Evidence map›Paper›PMID 39962419›Full record

ReviewBMC genomics2025

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

Linnea K Andersen, Neil F Thompson, Jason W Abernathy, Ridwan O Ahmed, Ali Ali, Rafet Al-Tobasei, Benjamin H Beck, Bernarda Calla, Thomas A Delomas, Rex A Dunham and 36 more

Erratum issuedAbstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Review
  5. Article
  6. Article
  7. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

46 authors.

Linnea K Andersen *USDA-ARS Aquatic Animal Health Research Unit, Auburn, AL, USA.
Neil F Thompson *USDA-ARS Pacific Shellfish Research Unit, Newport, OR, USA. neil.thompson@usda.gov.
Jason W AbernathyUSDA-ARS Aquatic Animal Health Research Unit, Auburn, AL, USA.
Ridwan O AhmedDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
Ali AliDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
Rafet Al-TobaseiMiddle Tennessee State University, Murfreesboro, TN, USA.
Benjamin H BeckUSDA-ARS Aquatic Animal Health Research Unit, Auburn, AL, USA.
Bernarda CallaUSDA-ARS Pacific Shellfish Research Unit, Newport, OR, USA.
Thomas A DelomasUSDA-ARS National Cold Water Marine Aquaculture Center, Kingston, RI, USA.
Rex A DunhamSchool of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL, USA.
Christine G ElsikUniversity of Missouri, Columbia, MO, USA.
S Adam FullerUSDA-ARS Harry K Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, USA.
Julio C GarcíaUSDA-ARS Aquatic Animal Health Research Unit, Auburn, AL, USA.
Mackenzie R GaveryEnvironmental and Fishery Sciences Division, NOAA Northwest Fisheries Science Center, Seattle, WA, USA.
Christopher M HollenbeckTexas A&M AgriLife Research, College Station, TX, USA.
Kevin M JohnsonCalifornia Sea Grant, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
Emily KunselmanHubbs-SeaWorld Research Institute, San Diego, CA, USA.
Erin L LegackiUSDA-ARS National Cold Water Marine Aquaculture Center, Orono, ME, USA.
Sixin LiuUSDA-ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA.
Zhanjiang LiuDepartment of Biology, Tennessee Technological University, Cookeville, TN, USA.
Brittany MartinUSDA-ARS Aquatic Animal Health Research Unit, Auburn, AL, USA.
Joseph L MattTexas A&M University - Corpus Christi, Corpus Christi, TX, USA.
Samuel A MayUSDA-ARS National Cold Water Marine Aquaculture Center, Orono, ME, USA.
Caitlin E OlderUSDA-ARS Warmwater Aquaculture Research Unit, Stoneville, MS, USA.
Ken OverturfUSDA-ARS Small Grains and Potato Germplasm Research, Hagerman, ID, USA.
Yniv PaltiUSDA-ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA.
Eric J PeatmanHarvest Select Catfish Inc, Inverness, MS, USA.
Brian C PetersonUSDA-ARS National Cold Water Marine Aquaculture Center, Orono, ME, USA.
Michael P PhelpsWashington State University, Pullman, WA, USA.
Louis V PloughUSDA-ARS Pacific Shellfish Research Unit, Newport, OR, USA.
Mark P PolinskiUSDA-ARS National Cold Water Marine Aquaculture Center, Orono, ME, USA.
Dina A ProestouUSDA-ARS National Cold Water Marine Aquaculture Center, Kingston, RI, USA.
Catherine M PurcellNOAA Fisheries, Southwest Fisheries Science Center, La Jolla, CA, USA.
Sylvie M A QuiniouUSDA-ARS Warmwater Aquaculture Research Unit, Stoneville, MS, USA.
Guglielmo RaymoDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
Caird E RexroadUSDA-ARS Office of National Programs, Beltsville, MD, USA.
Kenneth L RileyOffice of Aquaculture, NOAA Fisheries, Silver Spring, MD, USA.
Steven B RobertsUniversity of Washington, Seattle, WA, USA.
Luke A RoySchool of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Alabama Fish Farming Center, Greensboro, AL, USA.
Mohamed SalemDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
Kelly SimpsonUSDA-ARS Aquatic Animal Health Research Unit, Auburn, AL, USA.
Geoffrey C WaldbieserUSDA-ARS Warmwater Aquaculture Research Unit, Stoneville, MS, USA.
Hanping WangThe Ohio State University, Columbus, OH, USA.
Charles D WatersNOAA Alaska Fisheries Science Center Auke Bay Laboratories, Juneau, AK, USA.
Benjamin J ReadingDepartment of Applied Ecology, North Carolina State University, Raleigh, NC, USA.
Aquaculture Genomics, Genetics and Breeding Workshop

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe 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.

conclusionThis 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.

Indexed as

AquacultureGenomicsAnimalsBreedingGenomeUnited StatesAquacultureBreedingEducation and workforce trainingGene-editingGeneticsGenome-to-phenomeGenomicsInterdisciplinary integrationMulti-omics dataPhenomics

Identifiers

PMID39962419
PMCPMC11834649

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.