Rootstock-induced dwarfing in cherries is caused by differential cessation of terminal meristem growth and is triggered by rootstock-specific gene regulation.

Use of dwarfing rootstocks has dramatically increased the profitability of fruit production by reducing production costs, reduced chemical use and higher density plantings. Despite the importance of rootstock-induced dwarfing, the cause of this phenomenon is not known. Using two commercially available graft combinations consisting of a sweet cherry scion, 'Bing', on a dwarfing rootstock (Gi5) or a semi-vigorous rootstock (Gi6), we discovered that the difference in grafted tree height was due to a significantly earlier cessation of terminal meristem growth of the scion on Gi5 compared to Gi6 rootstock, rather than shorter metamer length. We then carried out cDNA-AFLP analysis to investigate differential gene expression between the two graft combinations. Transcript-derived fragments (TDFs) identified as differentially expressed were cloned and printed on microarrays for further confirmation of the differential expression. A total of 99 TDFs were identified as differentially expressed between the 'Bing'/Gi5 and 'Bing'/Gi6 samples, including genes involved in transcription regulation, brassinosteroid signaling, flavonoid metabolism and cell wall biosynthesis or modification. Rootstock vigor has a significant effect on gene expression at the scion and the graft union. Timing of the differential gene expression in the dwarf trees coincides with the earlier cessation of terminal shoot growth, suggesting that these differentially expressed genes may be involved in the dwarfing phenomenon.