Genomics of the Zygotic Transition in Rice

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PI: Venkatesan Sundaresan (University of California-Davis)Co-PI: Scott D. Russell (University of Oklahoma-Norman)Collaborator: Clarence Hedge (Langston University)Plants reproduce through pollination and fertilization, resulting in the fusion of an egg cell and a sperm cell to generate a single cell called a zygote. The zygote divides and grows to form an embryo inside the seed, which after germination gives rise to the entire adult plant. Thus, the zygote is a totipotent cell, with the capacity to regenerate all the tissues and organs of a plant. The growth of the zygote and the early embryo is initially dependent upon maternal factors provided by the egg cell. As the embryo develops, it later becomes independent of these maternal factors and relies only upon embryonically synthesized RNAs and proteins. The transition from the fertilized egg, reliant on maternal gene products, to independent growth controlled by embryonic genes and gene products, is called the Zygotic transition. During this transition, extensive changes occur to the zygotic genome: the DNA in the chromosomes is re-packaged, genes are activated in the zygotic nucleus, and the maternally-supplied RNA is removed. The Zygotic transition is therefore a landmark event in the life-cycle of a plant. Due to the small size and inaccessibility of the plant zygote, very little is currently known about this fundamental transition. This project will address the problem by utilizing recent advances in genomics to exploit advantageous features of rice plants. In rice, the time from pollination to fertilization is one of the shortest of all flowering plants, and dissection of zygotes at precisely defined stages of development is feasible. The project will determine on a genome scale the changes in gene expression as the zygote progresses from fertilized egg to the first embryonic division, and gain insights into gene networks that underlie this transition. It is known that expression of many genes during seed development depends upon the parent-of-origin, i.e. expression of maternally-inherited and paternally-inherited genes are different, due to modifications of the DNA or its packaging called epigenetic changes. The project will evaluate individual contributions of the paternal and maternal genomes of the zygote in crosses between two different rice strains, to determine the extent of parent-of-origin effects on zygotic transcription, and genes that show such effects will be characterized for the nature of their epigenetic modifications. The zygote is a critical transition in the plant life cycle, when the genome is reprogrammed for the initiation of a new diploid generation that arises from this one cell. This project will therefore be addressing a significant gap in the understanding of plant reproduction.Understanding of the zygotic transition in embryos has agricultural applications for increased seed yields, for regeneration of plants from tissue culture, and for improved methods of breeding hybrids. The project will focus on rice, one of the most important food crops in the world, and also a major crop in many states of the USA. The project findings should also be applicable to other crops, especially cereals. For this purpose, the data generated by the project will be made available for wide access through public databases such as GenBank and Gramene, and the analysis through a publicly-accessible project website at the University of California-Davis. Additionally, the project will provide training in plant genomics to students and faculty from Langston University, a historically African-American institution, through summer internships at the University of Oklahoma, and at the University of California-Davis. The project will also provide training for undergraduate students and graduate students at University of Oklahoma, and for undergraduate students, graduate students, and postdoctoral fellows at the University of California-Davis.