CRISPR genome-editing of corals to understand the genetic response of corals to ocean warming

Project Information

CORALCARE

Grant agreement ID: 894412

DOI

10.3030/894412

Project closed

EC signature date 23 April 2020

Start date 1 November 2021

End date 31 October 2024

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 281 827,20

EU contribution

€ 281 827,20

Coordinated by

INSTITUT DE RECHERCHE POUR LE DEVELOPPEMENT
France

Periodic Reporting for period 2 - CORALCARE (CRISPR genome-editing of corals to understand the genetic response of corals to ocean warming)

Reporting period: 2023-11-01 to 2024-10-31

Summary of the context and overall objectives of the project

Coral reefs are the rainforest of the ocean. They host the greatest biodiversity in the world and are estimated to directly support over 500 million people globally. Due to global changes, more than half of the world’s corals have been lost in the last three decades alone. The frequency and severity of heat waves and other disturbances has now exceeded the innate capacity of coral reefs to recover, which are in a poor condition on a global scale. If the threats to corals are not addressed, 70 to 90 percent of coral reefs could be gone within our lifetimes. It is urgently needed to understand the mechanisms of coral response to ocean warming to develop solutions to mitigate coral reef decline. Coral genetics is the science that studies DNA in corals, and it can help understand which genes have a role in the genetic adaptation of corals to heat. The CORALCARE research project is investigating an innovative genetic approach, CRISPR/Cas9, for coral conservation. CRISPR/Cas9 makes it possible to edit genes to reveal the role these play in mediating thermal adaptation in corals. The research project is also addressing the technical challenges of the current CRISPR/Cas9 technique in corals for achieving higher throughput gene study.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Coral gene editing is performed in coral eggs, when mass coral spawning occurs once a year. During this annual window of a few nights during the spawning season on Australia’s Great Barrier Reef, CRISPR/Cas9 molecules were microinjected into coral eggs. The molecules act like a pair of molecular scissors capable of cutting DNA at a specific location in the genome, where a gene of interest is located so that gene can be switched off. The three genes Caspase-2, IGF2R and Sacsin, believed to be involved in the response of corals to heat stress, were targeted and knocked out. Coral larvae with a knocked-out gene are expected to lose the function associated with that gene and, therefore, exhibit different survival rates during heat stress. The study compared the survival rates of CRISPR-edited larvae and non-edited larvae under normal temperature and heat wave conditions. The aim was to determine whether the function of these genes was necessary for survival and for coping with the warming of the oceans. At the end of the heat wave, all the coral larvae survived equally, with or without these genes. This suggests that the three genes may not be crucial for corals to cope with heat waves. However, further analysis of the efficiency of microinjection and confirmation that these genes do not play a role will be necessary.
Many genes, possibly hundreds to thousands, and possibly different between species, are involved in how corals respond and adapt to heat. In order to identify these genes and validate their function using the CRISPR/Cas9 toolbox, another part of the CORALCARE project is searching for these candidate genes. To do this, gene expression was monitored in young larvae from four different coral species over the course of the first day of a heat wave. The gene expression data will be analysed, and the genes that show a change in their level of expression will indicate that they are being used by coral larvae to cope with ocean warming.
Microinjection of coral eggs is challenging and physically demanding. It takes several nights during a spawning event to microinject the hundreds of eggs required for studying a single gene. Therefore, chemically-mediated CRISPR gene editing is being developed to replace microinjection and enable higher throughput editing. This promises to allow one person to edit more than one gene per spawning event. Several chemicals were tested as transporters of CRISPR molecules into coral eggs. Among them, a peptide successfully carried and delivered CRISPR molecules into the eggs.
Most corals spawn once during the Australian summer between October and December. A handful of other coral species spawn during the Australian autumn between February and March. In 2023, we successfully spawned Acropora subabrolhosensis in captivity for the first time. This species of coral belongs to the small group of autumn spawners, which opens up a second window each year for researchers for gene editing.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

By investigating an innovative genetics-based approach for coral conservation, CORALCARE will help predict the ability of corals to adapt climate change. Three genes were targeted and studied during the 2022 and 2023 coral spawning events on the Australian Great Barrier Reef. The Sacsin gene in particular, plays a role in the response of corals to heat stress.
The first stage of the development of the new chemically mediated gene editing method will contribute to scale up gene editing future research by allowing the study of a larger number of genes.
Furthermore, new knowledge about the spawning times of a new autumn coral spawner, Acropora subabrolhosensis, was acquired. This opens up a new possibility each year for gene editing research.
Finally, the comparative analysis of the gene expression data collected from four coral species will produce new knowledge about more candidate genes that are potentially involved in the response of corals to heat stress, as well as what genes are used by coral larvae to cope with ocean warming during the first day of a heat wave.
CORALCARE has positively influenced the researcher's career. Gene editing in corals is under development in a very few labs in the world. SF has acquired skills in the field of gene editing and is now one of the handful of people in the world able to perform microinjection in coral eggs. SF has further developed skills in coral reproductive biology, fluorescence imaging, transcriptomics, student supervision, leadership, project and financial management. This has allowed her to establish herself as a coral scientist.
The work carried out enhances the innovation capacity of the fields of coral gene editing and coral reef conservation, by screening candidate genes and their role in thermal adaptation and by developing a high-throughput method of gene editing in corals. It addresses issues related to climate change and the environment by providing tools to understand the genetic mechanisms that take place in corals to cope with the heat stress in the oceans due to climate change. Coral reefs have immense societal value. The conservation of reefs and the ecosystem services they provide to humanity is of paramount importance.
The international collaboration between the Australian partner (AIMS, Bay’s Lab), the American partner (Carnegie Institute for Science, Cleves’ Lab) and the European partner (IRD, Berteaux-Lecellier’s Lab) is extremely important for Europe’s climate change science. The project reinforces EU climate research excellence internationally, and directly supports EU climate policy in fighting climate change.The community of coral scientists, natural resource managers and policy makers will benefit from the knowledge resulting from CORALCARE. In 2021 and 2022, SF has supported the Ambassador of Belgium in Canberra with scientific expertise on the health status of the Australian Great Barrier Reef (GBR), with the view to discussing its potential listing as endangered heritage by UNESCO. Likewise, SF has provided the Belgian group of experts for the UNESCO World Heritage Committee (WHC) with science-based knowledge, with the view to prepare their participation to the 45th session of the WHC on the listing of the GBR.

A researcher microinjecting coral eggs

Principle of CRISPR/Cas9 gene-editing in corals

Microinjection in coral eggs seen through microscope

Acropora millepora broodstock

Collection of coral gametes in Acropora subabrolhosensis

Microinjection setup and coral eggs seen with the naked eye

Spawning of Acropora millepora