Single nucleus analysis of Arabidopsis seeds reveals imprinting dynamics

Seeds are the basis of agriculture, yet their full transcriptional complexity has remained unknown. We used single-nucleus RNA-sequencing to characterize developing Arabidopsis thaliana seeds, with a focus on endosperm. Endosperm, a site of gene imprinting, mediates the relationship between the maternal parent and embryo. We identified new cell types in the chalazal endosperm region, which interfaces with maternal tissue for nutrient unloading. We further demonstrated that the extent of parental bias of maternally expressed imprinted genes varies with cell cycle phase, and that imprinting of paternally expressed imprinted genes is strongest in chalazal endosperm. These data indicate imprinting is heterogenous and suggest that parental conflict, which is proposed to drive the evolution of imprinting, is fiercest at the boundary between filial and maternal tissues.