Background: Imprinting is a phenomenon found in mammals and flowering plants in which genes are differentially expressed between parental alleles. Plant imprinting is assumed to occur in seeds, especially in the triploid endosperm, and is essential for seed development. Imprinting is thought to have evolved to control resource allocation in the developing seeds. In flowering plants, the endosperm is the only triploid tissue, containing two copies of the maternal genome and one copy of the paternal genome. It is therefore possible that imprinting arises due to the genomic imbalance inherent to a triploid tissue, whereby unequal allelic composition triggers the activation and/or silencing of parental alleles. In Arabidopsis thaliana, it is possible to generate triploid plants by crossing diploid and tetraploid parents. Reciprocal triploids in Arabidopsis have been shown to display differential plant and seed size, as well as disrupted imprinting in the endosperm. In order to test whether imprinting is solely triggered by genome dosage imbalance, and investigate genes possibly linked with the differential seed size observed in reciprocal triploids, we generated a whole-genome transcriptome dataset of reciprocal triploid hybrid late torpedo embryos to i) detect parental allelic contributions and ii) quantify gene expression differences.