DECODING THE SALMONID GENOME PROJECT: A NATIONAL RESOURCE FOR THE LARGE-SCALE FUNCTIONAL CHARACTERIZATION OF GENOMIC ELEMENTS USING GENE EDITED RAINBOW TROUT

The central goal of the research is to establish one of the first CRISPR-based genetic screens in an agricultural animal to identify the function of over 1000 genomic features in Rainbow Trout (Oncorhynchus mykiss). The research will create a national resource of gene edited fish to "Decode the Salmonid Genome" by producing fish with characterized novel genotypes that can be used by the agricultural and basic science communities to better understand the link between genotype and phenotype. The project will focus on editing genes, non-coding RNAs, associated single nucleotide polymorphisms, and regulatory sequences to gain insight into the complex biology associated with growth and environmental resilience in trout. If successful, the project will dramatically increase the number of characterized functional elements in trout and establish the precedent for expansion of new genome edited fish lines. The genome edited fish generated in the research will not only establish the technology for large-scale functional characterization of the initial 1000 genetic features but also provide generations of research into novel genetic combinations underlying complex polygenic traits. The research will address two specific objectives to accomplish the central research goal:Objective 1: Profile 500 genomic elements involved in RBT somatic growth. This objective will create rainbow trout with genetic modifications in over 500 growth associated genes to gain insight into the factors regulating body and tissue size in vertebrates. A large phenotypic screen assessing somatic growth will be performed on the gene edited fish to identify alleles that increase or decrease growth in trout.Objective 2: Screen 500 RBT genomic features for improved environmental resilience. The ability of cultured fish to thrive under a variety of conditions is a key goal of aquaculture producers. Objective 2 will investigate the genetic factors underlying this likely polygenic trait by creating over 500 genetic modifications across numerous trout families. The performance of these families in adverse thermal and hypoxic environmental conditions will be evaluated to identify genetic features that influence environmental resilience in trout.