Abstract
BackgroundKnowledge of genetic markers that are correlated to stress tolerance may improve spatial mapping of reef vulnerability and can inform restoration efforts, including the choice of genotypes for breeding and reseeding. In this manuscript we present two methods for screening transcriptome data for candidate genetic markers in two reef building corals, Acropora millepora and Pocillopora damicornis (types α and β). In A. millepora, Single Nucleotide Polymorphisms (SNPs) were pre-selected by targeting genes believed to be involved in the coral thermal stress responses. In P. damicornis (type α and β), SNPs showing varying allele frequencies between two populations from distinct environments were pre-selected. Allele frequencies at nine, five and eight of the pre-selected SNP loci were correlated against gradients of water clarity and temperature in a large number of populations along the Great Barrier Reef.ResultsA significant correlation between environmental category and SNP allele frequency was detected in up to 55% of the tested loci, which is an exceptional success rate for these types of tests. In P. damicornis, SNP allele frequencies of β-hexosaminidase and Elongation factor 1-α were significantly correlated to temperature in type α and to temperature and/or water clarity respectively in type β. Type α also showed a correlation between water clarity and SNP allele frequency in a gene of unknown function. In A. millepora, allele frequencies at five (β-gamma crystallin, Galaxin, Ubiquitin, Ligand of Numb X2 and Thioredoxin) SNP loci showed significant correlations.ConclusionsAfter validation of these candidate loci through laboratory or field assessment of relative stress tolerance of colonies harbouring different alleles, it is anticipated that a proportion of these markers may represent the first coral candidate Quantitative Trait Loci for environmental stress tolerance and provide an important genetic tool that can be incorporated into spatial management decisions and restoration efforts of coral reefs. One pertinent example would be to combine spatial data of tolerant populations with genetic connectivity and thus identify high priority conservation reefs and implement targeted coral husbandry and active restoration efforts that use locally- and stress-adapted genotypes.
Highlights
Knowledge of genetic markers that are correlated to stress tolerance may improve spatial mapping of reef vulnerability and can inform restoration efforts, including the choice of genotypes for breeding and reseeding
Given the known and forecasted impacts of climate change on coral reef ecosystems [2,3,4,5,6], a priority area in conservation initiatives should be the determination of the amount of adaptive genetic variation, i.e. variation at loci that have an effect on fitness [7], in key habit forming
Pocillopora damicornis Transcriptome sequencing After preliminary machine quality filtering, 947,623 sequences were obtained
Summary
Knowledge of genetic markers that are correlated to stress tolerance may improve spatial mapping of reef vulnerability and can inform restoration efforts, including the choice of genotypes for breeding and reseeding In this manuscript we present two methods for screening transcriptome data for candidate genetic markers in two reef building corals, Acropora millepora and Pocillopora damicornis (types α and β). Some of the more commonly reported methods include the detection of non-random population divergence at specific loci (FST outliers) [12,13,14], elucidating the genetic architecture of specific phenotypes [15], and associating the frequency distribution of alleles to one or more ecological variables (genetic-environment associations, GEAs) [16,17]. Evidence for genetic variation that is significantly associated to environmental heterogeneity, fitness and phenotype remains scarce [18,19,20]
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