Progress 07/01/24 to 06/30/25
Outputs
Target Audience:This research is aimed at the finfish aquaculture scientific community and related industry partners. While the work is primarily focused on fundamental science, it carries strong potential for practical applications in the aquaculture sector. The findings will deepen our overall understanding of fish growth and environmental physiology, with an emphasis on trout and salmon species. These insights can inform selective breeding initiatives for these and other aquaculture species, ultimately supporting the expansion of finfish seafood production. Changes/Problems:A significant challenge was identified during this reporting period that needed to be solved. Originally, when we developed the project we believed that making our quota of gene-edited fish would be the primary challenge for the research but we determined this year that we are much more capable of gene editing than we expected and that phenotyping the fish would be our primary obstacle to accomplishing our goals. This required the majority of the reporting period to overcome, as we had to develop completely new and innovative solutions to taking measurements on fish, including the use of AI computer vision analysis, something that was relatively new to our lab. Because we hit a bottleneck in our phenotyping, our production of new gene-edited lines was slowed, but now we are at full pace and beginning to ramp back up our production of novel animal models. We are now on pace to meet or even exceed our expectations for model system generation. What opportunities for training and professional development has the project provided?The project provided extensive training opportunities for graduate students, postdoctoral researchers, and undergraduate students. This included teaching students advanced molecular biology, CRISPR genome editing technology, and transgenesis. Students were also introduced to new physiology techniques such as respirometry and cardiovascular physiology experiments (e.g., ECGs). They were able to acquire significant knowledge of current aquaculture techniques through direct hands-on experience working with fish. How have the results been disseminated to communities of interest?We presented the findings of our current research at the Plant and Animal Genome Conference in San Diego, the Triennial Aquaculture meeting in New Orleans, and the Coastwide Salmon Genetics meeting in Anchorage. The results of our research have also been shared directly with salmon and trout aquaculture producers who have a vested interest in the project and help support our research. What do you plan to do during the next reporting period to accomplish the goals?The next reporting period will be an exciting time when our first gene-edited trout lines start to become mature and we are able to fully ramp up our phenotyping pipeline. We expect to identify new novel genetic traits in trout that have never previously been identified, which could help advance US aquaculture production.
Impacts
What was accomplished under these goals?
The past project year was a turning point for the project. We were able to develop a challenging phenotyping workflow that will enable use to rapidly exploit our genome editing capabilities which far exceeded what we believed was possible. To accomplish this we had to develop innovative AI image analysis platforms and high-throughput phenomics pipelines that have not been in place in the field. In addition to developing these experimental pipelines we had our first functional hits from our each CRISPR gene editing screens. We were also able to identify a family of genes (egln1-3) that have an important role in the response of trout to hypoxia stress. These model fish may provide important information on how to develop trout lines that can tolerate acute drops in dissolved oxygen during culture conditions.
Publications
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Progress 07/01/23 to 06/30/24
Outputs
Target Audience:The target audience for the research is the finfish aquaculture scientific community and industry groups. The research is basic science in nature with significant potential for downstream applications in the aquaculture industry. The discoveries made in the research will advance our general understanding of fish growth and environmental physiology with specific focus on trout and salmon species. The insights we gain can be applied to selective breeding programs for these and other aquaculture species, helping to increase finfish seafood production. Changes/Problems:We have made one strategy change to speed the pace of research and obtain results faster than originally proposed. Instead of growing the gene edited lines to adulthood and cloning their offspring we will use high-efficiency gene editing to edit the F0 generation and assess the phenotypes in new juveniles. This will allow us to produce results in months rather than years but the pace of making the 1000 edits will be more gradual because we need to make many more families to reach this goal. Overall though, by the end of the research we believe this new strategy will allow us to make many more edited fish than was previously planned. What opportunities for training and professional development has the project provided?The research has provided abundant opportunities for the training of students and for their professional development. Both undergraduate and graduate students have been involved in the research as well as postdoctoral researchers. They are not only learning advanced genetic engineering skills but also how to manage fish in an aquaculture setting. The project has also provided support for student travel to network and improve collaboration since the project benefits significantly from the expertise of general aquaculture community. How have the results been disseminated to communities of interest?We have communicated the results at numerous scientific meetings, such as the Aquaculture America Conference, the Plant and Animal Genome Conference, and the International Conference on Integrated Salmon Biology in 2023/2024. The research has also been discussed with the two largest producers of rainbow trout in the naition, Troutlodge and Riverence. What do you plan to do during the next reporting period to accomplish the goals?In the next reporting period we will begin to produce high-throughput phenotypes of the genome-edited lines to identify high-performing families. This will be conducted on the lines that we currently have as well as new lines that we create in the new year. We estimate that we will at least be able to double the number of lines we have produced thus far with the goal of reaching 500 edits by years end. These experiments will continue to train students in advanced genetic engineering, fish physiology, as well as aquaculture production.
Impacts
What was accomplished under these goals?
In the first year of the project we have established the foundation for rapid expansion of our genome-edited lines to meet the objectives to edit 1000 genetic loci. We have so far created approximately 200 edits in 100 unique genetic lines. After initiating the research we realized that our original plan to breed out broodstock and clone their offspring would take many years to provide results so we have adjusted our focus and are now focusing on less edits per individual family but many more families. Instead of waiting for F1 offspring from each family, our new strategy allows us to have high editing efficiency in the F0 generation and we can assess phenotypes in large numbers of juveniles within months instead of years. This will mean that the number of families produced will be more gradual than originally proposed but in the end we will likely be able to produce significantly more gene edits than we originally proposed and the impact of the research will be much greater.
Publications
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