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ARS Home » Southeast Area » Stuttgart, Arkansas » Harry K. Dupree Stuttgart National Aquaculture Research Cntr » Research » Publications at this Location » Publication #368823

Research Project: Developing Nutritional, Genetic, and Management Strategies to Enhance Warmwater Finfish Production

Location: Harry K. Dupree Stuttgart National Aquaculture Research Cntr

Title: SNP discovery and panel development for genetic identification and hybridization analysis in walleye Sander vitreus

item ZHAO, HONGGANG - Auburn University
item LEWIS, MATTHEW - Auburn University
item SILLIMAN,, KATHERINE - Auburn University
item JOHNSON, SARAH - Auburn University
item KRATINA, GARRET - Auburn University
item RIDER, STEVE - Alabama Wildlife And Freshwater Fisheries
item STEPIEN, CAROL - National Oceanic & Atmospheric Administration (NOAA)
item HALLERMAN, ERIC - Virginia Tech
item Beck, Benjamin
item Fuller, Adam
item PEATMAN, ERIC - Auburn University

Submitted to: Genbank
Publication Type: Database / Dataset
Publication Acceptance Date: 9/24/2019
Publication Date: 4/20/2020
Citation: Zhao, H., Lewis, M., Silliman,, K., Johnson, S., Kratina, G., Rider, S.J., Stepien, C.A., Hallerman, E.M., Beck, B.H., Fuller, S.A., Peatman, E. 2020. SNP analyses highlight a unique, imperiled southern walleye (Sander vitreus) in the Mobile River Basin. Genbank Accession No. SOZC00000000.

Interpretive Summary:

Technical Abstract: Walleye (Sander vitreus) is a freshwater species inhabiting a wide range of habitats across North America. Owing to its economic importance and popularity as a sportfish, this species has been widely introduced beyond its indigenous range. Previous genetic studies have revealed a genetically distinct strain of walleye in Mobile River Basin drainages, but little is known about its genetic structure and how this southern strain relates to northern walleye populations. Another unresolved question is the hybridization status of walleye in Mobile River Basin following northern walleye introductions. In this study, we used genotyping-by-sequencing (GBS) data from 60 walleye individuals to infer genetic diversity and structure among northern and southern (Mobile River Basin) walleye populations. Genetic assessment with 2,782 GBS SNPs confirmed a unique genomic pattern in southern walleye group (FST = 0.805 vs. northern Lake Erie walleye). We also found strong evidence for a historical declining population trend with reduced genetic diversity and effective population size in a southern walleye population spawning in Hatchet Creek, Alabama. Additionally, a SNP assay with 68 diagnostic markers was developed for rapid and accurate identification of genetic purity and classification of various (northern/southern) hybrid classes among walleye individuals. Utilizing this SNP assay, we genotyped an additional 545 walleye individuals across 23 populations and characterized broad-scale genetic structure, distinguishing three groups comprised of the Mobile River Basin, Great Lakes/upper Mississippi, and southern Ohio drainage populations. Using both GBS and SNP assay data, we demonstrated that a suite of 68 SNPs could collectively classify advance-generation hybrids and enable us to identify an anthropogenic hybrid zone resulting from the previous introduction of northern walleye into the Black Warrior River. Our results highlight the need for further characterization and conservation management of southern walleye in Mobile River Basin, with our 68-SNP assay already being implemented in ongoing stream survey and captive breeding programs. Raw Illumina reads for walleye genotyping by sequencing (GBS) archived to the public database: National Center for Biotechnology Information - Sequence Read Archive (NCBI-SRA) under BioProject accession number PRJNA555395.