This Is AuburnElectronic Theses and Dissertations

Genetic Resources for Improved Selection and Management of Aquaculture and Conservation Fish Species




Zhao, Honggang

Type of Degree

PhD Dissertation


Fisheries and Allied Aquacultures


Molecular markers are versatile tools for conservation genetics allowing the identification of populations in genetic crisis, resolving taxonomic uncertainties, and establishing management units within fish species. Advances in biotechnologies have enabled SNP discovery and genotyping in a cost-effective and parallel manner. At the same time, huge progress has been achieved for high-throughput SNP genotyping and marker applications thanks to the introduction of assay-based genotyping platforms. Here, I describe SNP discovery and panel development in three key aquatic species in the southeastern United States: Florida bass (Micropterus floridanus), white bass (Morone chrysops), and walleye (Sander vitreus). Florida bass are arguably the most important freshwater sportfish in North America. In my first study, I carried out genotyping-by-sequencing (GBS) and developed SNP panels for Florida bass parentage assignment. Parentage analysis demonstrated that the developed marker panels were capable of accurate parentage assignment and are more powerful than existing microsatellite tools for the species. The SNP resources created in this study should facilitate parentage-based research and breeding, genetic tagging, and conservation of Florida bass. White bass are temperate bass species with high commercial and ecological value in North America. Population structure analyses using GBS data revealed two distinct genetic clusters among a domesticated white bass line and five potential founder stocks. Additionally, a 57-SNP assay was successfully developed to assign bass individuals back to their origin populations. The developed panels should augment ongoing efforts toward white bass conservation and selective breeding. Walleye are ecologically and economically important fish found in freshwater river and lake systems in North America. Southern walleye in Mobile River Basin were previously identified as a long-isolated lineage that genetically diverged from other walleye populations in North America. Here, I utilized GBS data to infer genetic diversity and structure among northern and southern walleye populations. Additionally, a SNP assay with 68 diagnostic markers was developed for rapid and accurate identification of genetic purity and classification of various hybrid classes. The availability of high-quality GBS datasets and a large set of diagnostics SNPs should greatly facilitate conservation and population genomics studies in this key species.