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Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research
Abdelrahman, Hisham1; ElHady, Mohamed2; Alcivar-Warren, Acacia3; Allen, Standish4; Al-Tobasei, Rafet5; Bao, Lisui1; Beck, Ben6; Blackburn, Harvey7; Bosworth, Brian8; Buchanan, John9; Chappell, Jesse1; Daniels, William1; Dong, Sheng1; Dunham, Rex1; Durland, Evan10; Elaswad, Ahmed1; Gomez-Chiarri, Marta11; Gosh, Kamal1; Guo, Ximing12; Hackett, Perry13; Hanson, Terry1; Hedgecock, Dennis14; Howard, Tiffany1; Holland, Leigh1; Jackson, Molly15; Jin, Yulin1; Kahlil, Karim1; Kocher, Thomas16; Leeds, Tim17; Li, Ning1; Lindsey, Lauren1; Liu, Shikai1; Liu, Zhanjiang1; Martin, Kyle18; Novriadi, Romi1; Odin, Ramjie1; Palti, Yniv; Peatman, Eric1; Proestou, Dina19; Qin, Guyu1; Reading, Benjamin20; Rexroad, Caird21; Roberts, Steven22; Salem, Mohamed5; Severin, Andrew23; Shi, Huitong1; Shoemaker, Craig6; Stiles, Sheila24; Tan, Suxu1; Tang, Kathy F. J.25; Thongda, Wilawan1; Tiersch, Terrence26; Tomasso, Joseph1; Prabowo, Wendy Tri1; Vallejo, Roger17; van der Steen, Hein27; Vo, Khoi1; Waldbieser, Geoff; Wang, Hanping28; Wang, Xiaozhu1; Xiang, Jianhai29; Yang, Yujia1; Yant, Roger30; Yuan, Zihao1; Zeng, Qifan1; Zhou, Tao1; Aquaculture Genomics Genetics & Br
2017-02-20
Source PublicationBMC GENOMICS
Volume18
SubtypeArticle
AbstractAdvancing 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.
KeywordAquaculture Genetic Resources Genome Transcriptome Qtl Rna-seq Snp Fish Shellfish
DOI10.1186/s12864-017-3557-1
Indexed BySCI
Language英语
WOS IDWOS:000394419000002
Citation statistics
Cited Times:3[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Version出版稿
Identifierhttp://ir.qdio.ac.cn/handle/337002/136407
Collection实验海洋生物学重点实验室
Affiliation1.Auburn Univ, Sch Fisheries Aquaculture & Aquat Sci, Auburn, AL 36849 USA
2.Auburn Univ, Dept Biol Sci, Auburn, AL 36849 USA
3.Environm Genom Inc, POB 196, Southborough, MA 01772 USA
4.Virginia Inst Marine Sci, Aquaculture Genet & Breeding Technol Ctr, Gloucester Point, VA 23062 USA
5.Middle Tennessee State Univ, Dept Biol, Murfreesboro, TN 37132 USA
6.USDA ARS, Aquat Anim Hlth Res Unit, 990 Wire Rd, Auburn, AL 36832 USA
7.USDA ARS, NL Wheat & Corn Collect Glance GRP, Natl Anim Germplasm Program, 1111 S Mason St, Ft Collins, CO 80521 USA
8.USDA ARS, CGRU, 141 Expt Stn Rd, Stoneville, MS 38701 USA
9.Ctr Aquaculture Technol, 8395 Camino Santa Fe,Suite E, San Diego, CA 92121 USA
10.Oregon State Univ, Dept Fisheries & Wildlife, Corvallis, OR 97331 USA
11.Dept Fisheries Anim & Vet Sci, 134 Woodward Hall,9 East Alumni Ave, Kingston, RI 02881 USA
12.Rutgers State Univ, Dept Marine & Coastal Sci, Haskin Shellfish Res Lab, 6959 Miller Ave, Port Norris, NJ 08349 USA
13.Dept Genet Cell Biol & Dev, 5-108 MCB,420 Washington Ave SE, Minneapolis, MN 55455 USA
14.Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90089 USA
15.Taylor Shellfish Farms, 130 SE Lynch RD, Shelton, WA 98584 USA
16.Univ Maryland, Dept Biol, 2132 Biosci Res Bldg, College Pk, MD 20742 USA
17.ARS, Natl Ctr Cool & Cold Water Aquaculture, USDA, Kearneysville, WV 25430 USA
18.Troutlodge, 27090 Us Highway 12, Naches, WA 98937 USA
19.Univ Rhode Isl, USDA ARS NEA NCWMAC Shellfish Genet, 469 CBLS,120 Flagg Rd, Kingston, RI 02881 USA
20.North Carolina State Univ, Dept Appl Ecol, Raleigh, NC 27695 USA
21.USDA ARS, Off Natl Programs, George Washington Carver Ctr, Room 4-2106,5601 Sunnyside Ave, Beltsville, MD 20705 USA
22.Univ Washington, Sch Aquat & Fishery Sci, Seattle, WA 98105 USA
23.Iowa State Univ, Off Biotechnol, Genome Informat Facil, Ames, IA 50011 USA
24.USDOC NOAA, Natl Marine Fisheries Serv, NEFSC, Milford Lab, Milford, CA 06460 USA
25.Univ Arizona, Sch Anim & Comparat Biomed Sci, Tucson, AZ 85721 USA
26.Louisiana State Univ, Aquat Germplasm & Genet Resources Ctr, Sch Renewable Nat Resources, Ctr Agr, Baton Rouge, LA 70820 USA
27.Stonebridge Breeding Ltd, Gate House, Abbotswood WR11 4NS, Evesham, England
28.Ohio State Univ, South Ctr, Aquaculture Genet & Breeding Lab, Piketon, OH 45661 USA
29.Chinese Acad Sci, Key Lab Expt Marine Biol, Inst Oceanol, Qingdao 266071, Peoples R China
30.Hybrid Catfish Co, 1233 Montgomery Dr, Inverness, MS 38753 USA
Recommended Citation
GB/T 7714
Abdelrahman, Hisham,ElHady, Mohamed,Alcivar-Warren, Acacia,et al. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research[J]. BMC GENOMICS,2017,18.
APA Abdelrahman, Hisham.,ElHady, Mohamed.,Alcivar-Warren, Acacia.,Allen, Standish.,Al-Tobasei, Rafet.,...&Aquaculture Genomics Genetics & Br.(2017).Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.BMC GENOMICS,18.
MLA Abdelrahman, Hisham,et al."Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research".BMC GENOMICS 18(2017).
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