Submitted to: National Center for Biotechnology Information (NCBI)
Publication Type: Database / Dataset
Publication Acceptance Date: 4/10/2017
Publication Date: 3/28/2018
Citation: Abernathy, J.W., Fuller, S.A. 2018. Hepatic gene expression analysis between low and high growing hybrid striped bass. National Center for Biotechnology Information (NCBI). Accession # GSE97547.
Technical Abstract: Hybrid striped bass (HSB), produced from a cross between white bass (Morone chrysops) and striped bass (Morone saxatilis) represent a significant market for US aquaculture. One of the major constraints to an increase in production and profitability of producers arises from the variation in growth observed when rearing these fish to market size. We therefore set out to study the genetics behind growth variation in HSB. Domesticated F8 white bass and F4 striped bass were bred in a partial diallel breeding design to create HSB and reared in replicate family tanks until large enough to tag with a PIT tag. Thirty-two fish from each of 44 half-sib families were tagged and initial length and weight was recorded before being randomly assigned to one of four 0.04 hectare communal ponds resulting in 5632 individually tagged fingerlings. Fish were allowed to grow for 115 days prior to harvest. At harvest tags were scanned to reveal family of origin, final length and weight were taken. The largest and smallest HSB were sacrificed and liver samples taken. Equimolar amounts of total RNA were pooled from the extreme fish for high-throughput Illumina RNA sequencing. Raw sequence reads were screened for quality then aligned to a de novo assembled HSB liver transcriptome. Read-counts were compiled from sequence alignments and used to assess differential gene expression between low growing (small) and fast growing (big) HSB. Raw sequencing data, the HSB liver transcriptome, read-count information and a complete description of computational methods have been made available to the public at the NCBI GEO database under the accession number GSE97547.