Using genomes to predict coral bleaching

Genetic sequencing can reveal evolutionary differences in reef-building corals that may help identify strains that adapt to warmer seas, researchers say.

In a recent study, they analysed 237 samples collected at 12 locations along Australia’s Great Barrier Reef.

Sequencing allowed them to look across the genome for signatures where adaptation occurred and to find genetically distinct variations associated with bleaching tolerance.

It also revealed a considerable amount of genetic diversity in the gene sacsin, which is involved in heat stress response. Such diversity suggests local environmental adaptation.

“What we discovered is that no single gene was responsible for differences in a coral’s response to bleaching, but instead many genetic variants influence the trait,” says Zachary Fuller from Columbia University, US, first author of a paper in the journal Science.

“On their own, each has a very small effect, but when taken together we can use all these variants to predict which corals may be able to survive in the face of hotter seas.”

The study brought together researchers from a number of US institutions and the Australian Institute of Marine Science. They worked with Acropora millepora, a shallow-water coral known to be susceptible to bleaching

When sea temperatures get too hot, corals will expel the vital photosynthetic algae that live within their tissues, causing the coral to turn white, and ultimately die.

However, the thermal limits of corals and their responses to bleaching events vary within species. While it’s thought that these tolerances are partly heritable, due to the lack of high-quality genomic resources for coral species, the genes responsible have remained elusive.

The new findings, the researchers suggest, offer a pathway for biologists to search for strains that can better cope with ocean warming and could enable similar approaches to be used in other species.

“These results set the stage for genomics-based approaches in conservation strategies,” they write.

In a related commentary in Science, Rachael A Bay and Leslie Guerrero from the University of California Davis note that bleaching is a complex trait because it is highly polygenic – encoded by many genes across the genome rather than a few key genes.

This makes identifying the causative genetic variants difficult.

“Fuller et al. borrowed tools first used in human disease and agricultural applications to calculate ‘polygenic scores’, combining the effects of many variants across the genome,” they write.

“In humans, this method was first used to predict the risk for schizophrenia and bipolar disease. Since, it has been used to predict traits as diverse as milk fat in dairy cows and cancer risk in humans.”

The new study provides a framework for integration of environmental and genomic data that could be used to predict the bleaching susceptibility of a coral even before a heat wave occurs and could be applied to any species of conservation concern, Bay and Guerrero add.

However, it does remain to be seen “whether this polygenic score is reliable across independent samples and distant geographies”.