Genome expression in polyploid is usually considered to be quite different depending on the genetic context. While it is admitted that autotetraploids resulting from polyploidization events within species do not present major changes of genes expression, allotetraploid which result from hybridization between divergent species or lines were showed to present very important changes of expression compared to the diploid (2x) parental lines (genomic shock). In this work, we investigated the root citrus genome expression using custom Agilent Citrus microarray (4x44K format) of different couples of 2x and doubled diploid (4x) in absence of stress: Poncirus, Cleopatra Mandarin as well in the Cleopatra Mandarin × Poncirus intergeneric hybrid. We also evaluated the plant hydraulic architecture of this plant material. Our goal was to evaluate if any change in root genome expression related to polyploidy could lead to plant hydraulic architecture changes.