Lycopersicon peruvianum is a wild species of tomato that exhibits gametophytic self-incompatibility (S), wherein the SI response is controlled by the genotype of the pollen. Cultivated tomato (L. esculentum) is a self-compatible species. Assisted by phenotypic markers, periclinal graft chimeras between these two species have been obtained. Fruit set analysis following breeding demonstrated that the available five chimeras (PPE, PEE, PEP, EPP, and EEP) are able to accept pollen from L. peruvianum, suggesting that there is a failure of the SI response. SI response is known to be dependent on S-locus associated proteins. These proteins are present in the style, which is mainly derived from the L1 and L2 layers of meristem. RNA analysis of the style tissue using a cloned S-locus cDNA as a probe showed that, except for EEP, all chimeras expressed the S-allele. This was also confirmed by SDS-PAGE analysis of stylar proteins that were present in variable amounts depending on the periclinal combination. Thus, the breakdown of SI is not associated with the lack of expression of the S-locus. Further work is being conducted to understand the nature of this breakdown.