Behind the Skeleton: Unraveling the Genetic Basis of Skeletal Variation in the Coral Platygyra daedalea

Abstract Environmental factors have long been recognized as the primary drivers of intraspecific morphological variation in corals, as demonstrated in numerous species. However, coral calcification is a process that depends on both environmental and biological factors. Understanding the extent to which genetics contributes to morphological variation in corals remains lacking, particularly in corals like Platygyra daedalea , a species with complex morphological variation that has been found to be neither induced environmentally nor driven by genetic divergence. To address this gap, we conducted a genome-wide association study using single-nucleotide polymorphism and phenotype data of eight skeletal traits, obtained through restriction enzyme site-associated DNA sequencing and micro-computed tomography, respectively. Here, we demonstrate that genetics contributes to the variation of specific Platygyra daedalea skeletal traits, particularly porosity ratio, interseptal distance, and septal thickness. Associated variants were located near genes involved in cell cycle regulation, ciliary function, cytoskeletal rearrangement, and skeletal protein formation. We also found some of these traits to correlate significantly with larger-scale morphological features such as valley width and valley depth, suggesting a potential influence of genetically shaped traits on broader skeletal structure.