The sexual endosperm is an angiosperm innovation central to flowering plant reproduction. Genomic interactions between parental alleles control its development and help determine seed viability. These interactions are characterized by genomic imprinting, where expression from certain genes is parent-specific. Unsuccessful imprinting has been linked to failed hybridization between plants of different species or ploidies. Here, we describe an endosperm-based barrier between Mimulus guttatus, a diploid, and M. luteus, an allotetraploid. Hybrid seeds suffer from underdeveloped endosperm, reducing viability, when M. guttatus is the seed parent, and from arrested endosperm and abortion when M. luteus is the seed parent. The two parental species differ in patterns of endosperm DNA methylation, expression dynamics, and their sets of imprinted genes; and transgressive patterns of methylation and expression emerge in their hybrids. The two inherited M. luteus subgenomes, which are genetically distinct but epigenetically similar, are expressionally dominant over the M. guttatus genome in the hybrid embryo and especially endosperm, where paternal imprints, in particular M. luteus', are perturbed. We suggest that diverged epigenetic landscapes between parental genomes result in epigenetic repatterning in hybrids that drive global shifts in expression patterns and can lead to endosperm-based hybridization barriers.

All data herein was derived from seeds produced from intraspecific or interspecific crosses among lines of Mimulus guttatus and M. luteus. All plants were stored and all crosses performed at the College of William and Mary in either growth chambers or a greenhouse under standardized growth conditions. Please refer to the ReadMe files in each directory (Cross_section_images, Expression_data, Methylation data, Morphology_data) and the 'Methods' section in the associated manuscript for further details regarding data collection and processing.

For details on file contents, please refer to the ReadMe files in each directory (Cross_section_images, Expression_data, Methylation data, Morphology_data). Raw sequence data is available on NCBI's Sequence Read Archive (SRA# = SUB9317876).