We have a funded PhD scholarship opportunity in the lab. Check out the details in this post or get in contact for more information. The Scholarship is officially listed on the UQ Graduate School page search for Peter Crisp. The position is a fully funded PhD scholarship for a domestic or international student (stipend + tuition + health cover). More details on the scholarship scheme can be found here on the UQ Graduate School Earmarked Scholarship page.
There has been a lot going on lately… including the grand opening of the Lab. We are here! Excited to be at UQ. Located in the John Hines Building, St Lucia.
The lab will be opening at the University of Queensland, St Lucia Campus, in the School of Agriculture and Food Sciences beginning Feb 2020. We will be looking for students! Contact me for more information.
Crop epigenomics and plant stress memory.
The field of epigenetics is concerned with the inheritance of traits that are not solely attributable to the underlying DNA sequence. We seek to understand the contribution of epigenetics to heritable phenotypic variation and resilience in plants.
I am continually fascinated by epigenetic inheritance and there remain many unanswered questions concerning the fundamental principles of epigenetic phenomena.
Epigenomic datasets including profiles of DNA methylation and chromatin modifications also provide a valuable resource for understanding gene regulation and genome architecture. In particular, we use epigenomic approaches to distill large genomes down to the relatively small fraction of regions that are functionally important for trait variation.
Potential role(s) of epigenetics in stress responses and acclimation is a topical issue but remains unresolved. We continue to work to identify cryptic, epigenetically regulated resilience alleles, a research area of great importance as we adapt agriculture to future climates.
Epigenetic engineering, inheritance, and the roles of DNA methylation
Cryptic stress resilience epialleles and stress recovery
Discovering hidden regulatory elements for crop improvement using epigenomics
For millennia, natural and artificial selection has combined favourable alleles for desirable traits in crop species. While modern plant breeding has achieved steady increases in crop yields over the last century, on the current trajectory we will simply not meet demand by 2045. Novel breeding strategies and sources of genetic variation will be required to sustainably fill predicted yield gaps and meet new consumer preferences. Here, we highlight that stepping up to meet this grand challenge will increasingly require thinking ‘beyond the gene’. Significant progress has been made in understanding the contributions of both epigenetic variation and cis-regulatory variation to plant traits. This non-genic variation has great potential in future breeding, synthetic biology and biotechnology applications.
The genomic sequences of crops continue to be produced at a frenetic pace. It remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Chromatin accessibility assays enable discovery of functional elements; however, to uncover the full portfolio of cis-elements would require profiling of many combinations of cell types, tissues, developmental stages, and environments. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define ∼100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs are found greater than 2 kb from genes. UMRs are highly stable in multiple vegetative tissues, and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf, and these represent regions with potential to become accessible in specific cell types or developmental stages. These UMRs often occur near genes that are expressed in other tissues and are enriched for binding sites of transcription factors. The leaf-inaccessible UMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMR space in four additional monocots ranges from 80 to 120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.
The guiding paradigm for our research is understanding the contribution of epigenetics to heritable phenotypic variation in crop plants and developing methods to harness that variation for crop improvement.
PhD in Plant Biology, 2016
Australian National University
BSc in Science with Honours, 2009
Australian National University
LLB in Laws with Honours, 2008
Australian National University