Updated: Dec 14, 2022
SNP SEQUENCING BASELINE DEVELOPMENT: ROUND 2!
At Coral Restoration Foundation we work with over 20 different species of hard corals, all ranging in shape and size! Staghorn (Acropora cervicornis) and elkhorn (Acropora palmata) corals were once the most prolific species on Florida’s Coral Reef and were the first 2 species CRF™ began outplanting back in 2007. But the other species in our care are just as vital components of a healthy reef ecosystem.
Pillar coral stand tall at Sombrero Reef in 2015 ©Alexander Neufeld/Coral Restoration Foundation™
One species has been in hyper focus in recent history, pillar coral. Pillar coral has seen a drastic decline in wild populations due to Stony Coral Tissue Loss Disease. Today pillar coral is part of a major rescue effort coordinated by multiple organizations and management agencies. CRF™ is one of those collaborators. Since restoration is vital to the survival of pillar coral, both within the Keys and throughout the world, CRF™'s role in the Coral Rescue Project is to care for pillar corals in our open ocean nursery and develop best practices to asexually propagate them!
The CRF™ Science Team cares for and propagates Pillar coral in our open ocean nurseries! ©Alexander Neufeld/Coral Restoration Foundation™
Recently, CRF™ sent samples of Orbicella spp. corals to Pennsylvania State University to develop what is called a SNP chip, a tool used for genotyping. We are now excited to announce that our Science Team is also supplying samples from our genetic bank for Single Nucleotide Polymorphism (SNP) sequencing for Dendrogyra cylindrus (aka Pillar coral) to scientists at Florida Fish and Wildlife Conservation Commission (FWC).
The work FWC is doing to develop this SNP chip will allow samples of multiple Dendrogyra cylindrus genotypes to be sequenced in the future! CRF has several putative genotypes of pillar coral that are not represented in other nurseries. Based on the genetic results of this sequencing for all pillar corals in Flordia, we will know how distantly related these individuals are and be able to develop informed coral swap plans to ensure genetic material is spread across multiple nurseries.
CRF™ Science Program Manager Amelia, and Science Program Associate Hayley, place samples of pillar coral in ethanol filled tubes! ©Haley Evans/Coral Restoration Foundation™
Despite our ability to estimate putative genotypes, which are genotypes based on collection location, it is always exciting to have the sequenced genome of corals. Through sequencing we can learn a lot of information about our corals that will help to influence our restoration techniques in the future. It is also helpful when working with other Florida Keys restoration groups for potential “coral swaps”, sharing information through our Coral Sample Registry, and setting up scientific collaborations with researchers interested in learning more about coral genetics.
Sending our pillar coral samples for SNP-chip sequencing has required days planning, coordinating, and of course sampling in the field from our science team! On December 7th our Science Program Manger Amelia, and Science Program Associate Hayley headed out to our Tavernier Nursery ready to collect fingernail sized samples of Pillar corals housed in our Genetic Bank. They used razor blades to fragment the corals, extracting small tissue samples that were placed in labelled test tubes filled with ethanol. The ethanol preserves the genetic material, or DNA, until the samples arrive at the lab and can be processed.
CRF™ Science Program Manager Amelia, and Science Program Associate Hayley, collect samples of pillar coral from a CRF™ coral nursery to be used in DNA sequencing! ©Haley Evans/Coral Restoration Foundation™
By genetically sequencing corals we in the restoration community get a better understanding of the genotypic diversity in coral nursery populations, particularly those corals being used for restoration. Instead of using putative genotypes based on locations scientists have the ability to see the exact genome of each individual to differentiate them! Though putative genotyping estimates are widely accepted in the restoration community, establishing the tools and resources to sequence coral genomes is an exciting step forward for collaborative research and innovation in the field.
Coral Chronicles Editor
Madalen Howard is CRF's Communications and Outreach Coordinator. Madalen comes to CRF™ via a winding road from the Tennessee hills, to the South Carolina low country, ending here in Florida’s Coral Reef. She earned her Bachelor's degree in Marine Biology and a Minor in Environmental Studies from the College of Charleston in 2016. Her experience ranges from field research to education, marketing and digital communications.
With CRF™ Madalen creates inclusive pathways to scientific discovery through content creation and by building and fostering relationships with press, digital media creators, and local community members. Throughout her life Madalen has had a skill connecting people with nature, and is excited to bring people into the world of coral restoration.