Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos

In animals, maternal gene products deposited into eggs regulate embryonic development before activation of the zygotic genome1. In plants, an analogous period of prolonged maternal control over embryogenesis is thought to occur based on some gene-expression studies2, 3, 4, 5, 6. However, other gene-expression studies and genetic analyses show that some transcripts must derive from the early zygotic genome7, 8, 9, 10, 11, 12, 13, 14, implying that the prevailing model does not fully explain the nature of zygotic genome activation in plants. To determine the maternal, paternal and zygotic contributions to the early embryonic transcriptome, we sequenced the transcripts of hybrid embryos from crosses between two polymorphic inbred lines of Arabidopsis thaliana and used single-nucleotide polymorphisms diagnostic of each parental line to quantify parental contributions. Although some transcripts seemed to be either inherited from primarily one parent or transcribed from imprinted loci, the vast majority of transcripts were produced in near-equal amounts from both maternal and paternal alleles, even during the initial stages of embryogenesis. Results of reporter experiments and analyses of transcripts from genes that are not expressed in sperm and egg indicate early and widespread zygotic transcription. Thus, in contrast to early animal embryogenesis, early plant embryogenesis is mostly under zygotic control.