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

Authors: ZHAO, HONGGANG - Auburn University; LI, CHAO - Qingdao Agricultural University; HARGROVE, JOHN - University Of Florida; BOWEN, BR - Department Of Natural Resources; THONGDA, WILAWAN - Auburn University; ZHANG, DONGDONG - Auburn University; MOHAMMED, HAITHAM - Auburn University; Beck, Benjamin; AUSTIN, JD - University Of Florida; PEATMAN, ERIC - Auburn University

Submitted to: Aquaculture
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/8/2017
Publication Date: 11/9/2017
Citation: Zhao, H., Li, C., Hargrove, J.S., Bowen, B., Thongda, W., Zhang, D., Mohammed, H., Beck, B.H., Austin, J., Peatman, E. 2017. SNP marker panels for parentage assignment and traceability in the Florida bass (Micropterus floridanus). Aquaculture. 485:30-38.

Interpretive Summary: The Florida bass (Micropterus floridanus) is a species native to peninsular Florida that is highly popular with recreational anglers for its tendency to attain a larger maximum size than its closely related sister species, the Northern largemouth bass, Micropterus salmoides. Stocking of Florida bass outside of their native range is 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 polymorphism (SNP) markers, in particular, can provide rapid and affordable genotyping of large numbers of fish. In this study, using a cost-effective genotyping-by-sequencing (GBS) method we found a total of 58 SNPs that were shown to assign parents to offspring with 100% accuracy, regardless of sex. Depending on the population, sex information, and genetic relationships between parents, we also demonstrated that smaller SNP subsets may be sufficient for parentage assignment. This study demonstrated the utility of this new and low-cost technique for SNP discovery. The SNP resources created in this study will facilitate research on the breeding, production for food, genetic selection, and conservation of Florida bass.

Technical Abstract: 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 than its sister taxon, the Northern largemouth bass, Micropterus salmoides. Stocking of Florida bass outside of their native range is 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 58,495 genome-wide SNPs and population-level genotypes for Florida bass using a cost-effective genotyping-by-sequencing (GBS) method. A total of 58 SNPs (run on two multiplexed Agena MassARRAY panels) 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 developed SNP marker 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.