SNP Chip Workshop (Restoration Genetics)

A critical need for coral restoration planning is the identification of genotypes in order to increase or at least maintain genotypic diversity within nurseries and in outplanting sites. High-resolution genetic tools are required for this task because Caribbean reef building corals, including Acropora spp, occur as large clonal stands that can only be delineated via genotyping. Previously, species-specific microsatellite markers were used to resolve genotypes and while these markers provided reliable results they are difficult to implement for restoration practitioners without access to a genetics laboratory. We have identified biallelic single nucleotide polymorphisms (SNP) markers from deep- and shallow-sequenced Acropora genomes to genotype individuals, distinguish populations and hybrid states. From these markers, we developed a custom SNP array and an open access web portal, Standard Tools for Acroporid Genotyping (STAG), to perform an automated bioinformatics protocol to obtain genotypes. The SNP array combined with STAG will allow for reliable, standardized identification of host genotype information. In this half-day workshop, we will provide a demonstration that walks the user through the three steps: data collection, genotype analysis with STAG, and navigation of the online database. Participants will explore whether or not the database contains previous observations of their test genotypes. For genets with matches in the database, information such as where and when they were sampled and associated phenotype data can be extracted. In the future, this database can be used for the definition of management units based on genetic differentiation among genets, sites, populations, and species. Our standardized approach to genotype corals will enhance data archiving of genetic diversity across the Caribbean and can be expanded to other threatened corals.

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