Genomic Signatures of Disease Resistance in Endangered Staghorn Corals

White Band Disease (WBD) has caused unprecedented declines in the Caribbean <em>Acropora</em> corals, which are now listed as critically endangered species. Highly disease resistant <em>Acropora</em> <em> cervicornis</em> genotypes exist, but we lack understanding of the genetic underpinnings of disease resistance. Using transmission experiments, a newly assembled genome, and whole genome resequencing of 76 <em>A. cervicornis</em> genotypes from Florida and Panama, we identified ten genomic regions and 73 single-nucleotide polymorphisms (SNPs) that are strongly associated with disease resistance and that include functional, protein coding changes in four genes involved in coral immunity and pathogen detection. Polygenic scores calculated from 10 genomic loci indicate that simple genetic screens can predict <em>A. cervicornis</em> disease resistance and that adaptive polygenic variation can be used to improve disease resistance in wild and nursery stocks of <em>A. cervicornis</em> across the Caribbean.