ORIGINAL PAPER Rootstock-regulated gene expression patterns in apple tree scions Philip J. Jensen & Izabela Makalowska & Naomi Altman & Gennaro Fazio & Craig Praul & Siela N. Maximova & Robert M. Crassweller & James W. Travis & Timothy W. McNellis Received: 23 December 2008 / Revised: 17 June 2009 / Accepted: 30 July 2009 / Published online: 27 August 2009 # Springer-Verlag 2009 Abstract Apple trees (Malus x domestica) do not repro- duce true-to-type from seed. Therefore, desirable cultivars are clonally propagated by grafting vegetative material onto rootstocks. Although cloned cultivars are genetically identical, rootstocks influence horticulturally important cultivar traits, including tree size, disease resistance, and abiotic stress tolerance. Here, ‘Gala’ scions were grafted to seven different rootstocks that produce a range of tree sizes and grown in a greenhouse. Global gene expression patterns in the scions were compared using a DNA microarray representing 55,230 apple transcripts. Each rootstock triggered a distinct, reproducible scion gene expression pattern. Two thousand nine hundred thirty-four scion transcripts were differentially regulated, by a factor of two or greater, by one or more rootstocks. Transcripts from genes predicted to be involved in responses to stress and biotic and abiotic stimuli were disproportionately repre- sented among the rootstock-regulated transcripts. Micro- array data analysis based on tree size identified 116 transcripts whose expression levels were correlated with tree size. The correlation of transcript level with tree size was tested for 14 of these transcripts using quantitative polymerase chain reaction in a population of orchard-grown ‘Mutsu’ cultivar trees grafted onto rootstocks from a breeding population of multiple crosses. Of those tested, transcripts encoding predicted sorbitol dehydrogenase, homeobox-leucine zipper, and hevein-like proteins were confirmed as being expressed at higher levels in larger trees, while a transcript predicted to encode an extensin-like protein was confirmed as being expressed at higher levels Communicated by A. Dandekar Electronic supplementary material The online version of this article (doi:10.1007/s11295-009-0228-7) contains supplementary material, which is available to authorized users. P. J. Jensen : T. W. McNellis (*) Department of Plant Pathology, The Pennsylvania State University, University Park, PA 16802, USA e-mail: twm4@psu.edu I. Makalowska Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland N. Altman Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA G. Fazio USDA/ARS, Plant Genetics Research Unit, Geneva, NY 14456, USA C. Praul Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA S. N. Maximova : R. M. Crassweller Department of Horticulture, The Pennsylvania State University, University Park, PA 16802, USA J. W. Travis The Pennsylvania State University Fruit Research and Extension Center, Biglerville, PA 17307, USA Tree Genetics & Genomes (2010) 6:57–72 DOI 10.1007/s11295-009-0228-7