PS Webinar Series: What the epigenome can tell us about the genomes of crop plants

Abstract -Despite the advances in genome sequencing and assembly, detailed annotation of plant genomes is now a bottleneck in genomic analysis and an impediment to realizing the full potential of genome editing for crop improvement. Here I will describe our recently developed approach that uses DNA methylation profiling of a single tissue (eg a leaf) to distil a genome down to the relatively small fraction of regions that are functionally valuable for trait variation throughout development.

Many crops have incredibly large genomes, ranging from the modest 730 megabases (Mb) sorghum genome to the massive 17,000 Mb hexaploid wheat genome. The identification of sequences of protein-coding genes and non-coding RNAs, with their associated promoter, terminator and intron sequences, has become relatively straightforward and accurate. However, it is becoming increasingly clear that there are other regions within the genome that play an enormous role in regulating and coordinating gene expression. These notably include cis-regulatory elements and enhancers/repressors. These regions are not easily identified bioinformatically, as they are often located a considerable distance from their target genes and do not have readily-distinguishable sequences.

Using DNA methylation profiling we are able to divide a genome into methylated and unmethylated regions. The unmethylated regions in a genome are highly stable during vegetative development and can reveal the locations of potentially expressed genes or cis-regulatory elements. This approach provides a framework toward complete annotation of genes and discovery of cis-regulatory elements and is broadly applicable to plant genomes.

Our recent paper and commentary

Biography - Dr Peter Crisp is an expert in crop genomics, epigenomics and molecular genetics. He leads a research group in the School of Agriculture and Food Science at the University of Queensland. His research group seeks to understand the contribution of epigenetics to heritable phenotypic variation in crop plants, focusing on cereals including barley, sorghum, wheat and maize. This includes the development of methods to harness epigenetic variation for crop improvement; understanding the role of epigenetics in stress responses; using innovative epigenomic approaches to distill large genomes down to the regions that are functionally important for trait variation and translating these discoveries using genome editing to develop new traits for crop improvement. Research in the Crisp Lab spans both wet lab and computational biology providing a powerful platform to integrate genetic, genomic and biotechnological approaches.

Dr Crisp is a graduate of the Australian National University. He completed a PhD in Plant Biology in Prof Barry Pogson’s lab in the ACR Centre of Excellence in Plant Energy Biology, working on gene regulation and stress responses in the context of chloroplast-nucleus signaling. From 2017-2019 he was a postdoc at the University of Minnesota working on crop epigenomics with Prof Nathan Springer and a member of the Centre for ​Precision Plant Genomics. In 2018 he was also a Mistletoe Research Fellow working with a US based start-up in association with ConservationX Labs. He joined the University of Queensland in 2020 as a Lecturer and an ARC DECRA Fellow. He has a passion for teaching and mentoring and strong commitment to reproducible research practices.

Crisp Lab website

Twitter: @pete_crisp