Review

. 2025 Feb 17;26(1):155.

doi: 10.1186/s12864-025-11247-z.

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

Linnea K Andersen^#¹, Neil F Thompson^#², Jason W Abernathy¹, Ridwan O Ahmed³, Ali Ali³, Rafet Al-Tobasei⁴, Benjamin H Beck¹, Bernarda Calla⁵, Thomas A Delomas⁶, Rex A Dunham⁷, Christine G Elsik⁸, S Adam Fuller⁹, Julio C García¹, Mackenzie R Gavery¹⁰, Christopher M Hollenbeck^{11

12}, Kevin M Johnson^{13

14}, Emily Kunselman¹⁵, Erin L Legacki¹⁶, Sixin Liu¹⁷, Zhanjiang Liu¹⁸, Brittany Martin¹, Joseph L Matt¹², Samuel A May¹⁶, Caitlin E Older¹⁹, Ken Overturf²⁰, Yniv Palti¹⁷, Eric J Peatman²¹, Brian C Peterson¹⁶, Michael P Phelps²², Louis V Plough^{5

23}, Mark P Polinski¹⁶, Dina A Proestou⁶, Catherine M Purcell²⁴, Sylvie M A Quiniou¹⁹, Guglielmo Raymo³, Caird E Rexroad²⁵, Kenneth L Riley²⁶, Steven B Roberts²⁷, Luke A Roy²⁸, Mohamed Salem³, Kelly Simpson¹, Geoffrey C Waldbieser¹⁹, Hanping Wang²⁹, Charles D Waters³⁰, Benjamin J Reading³¹; Aquaculture Genomics, Genetics and Breeding Workshop

Affiliations

¹ USDA-ARS Aquatic Animal Health Research Unit, Auburn, AL, USA.
² USDA-ARS Pacific Shellfish Research Unit, Newport, OR, USA. neil.thompson@usda.gov.
³ Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
⁴ Middle Tennessee State University, Murfreesboro, TN, USA.
⁵ USDA-ARS Pacific Shellfish Research Unit, Newport, OR, USA.
⁶ USDA-ARS National Cold Water Marine Aquaculture Center, Kingston, RI, USA.
⁷ School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL, USA.
⁸ University of Missouri, Columbia, MO, USA.
⁹ USDA-ARS Harry K Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, USA.
¹⁰ Environmental and Fishery Sciences Division, NOAA Northwest Fisheries Science Center, Seattle, WA, USA.
¹¹ Texas A&M AgriLife Research, College Station, TX, USA.
¹² Texas A&M University - Corpus Christi, Corpus Christi, TX, USA.
¹³ California Sea Grant, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
¹⁴ Biological Sciences Department, Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA, USA.
¹⁵ Hubbs-SeaWorld Research Institute, San Diego, CA, USA.
¹⁶ USDA-ARS National Cold Water Marine Aquaculture Center, Orono, ME, USA.
¹⁷ USDA-ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA.
¹⁸ Department of Biology, Tennessee Technological University, Cookeville, TN, USA.
¹⁹ USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, MS, USA.
²⁰ USDA-ARS Small Grains and Potato Germplasm Research, Hagerman, ID, USA.
²¹ Harvest Select Catfish Inc, Inverness, MS, USA.
²² Washington State University, Pullman, WA, USA.
²³ Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, USA.
²⁴ NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, CA, USA.
²⁵ USDA-ARS Office of National Programs, Beltsville, MD, USA.
²⁶ Office of Aquaculture, NOAA Fisheries, Silver Spring, MD, USA.
²⁷ University of Washington, Seattle, WA, USA.
²⁸ School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Alabama Fish Farming Center, Greensboro, AL, USA.
²⁹ The Ohio State University, Columbus, OH, USA.
³⁰ NOAA Alaska Fisheries Science Center Auke Bay Laboratories, Juneau, AK, USA.
³¹ Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA.

^# Contributed equally.

PMID: 39962419
PMCID: PMC11834649
DOI: 10.1186/s12864-025-11247-z

Review

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

Linnea K Andersen et al. BMC Genomics. 2025.

. 2025 Feb 17;26(1):155.

doi: 10.1186/s12864-025-11247-z.

Authors

Affiliations

¹ USDA-ARS Aquatic Animal Health Research Unit, Auburn, AL, USA.
² USDA-ARS Pacific Shellfish Research Unit, Newport, OR, USA. neil.thompson@usda.gov.
³ Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
⁴ Middle Tennessee State University, Murfreesboro, TN, USA.
⁵ USDA-ARS Pacific Shellfish Research Unit, Newport, OR, USA.
⁶ USDA-ARS National Cold Water Marine Aquaculture Center, Kingston, RI, USA.
⁷ School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL, USA.
⁸ University of Missouri, Columbia, MO, USA.
⁹ USDA-ARS Harry K Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, USA.
¹⁰ Environmental and Fishery Sciences Division, NOAA Northwest Fisheries Science Center, Seattle, WA, USA.
¹¹ Texas A&M AgriLife Research, College Station, TX, USA.
¹² Texas A&M University - Corpus Christi, Corpus Christi, TX, USA.
¹³ California Sea Grant, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
¹⁴ Biological Sciences Department, Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA, USA.
¹⁵ Hubbs-SeaWorld Research Institute, San Diego, CA, USA.
¹⁶ USDA-ARS National Cold Water Marine Aquaculture Center, Orono, ME, USA.
¹⁷ USDA-ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA.
¹⁸ Department of Biology, Tennessee Technological University, Cookeville, TN, USA.
¹⁹ USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, MS, USA.
²⁰ USDA-ARS Small Grains and Potato Germplasm Research, Hagerman, ID, USA.
²¹ Harvest Select Catfish Inc, Inverness, MS, USA.
²² Washington State University, Pullman, WA, USA.
²³ Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, USA.
²⁴ NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, CA, USA.
²⁵ USDA-ARS Office of National Programs, Beltsville, MD, USA.
²⁶ Office of Aquaculture, NOAA Fisheries, Silver Spring, MD, USA.
²⁷ University of Washington, Seattle, WA, USA.
²⁸ School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Alabama Fish Farming Center, Greensboro, AL, USA.
²⁹ The Ohio State University, Columbus, OH, USA.
³⁰ NOAA Alaska Fisheries Science Center Auke Bay Laboratories, Juneau, AK, USA.
³¹ Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA.

^# Contributed equally.

PMID: 39962419
PMCID: PMC11834649
DOI: 10.1186/s12864-025-11247-z

Erratum in

Correction: Advancing genetic improvement in the omics era: status and priorities for United States aquaculture.
Andersen LK, Thompson NF, Abernathy JW, Ahmed RO, Ali A, Al-Tobasei R, Beck BH, Calla B, Delomas TA, Dunham RA, Elsik CG, Fuller SA, García JC, Gavery MR, Hollenbeck CM, Johnson KM, Kunselman E, Legacki EL, Liu S, Liu Z, Martin B, Matt JL, May SA, Older CE, Overturf K, Palti Y, Peatman EJ, Peterson BC, Phelps MP, Plough LV, Polinski MP, Proestou DA, Purcell CM, Quiniou SMA, Raymo G, Rexroad CE, Riley KL, Roberts SB, Roy LA, Salem M, Simpson K, Waldbieser GC, Wang H, Waters CD, Reading BJ; Aquaculture Genomics, Genetics and Breeding Workshop. Andersen LK, et al. BMC Genomics. 2025 Mar 17;26(1):260. doi: 10.1186/s12864-025-11447-7. BMC Genomics. 2025. PMID: 40098073 Free PMC article. No abstract available.

Abstract

Background: The 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. These advancements were often coordinated, in part, by support provided over 30 years through the 1993-2023 National Research Support Project 8 (NRSP8, National Animal Genome Research Program, NAGRP) and affiliate projects focused on enabling genomic discoveries in livestock, poultry, and aquaculture species. These significant and parallel advances demand strategic planning of future research priorities. This paper, as an output from the May 2023 Aquaculture Genomics, Genetics, and Breeding Workshop, provides an updated status of genomic resources for United States aquaculture species, highlighting major achievements and emerging priorities.

Main text: Finfish and shellfish genome and omics resources enhance our understanding of genetic architecture and heritability of performance and production traits. The 2023 Workshop identified present aims for aquaculture genomics/omics research to build on this progress: (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. Research focuses should emphasize phenomics data collection, artificial intelligence, identifying causative relationships between genotypes and phenotypes, establishing pathways to apply genomic information and tools across aquaculture industries, and an expansion of training programs for the next-generation workforce to facilitate integration of genomic sciences into aquaculture operations to enhance productivity, competitiveness, and sustainability.

Conclusion: This collective vision of applying genomics to aquaculture breeding with focus on the highlighted priorities is intended to facilitate the continued advancement of the United States aquaculture genomics, genetics and breeding research community and industries. Critical challenges ahead include the practical application of genomic tools and analytical frameworks beyond academic and research communities that require collaborative partnerships between academia, government, and industry. The scope of this review encompasses the use of omics tools and applications in the study of aquatic animals cultivated for human consumption in aquaculture settings throughout their life-cycle.

Keywords: Aquaculture; Breeding; Education and workforce training; Gene-editing; Genetics; Genome-to-phenome; Genomics; Interdisciplinary integration; Multi-omics data; Phenomics.

PubMed Disclaimer

Conflict of interest statement

Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

**Fig. 1**
Current status of omics resources for species cultivated in United States aquaculture. The current status is indicated with various colors: Dark green: good status; light green, outstanding progress has been made, but additional work still needed; dark yellow: significant progress has been made, but significant amount of additional work still needed; light yellow, some progress has been made

**Fig. 2**
Major omics areas of focus from the phenome to genome and an example of how they can integrate to answer research questions

**Fig. 3**
Input from multiple groups impacts the success of aquaculture production from lab to farm to plate

See this image and copyright information in PMC

Cited by

Correction: Advancing genetic improvement in the omics era: status and priorities for United States aquaculture.
Andersen LK, Thompson NF, Abernathy JW, Ahmed RO, Ali A, Al-Tobasei R, Beck BH, Calla B, Delomas TA, Dunham RA, Elsik CG, Fuller SA, García JC, Gavery MR, Hollenbeck CM, Johnson KM, Kunselman E, Legacki EL, Liu S, Liu Z, Martin B, Matt JL, May SA, Older CE, Overturf K, Palti Y, Peatman EJ, Peterson BC, Phelps MP, Plough LV, Polinski MP, Proestou DA, Purcell CM, Quiniou SMA, Raymo G, Rexroad CE, Riley KL, Roberts SB, Roy LA, Salem M, Simpson K, Waldbieser GC, Wang H, Waters CD, Reading BJ; Aquaculture Genomics, Genetics and Breeding Workshop. Andersen LK, et al. BMC Genomics. 2025 Mar 17;26(1):260. doi: 10.1186/s12864-025-11447-7. BMC Genomics. 2025. PMID: 40098073 Free PMC article. No abstract available.

References

1. Biga P, Rexroad C, Bart A, Sullivan T, Green C, Fuglie K, Kim G, Surface J, Jermolowicz A, Thomason T et al: Aquaculture is agriculture colloquium: USDA's role in supporting farmers of fish, shellfish, and aquatic plants. In.: United States Department of Agriculture (USDA); 2021.
1. Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, et al. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics. 2017;18:1–23. 10.1186/s12864-017-3557-1. - PMC - PubMed
1. Rexroad C, Vallet J, Matukumalli LK, Reecy J, Bickhart D, Blackburn H, Boggess M, Cheng H, Clutter A, Cockett N. Genome to phenome: improving animal health, production, and well-being–a new USDA blueprint for animal genome research 2018–2027. Front Genet. 2019;10:327. 10.3389/fgene.2019.00327. - PMC - PubMed
1. Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Jin YH, Jenkins TL, Selly SLC, Martin SAM, Stevens JR, Santos EM, et al. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet. 2020;21(7):389–409. 10.1038/s41576-020-0227-y. - PubMed
1. Huang Y, Li Z, Li M, Zhang X, Shi Q, Xu Z. Fish genomics and its application in disease-resistance breeding. Rev Aquac. 2024. 10.1111/raq.12973.

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions

LinkOut - more resources

Full Text Sources
- BioMed Central
- PubMed Central

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

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

Affiliations

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

Authors

Affiliations

Erratum in

Abstract

Conflict of interest statement

Figures

Similar articles

Cited by

References

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources

Erratum in

Abstract

Conflict of interest statement

Figures

Similar articles

Cited by

References

Publication types

MeSH terms

Related information

LinkOut - more resources

Full Text Sources