SNP marker panels for parentage assignment and traceability in the Florida bass (Micropterus floridanus)

The Florida bass (Micropterus floridanus) is a species endemic to peninsular Florida that is held in high esteem by bass anglers for its tendency to attain a larger maximum size and aggressiveness relative to that of its sister taxon, the Northern largemouth bass, Micropterus salmoides. Hatchery rearing and stocking of Florida bass outside of their native range are commonplace, particularly in the southern United States. In many cases, however, there has been minimal assessment of the persistence and success of these fish. Genetic markers are an important tool for tagging and tracing the contributions of particular lines and crosses of fish. Single nucleotide polymorophism (SNP) markers, in particular, can provide rapid and affordable genotyping of large numbers of fish. In the present study, we generated 58,450 genome-wide SNPs and population-level genotypes for Florida bass using a cost-effective genotyping-by-sequencing method. A total of 58 SNPs were shown to assign parents to offspring with 100% accuracy, irrespective of sex and with the presence of full-sib relationships. Depending on the population, sex information, and genetic relationships between parents, we also demonstrated that smaller SNP subsets may be sufficient for parentage assignment. The accuracy and assignment power of the SNP panels were found to compare favorably to those of 10 microsatellites genotyped on the same parents and progeny. This study demonstrated the utility of simple and low-cost GBS techniques for SNP discovery and the relatively small number of variable SNPs needed for accurate parentage assignment in Florida bass. The SNP resources created in this study should facilitate parentage-based research and breeding, genetic tagging, and conservation of Florida bass.