SNP panel development for genetic management of wild and domesticated white bass (Morone chrysops)

Authors: ZHAO, HONGGANG - Auburn University; Fuller, Adam; THONGDA, WILAWAN - Auburn University; Abernathy, Jason; Beck, Benjamin; PEATMAN, ERIC - Auburn University

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/12/2018
Publication Date: 11/14/2018
Publication URL: http://handle.nal.usda.gov/10113/6277468
Citation: Zhao, H., Fuller, S.A., Thongda, W., Abernathy, J.W., Beck, B.H., Peatman, E. 2018. SNP panel development for genetic management of wild and domesticated white bass (Morone chrysops). Animal Genetics. 50(1):92-96. https://doi.org/10.1111/age.12747.
DOI: https://doi.org/10.1111/age.12747

Interpretive Summary: White bass (Morone chrysops), striped bass, and their interspecific hybrid are important game fishes, while the hybrid striped bass is an important aquaculture species in the United States. Numerous state, federal, and private hatcheries, therefore, rear these species for stocking purposes as well as food fish. While striped bass populations (both wild and domesticated) have been extensively evaluated, relatively little effort has been directed toward the study and improvement of white bass. In this study, we developed single nucleotide polymorphism (SNP) markers, a variation in a single base pair in a DNA sequence, to examine the genetic relationships among a long-term domesticated white bass line and five potential founder stocks for selective breeding collected from rivers in Arkansas, Texas, and Alabama. Using a technology called genotyping-by-sequencing (GBS), we generated 13,872 SNPs across these six populations. By using very specific statistical filtering criteria for the SNP-calling parameters, we identified 426 highly informative SNP loci. Population genetic and structure analyses using these SNPs revealed only moderate genetic differentiation between populations and indicated two major genetic clusters or groups. A final set of 57 SNPs was selected for assay design and validation using 96 additional samples. The developed SNP panels successfully assigned additional individuals to their population of origin with 100% accuracy. The SNP resources developed in this study should help ongoing efforts in selective breeding and conservation of white bass.

Technical Abstract: White bass (Morone chrysops), striped bass, and their interspecific hybrid are important game fishes, while the hybrid striped bass is an important aquaculture species in the United States. Numerous state, federal, and private hatcheries, therefore, rear these species for stocking purposes as well as food fish. While striped bass populations (both wild and domesticated) have been extensively evaluated, relatively little effort has been directed toward the study and improvement of white bass. In this study, we developed SNP resources to examine the genetic relationships among a long-term domesticated white bass line and five potential founder stocks for selective breeding collected from drainages in Arkansas, Texas, and Alabama. Using genotyping-by-sequencing (GBS), we generated 13,872 genome-wide SNP loci across the six populations. Stringent filtering of SNP-calling parameters identified 426 highly informative SNP loci. Population genetic and structure analyses using these loci revealed only moderate genetic differentiation between populations (global Fst = 0.083) and indicated two major genetic clusters. A final set of 57 SNPs was selected for assay design and validation using 96 additional samples. The developed SNP panels assigned additional genotyped individuals to their population of origin with 100% accuracy. The SNP resources developed in this study should facilitate ongoing efforts in selective breeding and conservation of white bass.