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Not AvailableSelf incompatibility occurs in greater frequency among the members of gramineae and controlled by two loci system. Sugarcane as any other polyploid crop with high level of heterozygosity show gametophytic incompatibility which is of special interest to breeders since it encourages outcrossing, prohibits selfing and contributes to propagation of species. Enzymes detected in sugarcane pollen have been found to play a crucial role in the control of incompatibility and among them esterase isozyme has been shown to be of both sporophytic and gametophytic origin and provide a source of markers for studying development of pollen pistil interaction The present study reports a biochemical approach to identify isozyme markers that control incompatibility reaction operating in sugarcane. Two isoenzyme systems, namely, esterase and glutamate dehydrogenase were studied to assess the variation in the protein content and their expression in the pistils, pollen and stigma of compatible and incompatible sugarcane clones that are used as parents in breeding programmes. Esterase and glutamate dehydrogenase isozyme patterns were studied in the anthers of six pollen parents and stigmas of two pistil parents. In general, the anther esterase pattern of Co 86011, Co 62198, Co 91004, Co 99002 and Co 1148 on the stigmas of Co 88028 indicated qualitative differences among them. Co 86011 had one intense band which was not present in other pollen parents might be the cause for the compatible reaction in crosses effected using Co 86011 as pollen parent. Esterase activity was found to be high in Co 86011 pollen on Co 88028 stigma in comparison with Co 88025 stigma and pollen of Co 62198, Co 91004 and Co 99002. Three fast migrating GDH bands were detected in the anther and stigma extracts of the parents studied. The isozyme pattern of GDH indicated that GDH 2 was common for pollen and pistil parents, GDH 1 found only in self incompatible parents viz., Co 62198, Co 91004 and Co 99002 and GDH 3 only in the compatible parent Co 86011. The presence of esterases and its activity suggest that pollen esterases complexes with stigma enables pollen tube entry into the stigma and similarly the high esterase activity in the mature stigma of compatible parents suggests a possible role for these enzymes in compatible and GDH for incompatible pollinations.Not Availabl