Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

Authors: Andersen, Linnea; Thompson, Neil; Abernathy, Jason; AHMED, RIDWAN - University Of Maryland; ALI, ALI - University Of Maryland; AL-TOBASEI, RAFET - University Of Maryland; Beck, Benjamin; Calla, Bernarda; Delomas, Thomas; DUNHAM, REX - Auburn University; ELSIK, CHRISTINE - University Of Missouri; Fuller, Sidney; Garcia, Julio; GAVERY, MACKENZIE - Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Servic; HOLLENBECK, CHRISTOPHER - Texas A&M University; JOHNSON, KEVIN - Scripps Institute; KUNSELMAN, EMILY - Hubbs-Sea World; Legacki, Erin; Liu, Sixin; LIU, ZHANJIANG - Tennessee Technological University; MARTIN, BRITTANY - Auburn University; MATT, JOSEPH - Texas A&M University; May, Samuel; Older, Caitlin; Overturf, Kenneth; Palti, Yniv; PEATMAN, ERIC - Harvest Select Farms; Peterson, Brian; PHELPS, MICHAEL - Washington State University; Plough, Louis; Polinski, Mark; Proestou, Dina; PURCELL, CATHERINE - Southwest Fisheries Science Center; Quiniou, Sylvie; RAYMO, GUGLIELMO - University Of Maryland; Rexroad Iii, Caird; RILEY, KENNETH - National Oceanic & Atmospheric Administration (NOAA); ROBERTS, STEVEN - University Of Washington; ROY, LUKE - Auburn University; SALEM, MOHAMED - University Of Maryland; SIMPSON, KELLY - Auburn University; Waldbieser, Geoffrey; WANG, HANPING - The Ohio State University; WATERS, CHARLES - Auke Bay Laboratories, Alaska Fisheries Science Center, National Marine Fisheries Service, National; READING, BENJAMIN - North Carolina State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/15/2025
Publication Date: 2/17/2025
Citation: Andersen, L.K., Thompson, N., Abernathy, J.W., Ahmed, R.O., Ali, A., Al-Tobasei, R., Beck, B.H., Calla, B., Delomas, T.A., Dunham, R.A., Elsik, C.G., Fuller, S.A., Garcia, J.C., Gavery, M.R., Hollenbeck, C.M., Johnson, K.M., Kunselman, E., Legacki, E.L., Liu, S., Liu, Z., Martin, B., Matt, J.L., May, S.A., Older, C.E., Overturf, K.E., Palti, Y., Peatman, E.J., Peterson, B.C., Phelps, M.P., Plough, L.V., Polinski, M.P., Proestou, D.A., Purcell, C.M., Quiniou, S., Raymo, G., Rexroad Iii, C.E., Riley, K.L., Roberts, S.B., Roy, L.A., Salem, M., Simpson, K., Waldbieser, G.C., Wang, H., Waters, C.D., Reading, B.J. 2025. Advancing genetic improvement in the omics era: status and priorities for United States aquaculture. BMC Genomics. 26:155. https://doi.org/10.1186/s12864-025-11247-z.
DOI: https://doi.org/10.1186/s12864-025-11247-z

Interpretive Summary: Dramatic technological and methodological innovations have created a plethora of scientific tools that broadly fall under the “Omics” categorization. Such tools and resources have significantly advanced United States aquaculture by producing whole genome sequences, fully annotated genomes, as well as provided the raw materials to produce many molecular tools and methods. Such rapid advancement demands robust planning and identification of pressing opportunities and challenges that will further advance the United States aquaculture industry and the genetics, genomics and breeding research community. The topic of this paper is the identification of priority topics that are intended to facilitate the continued advancement of aquaculture and spur continued development within the aquaculture genomics, genetics and breeding research community. The priorities, ideas and suggestions described here were developed from Workshop for Aquaculture Genomics, Genetics, and Breeding researchers held in Raleigh, North Carolina in May 2023 organized, supported and hosted by the National Research Support Project 8 (NRSP8, National Animal Genome Research Program, NAGRP) Aquaculture species group. The research products within this paper will be used to guide future study topics and efforts within aquaculture genetics, genomics and breeding as well as facilitate inter-disciplinary studies that are vital to fully realize the power afforded by ‘Omics tools currently available, and those that will continue to be developed considering the highlighted priorities identified herein.

Technical Abstract: The technological and methodological innovations of the “Omics Era” have ushered in significant advancements in genetic improvement of agriculturally important animal species through transforming genetics, genomics and breeding strategies. Specifically, the availability of well-annotated, whole genome sequences and associated molecular markers has facilitated gene-by-environment interaction studies, genome-wide association studies, genomic selection, marker-assisted selection, gene editing, genotype-to-phenotype studies, population structure analysis, and demographic monitoring. These advancements were coordinated with support from the 1993-2023 National Research Support Project 8 (NRSP8) as well as the USDA Agricultural Research Service and USDA National Institute of Food and Agriculture. The significant, parallel advances made in genetics, genomics and breeding under these initiatives demand strategic planning of future research priorities. This paper is an output from the May 2023 Workshop for Aquaculture Genomics, Genetics, and Breeding researchers held in Raleigh, North Carolina. Considerable progress in genome research for finfish and shellfish species has generated omics resources that enhance our understanding of genetic architectures and heritabilities. The 2023 Workshop identified multiple aims for aquaculture genomics/omics research: 1) Advancing reference genome assembly quality; 2) Integrating multi-omics data to enhance analysis of production and performance traits; 3) Developing resources for the collection and integration of phenomics data; 4) Creating pathways for applying and integrating genomics information across animal industries; and 5) Providing training, extension, and outreach to support the application of genome to phenome in aquaculture. Research focuses should emphasize phenomics data collection, identifying causative relationship between genotypes and phenotypes, establish pathways to apply genomic information and applications across aquaculture industries, and expansion of training programs for the next-generation workforce to integrate genomic sciences into aquaculture operations, thereby enhancing productivity, competitiveness, and sustainability. A collective vision of applying genomics within aquaculture breeding and the highlighted priorities are intended to facilitate the continued advancement of the United States aquaculture industry and genomics, genetics and breeding research community. Critical challenges ahead include the commercial application of genomic tools and analytical frameworks. The scope of this project encompasses the use of omics tools and applications in the study of aquatic animals cultivated for human consumption in aquaculture settings throughout their lifecycle.