Assembling the methylome of an oilseed <em>Brassica</em> — ASN Events
  1. Schedule
  2. Symposium 6B: Gene Regulation and Epigenetics
  3. Assembling the methylome of an oilseed Brassica

Assembling the methylome of an oilseed Brassica (#94)

Justin Bloomfield 1 , John P Hammond 2 3 , Terry J Rose 1 , Abdul Baten 1 , Graham J King 1 4
  1. Southern Cross University, Lismore, NSW, Australia
  2. School of Agriculture, University of Reading, Reading, United Kingdom
  3. University of Western Australia, Perth, WA, Australia
  4. Huazhong Agricultural University, Wuhan, China

Superimposed on the underlying DNA sequence of plants and animals is a series of epigenetic marks that can provide considerable agility in terms of modulating gene expression, ontology, susceptibility to disease and response to the environment. Understanding the epigenetic processes corresponding with these functions may unlock hidden traits of agronomic importance. In oilseed Brassicas, reproductive development underpins yield quality of the final harvestable seed product. To understand the associated molecular epigenetic interactions we are developing the methylome of Brassica rapa oilseed line R-o-18, genome size ~300 Mbp.

Following resequencing and pseudochromosome construction of the R-o-18 genome, we performed multiple technical and biological whole genome bisulphite sequencing (WGBS) runs on Illumina MiSeq and HiSeq platforms. To determine the reproducibility of the WGBS technique we ran technical replicates differing at the library preparation and/or sequencing run stage. Raw data processing and read alignment was performed and optimised using both proprietary and open source software. Methylation calling using Bismark and BSMap were compared for read coverage and percent methylation in the CG, CHG and CHH contexts common in plants. Mean GC content of converted clean paired reads is approximately 10 % lower than unconverted DNA, and unique alignments of cleaned Illumina MiSeq WGBS data per run exceeds 5.2 million with a mean length of approximately 115 bp giving approximately 600 Mbp of unique alignments per run.

The distribution of methylation in different functional regions was assessed for 5’ upstream, intra-exonic, intra-intronic and exon/intron boundaries. Methylation of selected key genes in distinct tissues were analysed in depth. Results from the WGBS comparisons and the methylome development will be presented. Our work is contributing towards the development of a framework underpinning new crop management strategies both in terms of information-led agronomy and in harnessing epigenetic variation in crop breeding.