Genetic Considerations

Staghorn Corals in Cane Bay, St. Croix. Photo © Kemit-Amon Lewis/TNC

A major goal of population enhancement efforts includes ensuring that recovering coral populations are genetically diverse. Obtaining genetically distinct individuals and tracking the genotypes of corals in nurseries and during outplanting is important for the long-term success of restoration efforts and the coral populations being restored. This is especially important for coral species that are endangered or rare, because they likely already have reduced genetic diversity and may not be sexually reproducing successfully, eliminating the chances of new genetic combinations arising naturally.

Key terms are defined below as a reference:

Definitions - see the Coral Genetics Research and Restoration webinar for further description

  • Allele – alternative form of a gene that arises by mutation and is found at the same position on a chromosome. Alleles can also arrive via immigration from another population.
  • Genets – colonies formed by sexual reproduction that are genetically distinct. A distinct coral colony represents a single genet (in the majority of cases), but if asexual reproduction occurs, multiple colonies might belong to the same genet, in which case they are called ramets.
  • Ramets – colonies formed by asexual reproduction that are genetically identical.
  • Genetic diversity – the probability that two randomly sampled alleles are different. This reflects the extent of genetic dissimilarity between genets in a population.
  • Genotypic diversity – the proportion of genets within a population. Because corals can reproduce asexually, several colonies (or ramets) can belong to the same genet and therefore genotypic diversity can be less than colony number)

Genetic Risks Associated with Restoration

The genetic and genotypic diversity of coral populations being restored should always be taken into account when conducting restoration using coral gardening methods. These methods take advantage of asexual fragmentation, creating colonies that are genetically identical (i.e., ramets that belong to the same genet). If genotypic diversity is low at outplant sites during spawning for sexual reproduction, the population is at risk since low genotypic diversity can lead to reduced fertilization success.

Incorporating Genetics into Restoration

To minimize these risks, coral gardening practitioners should aim to culture and outplant as many genets as possible. The following tabs include information on how to incorporate genetic information into various aspects of coral gardening methods for coral restoration.

  • Collect 3-6 coral genets per reef from reef areas with different environmental conditions, ideally including areas that mimic projected future conditions
  • To capture the majority (>50%) of locally adaptive alleles (alleles that have given a coral its ability to thrive in its current environment), collect from at least 3 genets a given site, or reef; in order to capture 90%, collect from 10 genets (Baums et al. 2019).
  • Donor colonies (from which coral fragments are collected) should be greater than 5m apart and genotyped using molecular genetic methods if possible.
  • Corals should be collected using this methodology from a range of reef habitats with differing local environmental conditions, for a minimum of 20-25 genets per species in production in each nursery.
coral fragments block nursery

Ramets (coral fragments) of the same genet growing on a block nursery structure. Source: Coral Restoration Foundation. Photo © Tim Calver

  • Corals should be tracked over time based on their genet or lineage. This can be done by designating one genet per nursery structure or using tags or plugs/pucks with genet A space for “unknown genotypes” should be designated for colonies that break or become dislodged and their genet is unknown. Those colonies can still be outplanted with the understanding that the genet is unknown. If no molecular genetic data are available, lineage can be indicated with a unique ID corresponding to the donor colony.
  • Phenotypic traits that can help guide which nursery corals to continue to propagate include: low background levels of partial mortality (amount of tissue loss), rapid wound healing (days to heal from fragmentation), high skeletal growth rate (buoyant weight or “crown area”), bleaching and infectious disease resistance or resilience (no bleaching/infectious disease, slow disease progression rate, and/or quick recovery), and high sexual reproductive output (spawning and sperm motility) (Baums et al. 2019).
  • Genets that show poor fitness in the nursery can be replaced with others from the same reef (Baums et al. 2019). Excluding these colonies from the nursery is unlikely to affect representation of genetic diversity as long as representation from a variety of habitats is maintained. Survivors of genets slated for replacement can still be outplanted directly (see below).
  • Outplant a proportional representation of all genets from nursery stocks in each outplant site (Baums et al. 2019)
  • Outplanting 4-6 different genets in close proximity to increase the chances of successful sexual reproduction will help establish a self-sustaining population.
  • It is possible that some genets may be maladapted to the nursery but well-adapted to the reef; in those cases, a practitioner could consider eliminating the nursery stage and outplanting directly from the parent colony to the reef. A genet could also be maintained in the nursery despite poor performance if monitoring at outplant sites indicates that it is a high performer once outplanted (O’Donnell et al. 2018).

Genetic Tools

A number of molecular genetic methods exist to determine if corals in nurseries belong to different genets, as well as measure genetic diversity and genetic population structure (Baums et al. 2019). Two commonly used approaches include:

  • Microsatellite markers – analyzes the numbers of motifs (repeat base pairs) in an allele
    • Many microsatellite markers have already been developed for Caribbean corals and Symbiodiniaceae (Baums et al. 2019)
    • Benefits: flexible in the number of samples that can be run; data files are small; genetic analysis is straightforward
    • Drawbacks: labor-intensive to assay many loci, scoring of alleles is difficult to automate, results cannot easily be compared across laboratories
  • Single nucleotide polymorphisms (SNPs) - analyzes single base pair differences in a genome sequence
    • Benefits: easier to automate and outsource, more loci can be assayed at a time to give genome-wide information; methods are more reproducible between labs; sequencing-based methods do not require platform development and can be immediately applied to any species.
    • Drawbacks: analysis requires bioinformatics expertise to derive genotypes from sequencing output.
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