocal BC₁F₁ (F₁ X Swarna) cross, the transgene showed normal Mendelian segregation ratio 1:1. This trend was also observed in the BC₂F₂ where the transgene followed an expected seregation ratio of 3:1. Segregation distortion of the transgene has been explained on the basis of the position effect of gametophytic selection locus ga2. The results obtained here are significant for the molecular marker assisted transfer of the golden rice transgene to widely grown Indian rice varieties.