Epigenetic Profiling During Brassica Reproductive Development

The domesticated Brassicacomplex is comprised of three diploid species and their three amphidiploids.  Phenotypic plasticity within the genus has given rise to a wide range of crop plants grown throughout the world which have edible roots, hypocotyls, stems, leaves, inflorescences and seeds.   

Brassicas display phenotypic plasticity during growth, resulting from developmental responses to the environment, mediated by signal transduction pathways that appear to include epigenetic mechanisms. The distribution of epigenetic marks is known to vary across Brassicagenomes. In order to understand the molecular epigenetic interactions affecting developmental progression, we are profiling the epigenetic marks of DNA methylation (5mC) in the context of small RNA and transcript populations.  In oilseed crops, reproductive development is essential in determining the yield and quality of final harvestable seed product. We are particularly interested in the cross-talk between epigenetic status and mineral nutrition, particularly phosphate, during development of reproductive tissues.

We firstly re-sequenced the genome of the homozygous self-compatible fast cycling B. rapa oilseed line R-o-18, with 144 million Illumina reads from 18.2 GB, and aligned this with the reference Chiifu B. rapa genome.  We have then used whole genome bisulfite sequencing (BSS) and are analysing this in relation to sRNAs associated with defined stages of seed development. Our aim is to assemble 5mC, transcript and sRNA profiles for defined tissues and stages of reproductive development, and then investigate the networks of regulation that may be modulated in different growing environments.