Обзорная статья

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

The Aquaculture Genomics, Genetics and Breeding WorkshopSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USAHisham A. AbdelrahmanSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAMohamed A. Abd El-HadyDepartment of Biological Sciences, Auburn University, Auburn, AL 36849, USAAcacia Alcivar‐WarrenEnvironmental Genomics Inc., P. O. Box 196, Southborough, MA 01772-1801, USAStandish K. AllenAquaculture Genetics & Breeding Technology Center, Virginia Institute of Marine Science, Gloucester Point, VA 23062, USARafet Al-TobaseiDepartment of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USALisui BaoAquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USABenjamin H. BeckAquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL 36832, USAHarvey D. BlackburnUSDA-ARS-NL Wheat & Corn Collections at a Glance GRP, National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO 80521-4500, USABrian G. BosworthUSDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS 38701, USAJohn BuchananCenter for Aquaculture Technologies, 8395 Camino Santa Fe, Suite E, San Diego, CA 92121, USAJesse A. ChappellSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAWilliam H. DanielsSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USASheng DongSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USARex A. DunhamSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAEvan DurlandDepartment of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331, USAAhmed ElaswadSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAMarta Gómez-ChiarriDepartment of Fisheries, Animal & Veterinary Science, 134 Woodward Hall, 9 East Alumni Avenue, Kingston, RI 02881, USAKamal GoshSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAXiming GuoHaskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USAPerry B. HackettDepartment of Genetics, Cell Biology and Development, 5-108 MCB, 420 Washington Avenue SE, Minneapolis, MN 55455, USATerry HansonSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USADennis HedgecockDepartment of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USATiffany HowardSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USALeigh HollandSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAMolly JacksonTaylor Shellfish Farms, 130 SE Lynch RD, Shelton, WA 98584, USAYulin JinSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAKarim KhalilSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAThomas D. KocherDepartment of Biology, University of Maryland, 2132 Biosciences Research Building, College Park, MD 20742, USATimothy D. LeedsNational Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV 25430, USANing LiSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USALauren LindseySchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAShikai LiuSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAZhanjiang LiuTroutlodge, 27090 Us Highway 12, Naches, WA, 98937, USAKyle E. MartinSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USARomi NovriadiSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USARamjie OdinSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAYniv PaltiNational Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV 25430, USAEric PeatmanSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USADina A. ProestouUSDA ARS NEA NCWMAC Shellfish Genetics at the University Rhode Island, 469 CBLS, 120 Flagg Road, Kingston, RI 02881, USAGuyu QinSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USABenjamin J. ReadingDepartment of Applied Ecology, North Carolina State University, Raleigh, NC 27695-7617, USACaird E. RexroadUSDA ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD 20705, USASteven RobertsSchool of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USAMohamed SalemDepartment of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USAAndrew SeverinGenome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011, USAHuitong ShiSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USACraig A. ShoemakerAquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL 36832, USASheila StilesUSDOC/NOAA, National Marine Fisheries Service, NEFSC, Milford Laboratory, Milford, Connectcut 06460, USASuxu TanSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAKathy F.J. TangSchool of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USAWilawan ThongdaSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USATerrence R. TierschAquatic Germplasm and Genetic Resources Center,Joseph R. TomassoSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAWendy Tri PrabowoSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USARoger L. VallejoNational Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV 25430, USAH. van der SteenStonebridge breeding Ltd, Gate House, Abbotswood, Evesham WR11 4NS, UKKhoi VoSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAGeoff WaldbieserUSDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS 38701, USAHan‐Ping WangAquaculture Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, OH 45661, USA. 29 Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China. 30 Hybrid Catfish Company, 1233 Montgomery Drive, Inverness, MS 38753, USAXiaozhu WangSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAJianhai XiangSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USAYujia YangSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USARoger YantSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USAZihao YuanSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAQifan ZengSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USATao ZhouSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA

2017en

ABI

Аннотация

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.

Перевод пока недоступен

Идентификаторы

DOI: 10.1186/s12864-017-3557-1

Цитирования и источники

Цитирований: 2Использованных источников: 0

Показатели — AkademScholar