The formation of gametes, the sperm and egg cells, and their fusion to form the zygote, is critical for plant reproduction. The zygote is a single cell that will initiate formation of an embryo within the seed, and ultimately gives rise to the next plant generation.  Gamete and zygote formation both involve major changes at the genome level, both in large scale gene expression and epigenetic changes that reprogram the genome. Despite their critical role in plant reproduction, detailed characterization of gametes and zygotes in plants had previously not been possible due to technical difficulties in obtaining sufficient numbers of isolated cells for analysis. Using rice as a model, this project developed methods to overcome these technical hurdles, and provided new insights into these previously inaccessible cells,  through genome-scale characterization of messenger RNA and small interfering RNA, as well as DNA methylation.

The research has yielded many new and surprising findings.  The zygote was found to have  large scale upregulation of thousands of genes compared to the egg or sperm.  Most of these genes were initially expressed  only the from maternal genome.  An exception was a gene called BBM1 (BabyBoom1), that was inactive in egg cells and expressed in fertilized egg cells, but only from the paternal genome initially.  It was shown that BBM1 is a paternal trigger for embryogenesis, and if it is artificially switched on in egg cells using transgenic rice plants, then embryos can be formed without fertilization. That a single gene can bypass the fertilization requirement for embryo formation in seeds was unexpected.  When these rice plants expressing BBM1 in the egg cell were mutated to eliminate meiosis, a process that causes segregation of genes, progeny plants were obtained that were genetically identical to the mother plant.  

This discovery has major implications for agriculture, as it provides a simple method for producing hybrid seeds from rice, which can be applied to other cereal crops. High yields from crops can be achieved by the use of hybrid plants, which are much more vigorous than inbred plants. However, seeds of hybrids are relatively expensive due to the additional steps required to generate them by cross pollination. Consequently, hybrids are underutilized for many crops grown by smallholder farmers, including rice, a major staple crop in the developing world. By developing a method for producing a hybrid crop plant that can self-reproduce through seeds while maintaining its hybrid constitution, this barrier for smallholder farmers could be overcome, and have an impact on world food production.

The differences in expression of the maternal and paternal genomes are likely to arise from underlying differences in the epigenetic modifications in the genomes of gametes and zygotes.  The distribution of small interfering RNAs (siRNAs), a class of RNAs that is dependent upon epigenetic changes to the genome, as well as capable of directing epigenetic modifications, was studied using techniques developed for the small numbers of these cells that can be isolated.  It was found that the sperm and egg had genome-wide distributions of these siRNAs that were very different from each other, as well as very different from non-reproductive cells of the plant.  These findings showed that major reprogramming of the genomes occurs during gamete formation.  Furthermore, it was shown that the formation of the zygote is accompanied by a reversion to the siRNA distribution seen in vegetative cells, indicating that resetting of the epigenome occurs soon after fertilization.

In summary, the project has filled major gaps in the understanding of a fundamental transition in the life cycle of plants. Results from this project have been used to design a method for the clonal propagation of hybrid plants through seeds, which has a potentially large impact on crop breeding and agriculture.

Last Modified: 06/24/2021
Modified by: Venkatesan Sundaresan