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ARS Home » Southeast Area » Stuttgart, Arkansas » Harry K. Dupree Stuttgart National Aquaculture Research Cntr » Research » Publications at this Location » Publication #358948

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

Location: Harry K. Dupree Stuttgart National Aquaculture Research Cntr

Title: Development and enhancement of white bass Morone chrysops resources for genetic improvement of hybrid striped bass

item Abernathy, Jason
item ANDERSON, LINNEA - North Carolina State University
item Rawles, Steven - Steve
item SCHILLING, JUSTIN - North Carolina State University
item Fuller, Adam
item McEntire, Matthew - Matt
item READING, BENJAMIN - North Carolina State University
item Beck, Benjamin
item PEATMAN, ERIC - Auburn University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 2/21/2019
Publication Date: 3/11/2019
Citation: Abernathy, J.W., Anderson, L.K., Rawles, S.D., Schilling, J., Fuller, S.A., McEntire, M.E., Reading, B.J., Beck, B.H., Peatman, E. 2019. Development and enhancement of white bass Morone chrysops resources for genetic improvement of hybrid striped bass [abstract]. Aquaculture 2019, March 7-11, 2019, New Orleans, Louisana. p. 10.

Interpretive Summary:

Technical Abstract: The white bass (Morone chrysops) is a parental species of hybrid striped bass, a fish of increasing commercial importance throughout the US. Our goal is to advance progress in the genetic improvement of hybrids by building white bass resources to facilitate selective breeding for agriculturally-important traits. Toward our goal, we created a first-generation white bass genome assembly, which was accomplished using high-throughput Illumina DNA sequencing combined with Chicago and Dovetail Hi-C + HiRise scaffolding. This approach produced a 645.14 Mb genome assembly (L90 = 23 scaffolds). Scaffolds ranged in size from 32.2 Mb (scaffold 1) to 15.4 Mb (scaffold 24). A substantial drop-off in size of the next largest contiguous sequence built by this platform was observed (scaffold 25 = 27 kb), indicative that the haploid chromosomes (n=24) for white bass had largely been captured in our assembly. An initial scan of the white bass genome for functional gene products was performed using the Augustus pipeline. Ab-initio gene prediction using training sets from the Danio rerio genome produced 28,356 protein-coding genes while evidence-based prediction from alignments of the white bass transcriptomic sequences produced 24,176 protein-coding genes, for an average of 26,266 protein-coding genes within the genome. Genome size (~645 Mb) and coding content (~26 K genes) are consistent with related Moronidae striped bass and seabass. To complement our genome assembly, we generated over 2.8 billion paired-end 150 bp reads using RNA sequencing for transcriptomics studies from both tissue-specific and whole fish efforts. These additional sequences will allow for improvement of our white bass transcriptome, provide for a source of gene-associated variation and serve as a guide for annotation of the genome assembly. In addition to our sequencing efforts, wild white bass gathered from Arkansas, Texas and Alabama along with available domesticated strains are being used to establish a base breeding population for familywise evaluations of growth and nutrient utilization on alternative, sustainable diets. A genotyping-by-sequencing panel has been developed from white bass populations on station, where single-nucleotide polymorphisms (SNPs) identified can discriminate domestic stocks from wild-sourced individuals. Additional genetic markers are being developed to rapidly identify sex and parentage. The combination of these resources substantially expands the genetic toolbox for white bass, while the application toward white bass breeding will aid in its improvement through selective breeding.