Grafting has widely used in the agriculture of fruit-bearing crops and trees because rootstocks have a profound influence on many aspects of scion development and scion responses to the environmental changes including biotic and abiotic stress tolerance. These effects appear to result from the change of gene expression on scion, but only limited numbers of papers have been published demonstrating it. To identify altered expression of genes in Chinese cabbage, Chiifu(Brassica rapa ssp. pekinensis, inbred line) shoot was grafted on three Brassica rootstocks: mustard, turnip and broccoli. After head formation, Br300K microarray experiment was conducted using total RNAs from scion leaves collected in two different seasons, spring (June) and fall (October). A large number of differentially expressed genes (DEGs) were identified both in two seasonal samples, but DEGs were more notable in June sample than in October sample. However, the number of DEGs by three rootstocks were high in October with respect to up-regulation, but high in June for down-regulation. Categories of DEGs included metal ion binding, response to hormonal stimuli, response to endogenous stimuli, regulation of transcription, oxidation reduction and response to stress. Up-regulated genes in both June and October samples were similar in mustard and turnip rootstocks, but different in broccoli rootstock. Two genes were found to respond to all experimental conditions: Brapa_ESTC049008 (hypothetical protein) as an up-regulated gene and Brapa_ESTC016027 (CNGC12) as a down-regulated gene. Together with the previous reports, these results suggest that grafting-induced gene expression depends on the species involved.

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