Pete Crisp

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Epigenomics in crops

The guiding paradigm for my research is understanding the contribution of epigenetics to heritable phenotypic variation in crop plants. Epigenetics refers to the heritable transmission of information that is not solely due to DNA sequence. My goal is to understand the role of epigenetics in trait variation in plants and learning when, how and why epigenetic traits (“epialleles”) can be passed through cell divisions to daughter cells or across generations.

Research Program

My researches focuses on DNA methylation, which is known to underlie epigenetic control of some traits and is often - but not universally - stably inherited in plants. There are many unanswered questions concerning the origin, inheritance, stability and functional relevance of epialleles in large crop genomes. These questions are critical for a complete understanding of fundamental principles of genetics and will greatly affect the potential application and utility of epigenetic information for plant breeding and modern agriculture.

Current research projects include:

  1. Characterizing unexpected inheritance patterns of DNA methylation in maize hybrids and their progeny

  2. Generating maize plants without methylation and the development of tools for epigenome engineering

  3. Identifying the accumulation and rate of epigenetic variation in clonal apple varieties

These projects utilize the crop species maize and apple, supplemented with work in models species wild foxtail millet (S. viridis) and Arabidopsis (A. thaliana). My research is driven by genomics and computational biology and I use classical forward and reverse genetic approaches. Genome editing is an important tool that I am developing to investigate epigenomes. While deploying this emerging technology to address fundamental research questions, I do so with an eye towards optimising these tools for precision epigenome engineering in crops.


Epigenomic variation in plants


Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions

Variation and Inheritance of Small RNAs in Maize Inbreds and F1 Hybrids

Monitoring the interplay between transposable element families and DNA methylation in maize

Opportunities to Use DNA Methylation to Distil Functional Elements in Large Crop Genomes

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture