Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm

Hybridization of closely related plant species is frequently connected to endosperm arrest and seed failure, for reasons that remain to be identified. In this study, we investigated the molecular events accompanying seed failure in hybrids of the closely related species pair Capsella rubella and C. grandiflora. Mapping of QTL for the underlying cause of hybrid incompatibility in Capsella identified three QTL that were close to pericentromeric regions. We investigated whether there are specific changes in heterochromatin associated with interspecific hybridizations and found a strong reduction of chromatin condensation in the endosperm, connected with a strong loss of CHG and CHH methylation and random loss of a single chromosome. Consistent with reduced DNA methylation in the hybrid endosperm, we found a disproportionate deregulation of genes located close to pericentromeric regions, suggesting that reduced DNA methylation allows access of transcription factors to targets located in heterochromatic regions. Since the identified QTL were also associated with pericentromeric regions, we propose that relaxation of heterochromatin in response to interspecies hybridization exposes and activates loci leading to hybrid seed failure. Author summary Seed failure in response to interspecific hybridizations is a well-known reproductive barrier preventing interbreeding of closely related species and thus maintaining species boundaries. This reproductive barrier is established in the endosperm, a nourishing tissue supporting embryo growth. In this study, we discovered that the endosperm of interspecific hybrids between the recently diverged species Capsella rubella and C. grandiflora suffers from mitotic abnormalities and random chromosome loss. We found that the endosperm has reduced levels of DNA methylation and chromatin condensation, likely accounting for the chromosome loss. Importantly, we found that genes located in pericentromeric regions were preferentially deregulated, suggesting that reduced DNA methylation exposes transcription factor binding sites in pericentromeric regions, leading to hyperactivation of genes and seed arrest. In support of the relevance of pericentromeric regions for hybrid seed arrest, we identified three QTL connected with the phenotype that were all located in pericentromeric regions. These results link epigenetic changes in hybrid endosperm with distinct genetic loci underpinning hybrid seed failure.