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Team Taps Coral Transcriptomes in Search for Environmental Response Markers

NEW YORK (GenomeWeb News) – Genetic features in coral from Australia's Great Barrier Reef may help to foretell the types of environmental conditions that these organisms can withstand and adapt to, a new study suggests.

In a paper published online last night in BMC Genetics, researchers from Australia, the US, and France used new and existing transcriptome information for coral from two reef building species — Acropora millepora and Pocillopora damicornis — to guide their search for markers coinciding with coral responses to temperature stress and water clarity. In both species, they tracked down variants with allele frequencies that corresponded to one or both of the environmental features considered.

If these and other environmental response-related sites in the genome hold up to future scrutiny, the study's authors explained, they could lead to quantitative trait loci that eventually prove useful for predicting which portions of a reef are prone to damage by pollution, warmer-than-usual waters, or other environmental stressors. Moreover, such genotype-phenotype profiling may help select organisms for rebuilding damaged reefs if such damage does occur.

"This work opens up possibilities for us to enhance reef resilience and recovery from impacts of climate change and pollution," corresponding author Petra Lundgren, a researcher with the Australian Institute for Marine Science, said in a statement. "For example, if in the future we need to restore coral populations, we can make sure that we use the most robust strains of corals to do so."

Genetic variation at the species and population levels is expected to influence how well reef building coral can adapt to and survive in ocean environments with changing temperatures, salinity profiles, and rainfall exposures. And coral's ability to respond to these and other potential stressors is particularly pertinent given the climate changes predicted over the coming years, authors of the new study noted.

For instance, temperature stress has been blamed for coral bleaching — a condition linked to the absence of endosymbiotic dinoflagellates that normally supply photosynthetic energy to coral. But coral are potentially sensitive to a variety of environmental changes.

"Not only is the temperature of the water they live in affected [by climate change]," said Lundgren, "but extreme weather and higher rainfall leads to increased levels of sediment, agricultural runoff, and fresh water on the reef."

In an effort to begin teasing apart gene-environment interactions in coral organisms, she and her colleagues did Roche 454 GS FLX Titanium sequencing on transcript from so-called nubbin samples collected from 20 common reef, P. damicornis, colonies.

The samples came from sites in and around the Great Barrier Reef, which includes thousands of individual reefs and stretches some 2,300 kilometeres (nearly 1,430 miles) along Australia's east coast.

Using the transcriptome data, the group searched for situations in which allele frequencies varied, either with water clarity or temperature for coral from two different P. damicornis types, known as alpha and beta.

From there, researchers narrowed in on suspicious SNPs at eight loci in the beta P. damicornis coral and five loci in the alpha type. These variants were subsequently tested in a larger set of alpha or beta samples collected along the Great Barrier Reef.

In parallel with analyses of newly generated coral transcriptome data, the researchers sorted through existing sequence data for A. millepora coral to find a handful of genes with potential ties to environmental responses.

For their wider analyses of A. millepora coral samples — again taken from Great Barrier Reef sites with varying temperature and water clarity profiles — the team genotyped variants at eight loci with Sequenom's MassArray system.

In each case, a subset of the loci tested in P. damicornis or A. millepora contained variants that were significantly associated with at least one of the two environmental conditions assessed.

For P. damicornis coral from both the alpha and beta types, the group uncovered correlations between allele frequencies of variants in an elongation factor-1-alpha gene and temperature. Variants in a beta-hexosaminidase gene stuck out based on apparent associations with temperature in the type alpha P. damicornis coral and water clarity in the beta type.

In the A. millepora coral, meanwhile, researchers saw SNPs in two genes that had significant links to water clarity and variants in another three genes that coincided with differences in temperature at the sampling sites.

"These represent the first genetic markers in corals for environmental stress tolerance," Lundgren and her co-authors concluded.

"After validation of these candidate loci, i.e., through laboratory or field assessment of relative stress tolerance of colonies harboring different alleles at these loci," they added, "it is anticipated that a proportion of these loci can be used as de facto QTLs."