Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

Aquaculture Genomics, Genetics and Breeding Workshop; Hisham Abdelrahman¹, Mohamed ElHady², Acacia Alcivar-Warren³, Standish Allen⁴, Rafet Al-Tobasei⁵, Lisui Bao¹, Ben Beck⁶, Harvey Blackburn⁷, Brian Bosworth⁸, John Buchanan⁹, Jesse Chappell¹, William Daniels¹, Sheng Dong¹, Rex Dunham¹, Evan Durland¹⁰, Ahmed Elaswad¹, Marta Gomez-Chiarri¹¹, Kamal Gosh¹, Ximing Guo¹², Perry Hackett¹³, Terry Hanson¹, Dennis Hedgecock¹⁴, Tiffany Howard¹, Leigh Holland¹, Molly Jackson¹⁵, Yulin Jin¹, Karim Khalil¹, Thomas Kocher¹⁶, Tim Leeds¹⁷, Ning Li¹, Lauren Lindsey¹, Shikai Liu¹, Zhanjiang Liu¹⁸, Kyle Martin¹⁹, Romi Novriadi¹, Ramjie Odin¹, Yniv Palti¹⁷, Eric Peatman¹, Dina Proestou²⁰, Guyu Qin¹, Benjamin Reading²¹, Caird Rexroad²², Steven Roberts²³, Mohamed Salem⁵, Andrew Severin²⁴, Huitong Shi¹, Craig Shoemaker⁶, Sheila Stiles²⁵, Suxu Tan¹, Kathy F J Tang²⁶, Wilawan Thongda¹, Terrence Tiersch²⁷, Joseph Tomasso¹, Wendy Tri Prabowo¹, Roger Vallejo¹⁷, Hein van der Steen²⁸, Khoi Vo¹, Geoff Waldbieser⁸, Hanping Wang²⁹, Xiaozhu Wang¹, Jianhai Xiang³⁰, Yujia Yang¹, Roger Yant³¹, Zihao Yuan¹, Qifan Zeng¹, Tao Zhou¹

Affiliations

¹ School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
² Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA.
³ Environmental Genomics Inc., P. O. Box 196, Southborough, MA, 01772-1801, USA.
⁴ Aquaculture Genetics & Breeding Technology Center, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA.
⁵ Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
⁶ Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA.
⁷ USDA-ARS-NL Wheat & Corn Collections at a Glance GRP, National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO, 80521-4500, USA.
⁸ USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA.
⁹ Center for Aquaculture Technologies, 8395 Camino Santa Fe, Suite E, San Diego, CA, 92121, USA.
¹⁰ Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA.
¹¹ Department of Fisheries, Animal & Veterinary Science, 134 Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA.
¹² Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
¹³ Department of Genetics, Cell Biology and Development, 5-108 MCB, 420 Washington Avenue SE, Minneapolis, MN, 55455, USA.
¹⁴ Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA.
¹⁵ Taylor Shellfish Farms, 130 SE Lynch RD, Shelton, WA, 98584, USA.
¹⁶ Department of Biology, University of Maryland, 2132 Biosciences Research Building, College Park, MD, 20742, USA.
¹⁷ National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA.
¹⁸ School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA. liuzhan@auburn.edu.
¹⁹ Troutlodge, 27090 Us Highway 12, Naches, WA, 98937, USA.
²⁰ USDA ARS NEA NCWMAC Shellfish Genetics at the University Rhode Island, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA.
²¹ Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695-7617, USA.
²² USDA ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD, 20705, USA.
²³ School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98105, USA.
²⁴ Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, 50011, USA.
²⁵ USDOC/NOAA, National Marine Fisheries Service, NEFSC, Milford Laboratory, Milford, Connectcut, 06460, USA.
²⁶ School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA.
²⁷ Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, 70820, USA.
²⁸ Stonebridge breeding Ltd, Gate House, Abbotswood, Evesham, WR11 4NS, UK.
²⁹ Aquaculture Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, OH, 45661, USA.
³⁰ Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
³¹ Hybrid Catfish Company, 1233 Montgomery Drive, Inverness, MS, 38753, USA.

PMID: 28219347
PMCID: PMC5319170
DOI: 10.1186/s12864-017-3557-1

Review

Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

Aquaculture Genomics, Genetics and Breeding Workshop et al. BMC Genomics. 2017.

. 2017 Feb 20;18(1):191.

doi: 10.1186/s12864-017-3557-1.

Authors

Affiliations

¹ School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
² Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA.
³ Environmental Genomics Inc., P. O. Box 196, Southborough, MA, 01772-1801, USA.
⁴ Aquaculture Genetics & Breeding Technology Center, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA.
⁵ Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
⁶ Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA.
⁷ USDA-ARS-NL Wheat & Corn Collections at a Glance GRP, National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO, 80521-4500, USA.
⁸ USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA.
⁹ Center for Aquaculture Technologies, 8395 Camino Santa Fe, Suite E, San Diego, CA, 92121, USA.
¹⁰ Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA.
¹¹ Department of Fisheries, Animal & Veterinary Science, 134 Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA.
¹² Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
¹³ Department of Genetics, Cell Biology and Development, 5-108 MCB, 420 Washington Avenue SE, Minneapolis, MN, 55455, USA.
¹⁴ Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA.
¹⁵ Taylor Shellfish Farms, 130 SE Lynch RD, Shelton, WA, 98584, USA.
¹⁶ Department of Biology, University of Maryland, 2132 Biosciences Research Building, College Park, MD, 20742, USA.
¹⁷ National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA.
¹⁸ School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA. liuzhan@auburn.edu.
¹⁹ Troutlodge, 27090 Us Highway 12, Naches, WA, 98937, USA.
²⁰ USDA ARS NEA NCWMAC Shellfish Genetics at the University Rhode Island, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA.
²¹ Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695-7617, USA.
²² USDA ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD, 20705, USA.
²³ School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98105, USA.
²⁴ Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, 50011, USA.
²⁵ USDOC/NOAA, National Marine Fisheries Service, NEFSC, Milford Laboratory, Milford, Connectcut, 06460, USA.
²⁶ School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA.
²⁷ Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, 70820, USA.
²⁸ Stonebridge breeding Ltd, Gate House, Abbotswood, Evesham, WR11 4NS, UK.
²⁹ Aquaculture Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, OH, 45661, USA.
³⁰ Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
³¹ Hybrid Catfish Company, 1233 Montgomery Drive, Inverness, MS, 38753, USA.

PMID: 28219347
PMCID: PMC5319170
DOI: 10.1186/s12864-017-3557-1

Erratum in

Erratum to: Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.
Aquaculture Genomics, Genetics and Breeding Workshop; Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin Y, Khalil K, Kocher T, Leeds T, Li N, Lindsey L, Liu S, Liu Z, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin G, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi H, Shoemaker C, Stiles S, Tan S, Tang KF, Thongda W, Tiersch T, Tomasso J, Prabowo WT, Vallejo R, van der Steen H, Vo K, Waldbieser G, Wang H, Wang X, Xiang J, Yang Y, Yant R, Yuan Z, Zeng Q, Zhou T. Aquaculture Genomics, Genetics and Breeding Workshop, et al. BMC Genomics. 2017 Mar 16;18(1):235. doi: 10.1186/s12864-017-3614-9. BMC Genomics. 2017. PMID: 28302067 Free PMC article. No abstract available.

Abstract

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.

Keywords: Aquaculture; Fish; Genetic resources; Genome; QTL; RNA-Seq; SNP; Shellfish; Transcriptome.

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Figures

**Fig. 1**
Schematic presentation of the goals and current status of aquaculture genomics and genetics research. The major aquaculture species in the United States are grouped into teleost fish and invertebrate species, with the species names listed in the first column. Major milestones of research goals are listed in the first row, while current status for each species is indicated in the appropriate cells 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

See this image and copyright information in PMC

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Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

Affiliations

Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

Authors

Affiliations

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