For rejection reaction the physiological and biochemical processes are set in the pistil by the recognition reaction specific to the type of pollen that lands on stigma. In contrast to systems where inhibition can occur on stigma itself thus preventing germination of pollen or its entry into style, in GSI system it may occur in style leading to either inhibition of pollen tube growth or its bursting.
The pollen wall and its protein content plays an important role in pollen stigma interaction. Through cytochemical studies it has been observed that the pollen wall is perforated by protoplasmic strands giving the appearance of a living physiological structure playing a very responsible role in the process of interchange between the pollen grain and the substrate. The incorporation of proteinaceous substances in the exine and the intine has been demonstrated by EM studies of the pollen wall during development. A good amount of mobile proteins of the pollen grains is S-gene specific. The recognition proteins of incompatibility are held extra-cellularly in the pollen wall. In GSI plants, these proteins are present in the intine while in SSI plants they occur in the exine.