Investigating gene editing to support coral adaptation to climate change

Coral reefs are under threat globally, primarily from climate change. There is an increasing need to understand the resilience of corals and their capacity to cope with rising temperatures – among individual coral colonies, within and among populations, and among species. Resilience is driven largely by genetic diversity – the ultimate fuel for adaptation under changing conditions.

Our research seeks to identify genes that underpin characteristics like heat and bleaching tolerance, and growth, using gene editing techniques with the CRISPR/Cas9 system. By introducing precise DNA edits into corals’ DNA, we can change the regulation of certain genes and thus test their function under current and simulated future conditions.

person in blue gown and gloves at microscope — Conducting CRISPR research on corals at AIMS' National Sea Simulator Image: M. Roman

Understanding the genetic basis of climate-related traits will enable the development of field-ready tools to identify resilient colonies and species, and more broadly understand how corals will be impacted by future climate change. This information can also be used to support the enhancement of coral traits in natural populations.

Our research also seeks to develop strategies to monitor and track the resilience of corals, both on a colony and population level. We will do this by combining two novel genomic technologies: CRISPR-Cas9 mediated gene editing and environmental DNA (eDNA) metabarcoding.

Research for 2024/2025

Over the next year we will focus on increasing our understanding of coral heat tolerance and ability to monitor coral resilience. We will examine both larval and juvenile stages of the coral animal.

The team aims to:

develop a system to monitor genetic diversity from seawater eDNA for a variety of coral species.

develop a system to monitor individual coral colonies by inserting genetic barcodes in corals’ DNA with CRISPR.

develop a rapid test for coral heat tolerance using CRISPR technology.

These ambitious projects will help us gain a deeper understanding of coral biology and lead the way to developing systems that can predict resilience in the wild via genetic markers and monitor that resilience on both an individual colony and population level.

a close up of a small needle injecting into oval eggs on glass — Microinjecting fertilised A. millepora eggs Image: P. Cleves

Monitoring coral population diversity using eDNA

eDNA (or environmental DNA) refers to DNA shed from organisms into their surrounding environment. It is a highly scalable, and non-invasive approach to identifying what species are in a sample (in the case of the ocean, a water sample). However, use of eDNA monitoring to date is mostly limited to the presence or absence of a species, and not population diversity.

The team aims to extend the use of eDNA to develop a monitoring system that can track both genetic diversity of a population, and individuals within that population from samples of reef water.

How do you measure genetic diversity from eDNA?

After we collect water samples from a reef, we can extract the DNA from that water. We then use ‘molecular magnets’ to sift through this DNA from the sampling area to see how many unique reads of DNA we find. This tells us about the genetic diversity of the population where the sample was taken. The more unique sequences we find, the higher the genetic diversity of the population.

Developing ‘genetic barcodes' for monitoring individual colonies and tracking their offspring

The CRISPR-Cas9 genome editing system can be used to create genetic barcodes in individuals. This can be done by creating random mutations in a corals DNA that have no effect on the animal – similar to a tag. These sites of random mutations represent a unique genetic barcode that can be used not only to track the individual over its lifetime but potentially also its offspring. If this research shows the approach is viable, it is envisaged it could be co-developed with an eDNA detection capability to provide an essential tool for restoration and adaptation management.

Monitoring of these genetic barcodes can be merged with the above general genetic diversity monitoring to track coral at both the individual colony and population level. This would be extremely valuable for informing coral reef management and restoration, as it can give insight into how out-planted (barcoded) coral colonies are surviving, spreading, and integrating into the natural population and how general genetic diversity is changing in response to restoration efforts.

black background with a few coral polyps under red light under a microscope — Image: M. Monnier

Developing a rapid test for coral heat tolerance using CRISPR technology

We aim to develop a way to test a corals' heat tolerance by measuring their gene expression in response to acute heat stress.

By observing how a coral upregulates (or increases activation of) certain genes in response to heat stress, we can predict its heat tolerance. When a coral upregulates a gene, it increases the amount of RNA produced by that gene. We can use CRISPR systems to measure RNA for specific genes, which can be visualised using a marker, similar to commonly used rapid RNA tests for COVID-19. This approach would provide a holistic, low-cost, high-throughput method for screening heat tolerance in corals.

Why measure gene expression?

A coral's heat tolerance is a trait influenced by many factors, such as its genetics, life history, and the composition of its symbionts. Measuring each of these factors individually to assess overall heat tolerance is almost impossible. Instead, we can measure gene expression, which examines how genes are turned on and off. This approach provides a way to measure how all those factors work together to determine heat tolerance.

Think of it like a musical orchestra, where the quality of a performance is determined by many factors (i.e., different musicians, instruments, and practice schedules). Rather than analysing all those factors individually, the best way to predict the quality of the concert would be to listen to them play a song. Similarly, we measure gene expression while under heat stress to see how all parts work together in corals.

CRISPR/Cas9 research to date

Over the past five years, we have developed technology to make precise changes in the coral genome using CRISPR/Cas9.

In 2018, we identified a key gene, HSF1, that controls coral tolerance to heat stress. This is the first gene to be shown to control coral survival to heat.

In 2020, we identified a gene we believe is involved in corals' ability to biomineralise their skeletons.

From 2021, we have built a database of key genes for CRISPR screens from several Acropora coral species, to increase the knowledge of the genetic basis of heat stress in corals and feed the possibilities of CRISPR screens.

In 2022 and 2023, we continued to identify genes that control survival to acute heat stress and have explored how the regulation of these genes effect survival over time and across species.

Researchers

Dr Line Bay, AIMS

Dr Phillip Cleves, Carnegie Institution for Science

Dr Luke Thomas, AIMS

Max Moonier, AIMS and UWA

Dr Severine Fourdrilis, AIMS

Dr Ryan Lister, UWA

This research is supported by

Carnegie Institution for Science

Australian Institute of Marine Science

The European Union’s Marie Skłodowska-Curie Actions

University of Western Australia

This page was updated in October 2024