Virginia leads the nation in production of aquacultured hard clams, Mercenaria mercenaria (Linnaeus, 1758), with an estimated farm gate value of $38.8 million in 2018. Despite the high economic value, there are few genomic resources available to support the hard clam aquaculture industry.

To develop effective genetic tools for industry, it is important to first understand population structure. Hard clams have a pelagic larval phase that allows for dispersal, but the level of genetic connectivity is not well understood. This study uses genotyping-by-sequencing to delineate the genetic stock structure of wild clams sampled along the East Coast of North America. Samples were collected from 15 locations from Prince Edward Island, Canada, to South Carolina, USA. Following DNA isolation, 452 individuals were sequenced and 153,842 single nucleotide polymorphisms (SNPs) were identified. The SNP loci were filtered for quality control and subsequently analyzed to delineate population structure and quantify levels of genetic divergence among populations. Data provides evidence of several genetically distinct populations with more structure than previously recognized. Data will be used to identify a subset of SNP markers capable of geographic discrimination and population assignment, and these will be tested on wild and hatchery clams to confirm their utility. The validated loci will be available as an assay panel that is tailored to address industry needs, such as tracking hatchery lines, monitoring genetic variation, and differentiating among wild and hatchery clams and among hatchery lines.