Epigenetic Mechanisms Regulating Gene Imprinting In Rice Seeds

01 Sep 2010 31 Aug 2017

Daniel Zilberman (PI) , Robert L Fischer (CoPI)


PI: Daniel Zilberman (University of California, Berkeley) Co-PI: Robert Fischer (University of California, Berkeley) Senior personnel: Pamela C. Ronald (University of California, Davis), Takashi Okamoto (Tokyo Metropolitan University)

Plant seeds consist of embryos supported by a nutritive tissue called endosperm. In the cereal crops, such as rice, the endosperm occupies the bulk of the seed and serves as a major source of food for humans and livestock. Full understanding of how seeds develop is important to future crop improvement, and there is now evidence that direct genomic changes help to regulate seed development. In particular, genetic and molecular studies, primarily in the model plant Arabidopsis thaliana, show that endosperm development is regulated by methylation, in which methyl groups are added to DNA and associated proteins. This type of direct change to the DNA is a form of epigenetic regulation and it can influence the size and quality of the seed, in part by regulating gene expression that is specific to a parental genome, known as genomic imprinting. Genome-wide changes in endosperm DNA methylation also interface with small RNA pathways and influence control of transposable elements, segments of DNA that move throughout the genome. In rice, as in most other important crops, the epigenetic landscape of gametes and seeds are unknown. To understand epigenetic regulation of rice seed development, this project will analyze DNA methylation, identify modifications to the DNA-associated proteins, called histones, and characterize small RNAs in rice seed tissues. This project will quantify gene expression, identify imprinted genes, and will use computational tools to identify rice pathways regulated by genomic imprinting. Comparisons of imprinted genes between rice and Arabidopsis will help clarify how genomic imprinting has evolved in flowering plants.

Nearly half of the world food supply is provided by the proteins, carbohydrates and nutrients stored in properly developed endosperm. Imprinted genes specifically influence seed yield by controlling resource allocation to the endosperm. The outcomes from this project will enable new technologies that increase crop yield to feed a growing population, thereby directly addressing the problem of hunger in our society. The project will attract new students to science by incorporating undergraduate students into the research program. In particular, students will be recruited from the Berkeley Biology Scholars Program, established to promote the success of undergraduate students from groups underrepresented in the biological sciences. All genomic data will be made available to the public through the Gene Expression Omnibus database (GEO; http://www.ncbi.nlm.nih.gov/geo/) and a dedicated web site that will be developed for this project.