Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana

Background: Crossing plants of the same species but different ploidies can have dramatic effects on seed growth, but little is known about the alterations to transcriptional programmes responsible for this. Parental genomic imbalance particularly affects proliferation of the endosperm, with an increased ratio of paternally to maternally contributed genomes ('paternal excess') associated with overproliferation, while maternal excess inhibits endosperm growth. One interpretation is that interploidy crosses disrupt the balance in the seed of active copies of parentally imprinted genes. This is supported by the observation that mutations in imprinted FIS-class genes of Arabidopsis thaliana share many features of the paternal excess phenotype. Here we investigated gene expression underlying parent-of-origin effects in Arabidopsis through transcriptional profiling of siliques generated by interploidy crosses and FIS-class mutants. Results: We found that fertilized fis1 mutant seeds have similar profiles to seeds with paternal excess, showing that the shared phenotypes are underpinned by similar patterns of gene expression. We identified genes strongly associated with enhanced or inhibited seed growth; this provided many candidates for further investigation including MADS-box transcription factors, cell cycle genes, and genes involved in hormone pathways. Conclusions: The work presented here is a step towards understanding the effects on seed development of the related phenomena of parental genome balance and imprinting.