Rootstock-Dependent Gene Expression in Apple Tree Scions

Project: Research project

Project Details


Apple trees do not reproduce true-to-type from seed. Instead, desirable cultivars are propagated by grafting vegetative material onto suitable rootstocks. Rootstocks can alter scion traits of importance to agriculture, including fruit size, flowering timing, the number of flowers and fruits produced, drought tolerance, disease resistance, cold tolerance, and tree stature. In effect, the traits of genetically identical apple cultivar scions can be very different depending on the rootstock to which they are grafted. This project harnesses this phenomenon to identify genes in apple trees that are involved in controlling agriculturally important traits. The central hypothesis driving this research is that scions grafted to different rootstocks have different overall patterns of gene activity, and that these differences in gene activity play a role in determining the trait differences between the trees. Global gene expression patterns in 'Gala' cultivar scions grafted to a series of different rootstocks will be compared. Genes whose expression level is rootstock-dependent will be identified (at least 500 unique genes). A DNA microarray comprised of the differentially expressed genes will be developed and used to survey a large number of scion/rootstock combinations in order to associate the expression of particular genes with particular traits.

This project will result in the identification of genes whose activity depends on the identity of the rootstock. The sequences of these genes will be made public though databases including GenBank ( and the Genome Database for Rosaceae ( The results of the microarray experiments will be made available to the public though GEO database ( The sequence and microarray data will be made publicly available through the GEO database as soon as the first manuscript describing the results is accepted for journal publication, and will remain accessible after the completion of the project into the foreseeable future. The microarrays themselves will be made available at cost to other non-profit research groups. The broader impacts of this work include minority undergraduate student summer training through the SROP program ( Each summer, two or three underrepresented undergraduates will be given the opportunity to participate in the project. In addition, one or more graduate students will receive training in genomics research and undergraduates will be engaged in research related to this project during the academic year. The results of this project may also be useful for the development of gene activity markers that could be used in apple breeding programs to try to predict the traits of a tree early on in its development.

Effective start/end date9/1/048/31/12


  • National Science Foundation: $2,269,241.00


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