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dc.contributor.authorAbdelrahman, Hisham
dc.contributor.authorElHady, Mohamed
dc.contributor.authorAlcivar-Warren, Acacia
dc.contributor.authorAllen, Standish
dc.contributor.authorAl-Tobasei, Rafet
dc.contributor.authorBao, Lisui
dc.contributor.authorBeck, Ben
dc.contributor.authorBlackburn, Harvey
dc.contributor.authorBosworth, Brian
dc.contributor.authorBuchanan, John
dc.contributor.authorChappell, Jesse
dc.contributor.authorDaniels, William
dc.contributor.authorDong, Sheng
dc.contributor.authorDunham, Rex
dc.contributor.authorDurland, Evan
dc.contributor.authorElaswad, Ahmed
dc.contributor.authorGomez-Chiarri, Marta
dc.contributor.authorGosh, Kamal
dc.contributor.authorGuo, Ximing
dc.contributor.authorHackett, Perry
dc.contributor.authorHanson, Terry
dc.contributor.authorHedgecock, Dennis
dc.contributor.authorHoward, Tiffany
dc.contributor.authorHolland, Leigh
dc.contributor.authorJackson, Molly
dc.contributor.authorJin, Yulin
dc.contributor.authorKhalil, Karim
dc.contributor.authorKocher, Thomas
dc.contributor.authorLeeds, Tim
dc.contributor.authorLi, Ning
dc.contributor.authorLindsey, Lauren
dc.contributor.authorLiu, Shikai
dc.contributor.authorLiu, Zhanjiang
dc.contributor.authorMartin, Kyle
dc.contributor.authorNovriadi, Romi
dc.contributor.authorOdin, Ramjie
dc.contributor.authorPalti, Yniv
dc.contributor.authorPeatman, Eric
dc.contributor.authorProestou, Dina
dc.contributor.authorQin, Guyu
dc.contributor.authorReading, Benjamin
dc.contributor.authorRexroad, Caird
dc.contributor.authorRoberts, Steven
dc.contributor.authorSalem, Mohamed
dc.contributor.authorSeverin, Andrew
dc.contributor.authorShi, Huitong
dc.contributor.authorShoemaker, Craig
dc.contributor.authorStiles, Sheila
dc.contributor.authorTan, Suxu
dc.contributor.authorTang, Kathy F. J.
dc.contributor.authorThongda, Wilawan
dc.contributor.authorTiersch, Terrence
dc.contributor.authorTomasso, Joseph
dc.contributor.authorPrabowo, Wendy Tri
dc.contributor.authorVallejo, Roger
dc.contributor.authorvan der Steen, Hein
dc.contributor.authorVo, Khoi
dc.contributor.authorWaldbieser, Geoff
dc.contributor.authorWang, Hanping
dc.contributor.authorWang, Xiaozhu
dc.contributor.authorXiang, Jianhai
dc.contributor.authorYang, Yujia
dc.contributor.authorYant, Roger
dc.contributor.authorYuan, Zihao
dc.contributor.authorZeng, Qifan
dc.contributor.authorZhou, Tao
dc.date.accessioned2017-04-05T21:03:53Z
dc.date.available2017-04-05T21:03:53Z
dc.date.issued2017-02-20
dc.identifier.citationAquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research 2017, 18 (1) BMC Genomicsen
dc.identifier.issn1471-2164
dc.identifier.doi10.1186/s12864-017-3557-1
dc.identifier.urihttp://hdl.handle.net/10150/623031
dc.description.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.
dc.description.sponsorshipAnimal Genomics, Genetics and Breeding Program of the USDA National Institute of Food and Agriculture [2015-67015-22907]; USDA NRSP-8 Aquaculture Coordinator's fundsen
dc.language.isoenen
dc.publisherBIOMED CENTRAL LTDen
dc.relation.urlhttp://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3557-1en
dc.rights© The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License.en
dc.subjectAquacultureen
dc.subjectGenetic resourcesen
dc.subjectGenomeen
dc.subjectTranscriptomeen
dc.subjectQTLen
dc.subjectRNA-Seqen
dc.subjectSNPen
dc.subjectFishen
dc.subjectShellfishen
dc.titleAquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future researchen
dc.typeArticleen
dc.contributor.departmentUniv Arizona, Sch Anim & Comparat Biomed Scien
dc.identifier.journalBMC Genomicsen
dc.description.noteOpen access journal.en
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
refterms.dateFOA2018-04-26T05:10:04Z
html.description.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.


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