Exposing the Contribution of Epialleles to Heritable Variation in Apomictic Dandelions

Unravelling the role of natural epigenetic variation in plant adaptation

To tackle climate change and other environmental changes, the ability to adapt rapidly is crucial for both natural populations and crops. This rapid adaptation is made possible by heritable trait variation, which in plants can come from both genetic and epigenetic sources.

Epigenetics involves changes that affect gene activity without altering the DNA sequence, such as DNA methylation, which is notably stable in plant genomes. While epigenetic changes have been proposed as a means to facilitate rapid adaptation, the extent to which they contribute to heritable trait variation remains unclear.

This project addresses these challenges by utilizing epigenomic editing techniques to investigate natural DNA methylation changes in dandelions that reproduce asexually through clonal seeds (apomixis), which results in limited genetic variation — making it feasible to separate genetic from epigenetic effects.

Project Goals

Identifying and validating natural epialleles

• Identify natural epigenetic variants (epialleles) in a single lineage of apomictic dandelions
• Determine the epiallelic impact on heritable gene expression variation
• Provide a quantitative assessment of the importance of epiallelic variation
• First use of epigenomic editing in a wild plant species to understand natural epigenetic variation
• Develop epigenomic editing techniques for application in asexual plants and clonally propagated crops

Originality & Innovation

From descriptive research to demonstrating causality

• Causal epigenetics: First application of epigenomic editing to unravel the functional relevance of natural epiallelic variation in a wild, non-model plant system
• Natural accumulation of variation: Apomictic dandelion lineages represent long-term natural experiments in which relevant levels of variation have accumulated, now analysable with the dandelion reference genome and long-read sequencing
• New Genomic Techniques: Translating epigenome editing from Arabidopsis to dandelion, contributing to the NGT toolbox for wild and non-model species

Project Team

Principal investigators and researchers

Prof. Koen Verhoeven

WP1 Lead / Coordinator

PhD Researcher

PhD1 - Verhoeven Lab (Coming soon)

Dr. Jason Gardiner

WP2 Lead

PhD Researcher

PhD2 - Gardiner Lab (Coming soon)

Collaborators

Working with leading experts in plant genomics and epigenetics

Prof. Eric Schranz

Biosystematics

Dr. Michael Seidl

Bioinformatics

Dr. Basudev Ghoshal

Virologist