Transcriptomic response and gene co-expression network analyses of white bass (Morone chrysops) after being fed protein substitution diets toward a more sustainable aquaculture

Authors: MULIYA SANKAPPA, NITHIN - Orise Fellow; Fuller, Adam; Rawles, Steven - Steve; Green, Bartholomew - Bart; ROSENTRATER, KURT - Iowa State University; McEntire, Matthew - Matt; Huskey, George; Beck, Benjamin; Webster, Carl; Abernathy, Jason

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 11/6/2023
Publication Date: 1/11/2024
Citation: Muliya Sankappa, N., Fuller, S.A., Rawles, S.D., Green, B.W., Rosentrater, K., Mcentire, M.E., Huskey Jr, G., Beck, B.H., Webster, C.D., Abernathy, J.W. 2024. Transcriptomic response and gene co-expression network analyses of white bass (Morone chrysops) after being fed protein substitution diets toward a more sustainable aquaculture. Meeting Abstract[abstract].

Interpretive Summary:

Technical Abstract: In the United States, white bass (Morone chrysops) are a common sportfish and one of the parental species of the commercially-successful hybrid striped bass (M. chrysops x M. saxatilis; HSB). Currently, largemouth bass (LMB; Micropterus salmoides) or HSB are raised on diets that include a substantial amount of marine fish meal (FM). In this study, we assessed variation in gene expression of white bass fed diets in which FM was partially or completely replaced by various combinations of soybean meal, poultry by-product meal, canola meal, soy protein concentrate, wheat gluten, or a commercial protein blend (Pro-CisionTM). Using information on nutritional availability for most of the dietary components, six isonitrogenous (40% protein), isolipidic (11%), and isocaloric (17.1 kJ/g) diets were created to satisfy the known nutrient and energy needs of LMB and HSB. One of the test diets was made up entirely of sources of plant protein. The test diets were fed to satiation twice daily for 60 days to juvenile white bass (40.2 g beginning weight), which were stocked into a flow-through aquaculture system (3 tanks/diet; 10 fish/tank). There were no studies regarding the utilization of alternative proteins in this species and analysis of their differentially expressed genes (DEGs). To generate DEGs, liver tissues from white bass fed each of the five test diets or control diet (n=9 biological replicates each diet) were sent for Illumina sequencing at depth of 25 M reads each sample with 150 bp paired-end configuration. Sequencing reads were assessed for quality control and then aligned to the white bass transcriptome for pairwise comparisons between treatments (diet). When compared to the FM control, RNA sequencing (RNAseq) and bioinformatic analyses of all test diets identified substantial DEGs. A total of 1,260 DEGs were found, with main gene ontologies identified as cell cycle, metabolic, and immunological gene activities. Next, RNAseq data underwent additional systems analyses to both (a) generate gene co-expression networks and (b) infer gene regulatory networks. Results from network analyses were used to both prioritize our list of potential candidate genes and pinpoint master regulators (hub genes) associated with FM replacement in this species. As the availability of marine fish meal decreases and more plant-based ingredients are used as dependable sources of protein, this information will be helpful as a resource for future modifications to the composition of diets fed to moronid species. Significant results from global gene expression analyses and gene network analyses will be presented and discussed.