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

Persistent Link:
http://hdl.handle.net/10150/623031
Title:
Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research
Author:
Abdelrahman, Hisham; ElHady, Mohamed; Alcivar-Warren, Acacia; Allen, Standish; Al-Tobasei, Rafet; Bao, Lisui; Beck, Ben; Blackburn, Harvey; Bosworth, Brian; Buchanan, John; Chappell, Jesse; Daniels, William; Dong, Sheng; Dunham, Rex; Durland, Evan; Elaswad, Ahmed; Gomez-Chiarri, Marta; Gosh, Kamal; Guo, Ximing; Hackett, Perry; Hanson, Terry; Hedgecock, Dennis; Howard, Tiffany; Holland, Leigh; Jackson, Molly; Jin, Yulin; Khalil, Karim; Kocher, Thomas; Leeds, Tim; Li, Ning; Lindsey, Lauren; Liu, Shikai; Liu, Zhanjiang; Martin, Kyle; Novriadi, Romi; Odin, Ramjie; Palti, Yniv; Peatman, Eric; Proestou, Dina; Qin, Guyu; Reading, Benjamin; Rexroad, Caird; Roberts, Steven; Salem, Mohamed; Severin, Andrew; Shi, Huitong; Shoemaker, Craig; Stiles, Sheila; Tan, Suxu; Tang, Kathy F. J.; Thongda, Wilawan; Tiersch, Terrence; Tomasso, Joseph; Prabowo, Wendy Tri; Vallejo, Roger; van der Steen, Hein; Vo, Khoi; Waldbieser, Geoff; Wang, Hanping; Wang, Xiaozhu; Xiang, Jianhai; Yang, Yujia; Yant, Roger; Yuan, Zihao; Zeng, Qifan; Zhou, Tao
Affiliation:
Univ Arizona, Sch Anim & Comparat Biomed Sci
Issue Date:
2017-02-20
Publisher:
BIOMED CENTRAL LTD
Citation:
Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research 2017, 18 (1) BMC Genomics
Journal:
BMC Genomics
Rights:
© The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License.
Collection Information:
This 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.
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.
Note:
Open access journal.
ISSN:
1471-2164
DOI:
10.1186/s12864-017-3557-1
Keywords:
Aquaculture; Genetic resources; Genome; Transcriptome; QTL; RNA-Seq; SNP; Fish; Shellfish
Version:
Final published version
Sponsors:
Animal Genomics, Genetics and Breeding Program of the USDA National Institute of Food and Agriculture [2015-67015-22907]; USDA NRSP-8 Aquaculture Coordinator's funds
Additional Links:
http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3557-1

Full metadata record

DC FieldValue Language
dc.contributor.authorAbdelrahman, Hishamen
dc.contributor.authorElHady, Mohameden
dc.contributor.authorAlcivar-Warren, Acaciaen
dc.contributor.authorAllen, Standishen
dc.contributor.authorAl-Tobasei, Rafeten
dc.contributor.authorBao, Lisuien
dc.contributor.authorBeck, Benen
dc.contributor.authorBlackburn, Harveyen
dc.contributor.authorBosworth, Brianen
dc.contributor.authorBuchanan, Johnen
dc.contributor.authorChappell, Jesseen
dc.contributor.authorDaniels, Williamen
dc.contributor.authorDong, Shengen
dc.contributor.authorDunham, Rexen
dc.contributor.authorDurland, Evanen
dc.contributor.authorElaswad, Ahmeden
dc.contributor.authorGomez-Chiarri, Martaen
dc.contributor.authorGosh, Kamalen
dc.contributor.authorGuo, Ximingen
dc.contributor.authorHackett, Perryen
dc.contributor.authorHanson, Terryen
dc.contributor.authorHedgecock, Dennisen
dc.contributor.authorHoward, Tiffanyen
dc.contributor.authorHolland, Leighen
dc.contributor.authorJackson, Mollyen
dc.contributor.authorJin, Yulinen
dc.contributor.authorKhalil, Karimen
dc.contributor.authorKocher, Thomasen
dc.contributor.authorLeeds, Timen
dc.contributor.authorLi, Ningen
dc.contributor.authorLindsey, Laurenen
dc.contributor.authorLiu, Shikaien
dc.contributor.authorLiu, Zhanjiangen
dc.contributor.authorMartin, Kyleen
dc.contributor.authorNovriadi, Romien
dc.contributor.authorOdin, Ramjieen
dc.contributor.authorPalti, Yniven
dc.contributor.authorPeatman, Ericen
dc.contributor.authorProestou, Dinaen
dc.contributor.authorQin, Guyuen
dc.contributor.authorReading, Benjaminen
dc.contributor.authorRexroad, Cairden
dc.contributor.authorRoberts, Stevenen
dc.contributor.authorSalem, Mohameden
dc.contributor.authorSeverin, Andrewen
dc.contributor.authorShi, Huitongen
dc.contributor.authorShoemaker, Craigen
dc.contributor.authorStiles, Sheilaen
dc.contributor.authorTan, Suxuen
dc.contributor.authorTang, Kathy F. J.en
dc.contributor.authorThongda, Wilawanen
dc.contributor.authorTiersch, Terrenceen
dc.contributor.authorTomasso, Josephen
dc.contributor.authorPrabowo, Wendy Trien
dc.contributor.authorVallejo, Rogeren
dc.contributor.authorvan der Steen, Heinen
dc.contributor.authorVo, Khoien
dc.contributor.authorWaldbieser, Geoffen
dc.contributor.authorWang, Hanpingen
dc.contributor.authorWang, Xiaozhuen
dc.contributor.authorXiang, Jianhaien
dc.contributor.authorYang, Yujiaen
dc.contributor.authorYant, Rogeren
dc.contributor.authorYuan, Zihaoen
dc.contributor.authorZeng, Qifanen
dc.contributor.authorZhou, Taoen
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.en
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
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