Expanding the Toolbox: SNP Tools for Aquaculture and Conservation Management in the Eastern Oyster (Crassostrea virginica) and the Black Basses (Micropterus spp.)

Abstract

Single nucleotide polymorphisms (SNPs) are considered as important molecular markers due to their several advantages, including their abundance, distribution in the genome, stability due to low mutation rates, ease of multiplexing, lower cost, amenability to high throughput assays, and low genotyping error rate. The rapid development of technology for SNPs has provided an efficient and cost-effective genetic marker tool for aquaculture and aquatic conservation in recent years for various purposes such as the determination of the population structure, population genomics, traceability, species identification, hybridization rates, and migratory dynamics. Here, relevant aspects of the Eastern oyster (Crassostrea virginica) and black basses (Micropterus spp.), key aquatic species in the southeastern United States, are examined. Culture of the Eastern oyster is rapidly expanding. Combined with their continuing role as an environmental sentinel species and ecological model, this trend necessitates improved molecular tools for breeding and selection, as well as population assessment and genetic conservation. The development and validation of two panels of 58 SNPs for the species are described. Population analyses revealed three distinct populations, based upon FST values and STRUCTURE, among wild oysters sampled from Delaware Bay (1), Northwest Florida (2), Alabama (2), Louisiana (2), and the Texas Gulf Coast (3), consistent with previous microsatellite and mtDNA analyses. In addition, utilizing the developed panels for parentage assignment in cultured oysters resulted in highly accurate parent-offspring pairing (99.37%). The SNP. markers could, furthermore, clearly discriminate between hatchery stocks and wild-sourced individuals Black basses are apex predators in North American streams, rivers, and lakes and are important game fishes. Translocation and introductions for angling, accompanied by intrinsically weak genetic barriers, have led to widespread introgressive hybridization and genetic swamping. Species-diagnostic (fixed allele) SNP markers have been utilized successfully in salmonids to monitor hybridization and maintain genetic integrity. Here, similar resources for black basses through initial genotyping-by-sequencing (GBS), followed by extensive validation in additional samples using two panels of 64 SNPs, were developed. Results from >1300 genotyped bass indicated that the developed panels robustly and clearly delineate the majority of species and their hybrids among black basses.