RESEARCH-PGR: Zygotic Genome Activation in Rice

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Fusion of the maternal and paternal gametes forms the zygote, and it marks the initiation of a new plant from a single cell. This is a critical stage in the life cycle of the plant. Extensive reprogramming of the pattern of gene expression through chemical modifications of DNA and associated proteins, also known as epigenetic processes, accompany zygote development. Previous studies have shown that the large-scale activation of plant zygotic genes occurs earlier than it does in animals; however, both the timing and the relative contributions of the maternal and paternal genetic material to zygotic gene activation are not well defined. Furthermore, a detailed characterization of the reprogramming and activation of the zygotic genome at the earliest stages has not been performed in a flowering plant due to the difficulties in isolating single-cell zygotes at precise time points during early development. This project will characterize genome-wide changes mediated by epigenetic mechanisms in zygotes from rice, an important crop plant. This study will address the early stages of zygote development starting at fertilization, and will utilize the latest technical advances in the isolation and molecular analysis of single cells. Understanding the formation of zygotes from gametes has agricultural applications for increased seed yields, for regeneration of plants from tissue culture, and for improved methods of breeding hybrids. The project will also provide training in plant biology and genomics to students and faculty from Langston University, a historically African-American institution in Oklahoma.Rice is an excellent model to study the mechanisms associated with genome reprograming during zygote genome activation. Rice has one of the shortest time from pollination to fertilization among flowering plants, a characteristic that makes feasible the isolation of precisely-staged zygotes for analysis. Epigenetic processes in zygotic genome activation will be elucidated by characterization of the small RNA transcriptomes and methylomes of the male and female gametes, and of zygotes derived from self-pollinated as well as hybrid crosses. The aims include identification of micro RNAs targeting maternal transcripts, short interfering RNAs targeting transposons for silencing, and potentially novel small RNAs involved in zygotic chromatin resetting. Loci with uniparental zygotic expression will be investigated for transmission or erasure of methylation marks. The analysis will incorporate mutants affecting RNA-dependent methylation pathways. The datasets will be used to generate models for parent-of-origin expression in embryogenesis, as well as for silencing of transposable elements and establishment of constitutive heterochromatic domains through the germline. The project outcomes will result in the closure of major gaps in the understanding of a fundamental transition in the life cycle of plants.