Performing Department
(N/A)
Non Technical Summary
The Decode the Salmonid Genome Project is a major research effort aimed at better understanding how changes in the genetic code in animals can influence biological traits. This knowledge will imporove the selection of higher producing agricultural animals that can produce more food on less feed and with less impact on the environment. Insight in to how the genome functions could also improve our understanding of animal and human health as well as how to better protect our precious natural species from biological or environmental threats. Unfortunately, our ability to characterize genome function in animals is currently limited by the time and resources required to make changes to the genetic code and then measure their effect on the whole organism. To overcome this limitation, the Decode the Salmonid Genome Project will use advances in CRISPR genome editing technology and a unique agricultural model system, the rainbow trout, to perform the first large-scale profiling of the genome in an agricultural species. The research aims to evaluate the function of over 1000 locations in the trout genome to gain insight into regions that are important for the growth of animals and their ability to tolerate high temperatures and low oxygen levels. To accomplish this, trout families will be engineered with CRISPR genome editing technology to have multiple genetic modifications (4-12). Numerous families will be produced to create a mixed population with over 1000 genetically modified locations. High and low performing families will then be identified using a high-throughput screening process that assesses the growth, thermal tolerance and hypoxia tolerance of each family. This will allow us to rapidly identify genetic changes that influence these key biological traits of interest.Through this effort, a National Resource of gene edited fish will be produced that contain unique genetic changes which can be studied by future interested research groups. The gene edited lines will form the foundation for more advanced studies investigating the interaction of these genetic changes on complex biological traits, something that is difficult or impossible to perform using current methods. The model systems produced in this research will also likely contain many novel production traits that can be identified and selected for to improve the genetics of US cultured salmon and trout species. Taken together the research will fundamentally advance our understanding of salmon and trout biology and the genetics underlying important aquaculture traits while also providing knowledge of conserved biological mechanisms that could have broader impacts on other agricultural sectors or even human health.
Animal Health Component
0%
Research Effort Categories
Basic
60%
Applied
20%
Developmental
20%
Goals / Objectives
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.
Project Methods
The novelty of the research hinges on our unique approach to genome edit rainbow trout at a scale not previously attempted. Currently, genetic studies are performed by systematically evaluating one gene at a time. While this approach is good for evaluating individual traits it is not effective at profiling large numbers of genomic features and requires extensive time and resources to complete. To overcome this obstacle we have developed a method to simultaneously edit numerous alleles in a single individual at low efficiency. This approach will be used to create numerous gene edited families, each containing multiple genetic modifications totaling over 500 unique modifications. The modifications will be focused on genes involved in growth or environmental resilience to produce at total of over 1000 genetic modifications. The research seeks to create these 1000 genetic modifications within the first year of the research by microinjecting thousands of rainbow trout eggs donated by local aquaculture farms.The founder animals that are created from the gene edited families will be grown to adulthood and the gametes used to produce offspring. A subset of individuals from each family will be cloned to produce homozygous individuals. Homozygous individuals from each family will be included in two large-scale phenotypic screens to identify genotypes that 1) improve or reduce growth or 2) increase or decrease thermal or hypoxia tolerance. These studies will be performed on over 800 size and age matched individuals with appropriate controls. The families that are identified through the phenotypic screen will be fully characterized to determine the molecular mechanisms underlying the phenotypic trait. By making crosses between gene edited families it will be possible in future generations to perform additional phenotypic screens to define the interaction of gene edited alleles to begin to evaluate the genetics of potential polygenic or additive traits.