Identifying the role of epigenetics in the origins of seed plant reproduction

Agriculture depends on the successful production of seeds by plants. Seeds are the product of plant sexual reproduction, a highly complex biological process involving the production of pollen, fertilization of cells inside a seed by pollination and fertilization-dependent reprogramming of those cells into entirely new tissues. We are beginning to understand that, as well as classical genetic mechanisms, each of these processes is also tightly regulated by epigenetic mechanisms such as DNA methylation. Without this additional regulation seed production fails, but our understanding of these extremely important mechanisms remains incomplete. Seed-based reproduction is a recent innovation in one plant group (‘the seed plants’). It evolved from an older method of plant sexual reproduction still found in the closest seedless relatives to the seed plants, the ferns, but the process through which seeds first evolved remains one of the great unsolved mysteries of Plant Science.

Very little is currently known about fern reproduction and the mechanisms that control it, but in recent years it has become possible to begin to investigate this through a new laboratory genetic model, the fern Ceratopteris richardii. Preliminary experiments in this species have raised the exciting hypothesis that epigenetic regulation of reproduction existed before the evolution of seeds, and as such modification of epigenetic mechanisms may have been crucial in the evolution of seed-based reproduction. Through this knowledge we will gain a greater understanding of how plants evolved seeds and the epigenetic mechanisms that are now so important to them and to agriculture.

Using a combination of wet-lab experiments and bioinformatic analysis in the model fern Ceratopteris, this project aims to determine the role of epigenetic regulation in fern reproduction and how these mechanisms compare to those known in seed-based reproduction processes.

To achieve this, we will focus on the following objectives:

1. We will characterize the role of DNA methylation changes that occur during fern spore production (the proposed evolutionary precursor to pollen), using next-generation sequencing (DNA-seq) and bioinformatic analysis.

2. We will test the role of DNA methylation in Ceratopteris fertilization and embryo development. This will be achieved through genetic engineering of Ceratopteris to modify genes critical to known methylation regulatory mechanisms (e.g. MET1) and the characterization of the downstream effects on the epigenetic regulation and genomic stability.

3. We will test the similarity of epigenetic mechanisms regulating reproduction between ferns and seed plants. This will be achieved by introducing fern copies of reproductive genes sensitive to DNA methylation into the laboratory model seed plant Arabidopsis thaliana and testing their effect on pollen and/or seed development.

Funding notes:

MIBTP is a BBSRC funded Doctoral Training Partnership between the University of Warwick, the University of Birmingham, the University of Leicester, Aston University, and Harper Adams University. Please see https://warwick.ac.uk/fac/cross_fac/mibtp/phd/application/ for eligibility requirements.

References:

Marchant et al. (2022) ‘Dynamic genome evolution in a model fern’, Nature Plants, 8, pp.1038-1051. Available at https://doi.org/10.1038/s41477-022-01226-7 Zhang et al. (2018) ‘Dynamics and function of DNA methylation in plants’, Nature Reviews Molecular Cell Biology, 19 pp. 489-506. Available at https://doi.org/10.1038/s41580-018-0016-z