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

BMC Genomics

Commentary

Standish Allen¹  Hanping Wang²  Craig Shoemaker³  Ben Beck³  Terrence Tiersch⁴  John Buchanan⁵  Benjamin Reading⁶  Mohamed ElHady⁷  Dennis Hedgecock⁸  Mohamed Salem⁹  Rafet Al-Tobasei⁹  Thomas Kocher^1,10  Evan Durland^1,11  Marta Gomez-Chiarri^1,12  Perry Hackett^1,13  Acacia Alcivar-Warren^1,14  Andrew Severin^1,15  Ximing Guo^1,16  Roger Yant^1,17  Jianhai Xiang^1,18  Roger Vallejo^1,19  Yniv Palti^1,19  Tim Leeds^1,19  Kathy F. J. Tang^2,20  Steven Roberts^2,21  Eric Peatman^2,22  Ning Li^2,22  Xiaozhu Wang^2,22  Terry Hanson^2,22  Shikai Liu^2,22  Hisham Abdelrahman^2,22  Ramjie Odin^2,22  Romi Novriadi^2,22  Yujia Yang^2,22  Karim Khalil^2,22  Joseph Tomasso^2,22  Suxu Tan^2,22  Lauren Lindsey^2,22  Jesse Chappell^2,22  Wendy Tri Prabowo^2,22  Tao Zhou^2,22  Tiffany Howard^2,22  Wilawan Thongda^2,22  Zihao Yuan^2,22  Zhanjiang Liu^2,22  Kamal Gosh^2,22  Guyu Qin^2,22  Qifan Zeng^2,22  Leigh Holland^2,22  Khoi Vo^2,22  Yulin Jin^2,22  William Daniels^2,22  Sheng Dong^2,22  Huitong Shi^2,22  Rex Dunham^2,22  Lisui Bao^2,22  Ahmed Elaswad^2,22  Hein van der Steen^2,23  Molly Jackson^2,24  Kyle Martin^2,25  Dina Proestou^2,26  Caird Rexroad^2,27  Harvey Blackburn^2,28  Geoff Waldbieser^2,29  Brian Bosworth^2,29  Sheila Stiles^3,30 

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

关键词: Aquaculture;    Genetic resources;    Genome;    Transcriptome;    QTL;    RNA-Seq;    SNP;    Fish;    Shellfish;   

DOI  :  10.1186/s12864-017-3557-1

 received in 2016-12-14, accepted in 2017-02-06,  发布年份 2017

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2017