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Zenger KR, Khatkar MS, Jones DB, Khalilisamani N, Jerry DR, Raadsma HW. Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters. Front Genet 2019; 9:693. [PMID: 30728827 PMCID: PMC6351666 DOI: 10.3389/fgene.2018.00693] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/11/2018] [Indexed: 11/20/2022] Open
Abstract
Within aquaculture industries, selection based on genomic information (genomic selection) has the profound potential to change genetic improvement programs and production systems. Genomic selection exploits the use of realized genomic relationships among individuals and information from genome-wide markers in close linkage disequilibrium with genes of biological and economic importance. We discuss the technical advances, practical requirements, and commercial applications that have made genomic selection feasible in a range of aquaculture industries, with a particular focus on molluscs (pearl oysters, Pinctada maxima) and marine shrimp (Litopenaeus vannamei and Penaeus monodon). The use of low-cost genome sequencing has enabled cost-effective genotyping on a large scale and is of particular value for species without a reference genome or access to commercial genotyping arrays. We highlight the pitfalls and offer the solutions to the genotyping by sequencing approach and the building of appropriate genetic resources to undertake genomic selection from first-hand experience. We describe the potential to capture large-scale commercial phenotypes based on image analysis and artificial intelligence through machine learning, as inputs for calculation of genomic breeding values. The application of genomic selection over traditional aquatic breeding programs offers significant advantages through being able to accurately predict complex polygenic traits including disease resistance; increasing rates of genetic gain; minimizing inbreeding; and negating potential limiting effects of genotype by environment interactions. Further practical advantages of genomic selection through the use of large-scale communal mating and rearing systems are highlighted, as well as presenting rate-limiting steps that impact on attaining maximum benefits from adopting genomic selection. Genomic selection is now at the tipping point where commercial applications can be readily adopted and offer significant short- and long-term solutions to sustainable and profitable aquaculture industries.
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Affiliation(s)
- Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
| | - Mehar S Khatkar
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - David B Jones
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Nima Khalilisamani
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Tropical Futures Institute, James Cook University Singapore, Singapore, Singapore
| | - Herman W Raadsma
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
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Jacobs A, Womack R, Chen M, Gharbi K, Elmer KR. Significant Synteny and Colocalization of Ecologically Relevant Quantitative Trait Loci Within and Across Species of Salmonid Fishes. Genetics 2017; 207:741-754. [PMID: 28760747 PMCID: PMC5629336 DOI: 10.1534/genetics.117.300093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 07/21/2017] [Indexed: 11/18/2022] Open
Abstract
The organization of functional regions within genomes has important implications for evolutionary potential. Considerable research effort has gone toward identifying the genomic basis of phenotypic traits of interest through quantitative trait loci (QTL) analyses. Less research has assessed the arrangement of QTL in the genome within and across species. To investigate the distribution, extent of colocalization, and the synteny of QTL for ecologically relevant traits, we used a comparative genomic mapping approach within and across a range of salmonid species. We compiled 943 QTL from all available species [lake whitefish (Coregonus clupeaformis), coho salmon (Oncorhynchus kisutch), rainbow trout (O. mykiss), Chinook salmon (O. tshawytscha), Atlantic salmon (Salmo salar), and Arctic charr (Salvelinus alpinus)]. We developed a novel analytical framework for mapping and testing the distribution of these QTL. We found no correlation between QTL density and gene density at the chromosome level but did at the fine-scale. Two chromosomes were significantly enriched for QTL. We found multiple synteny blocks for morphological, life history, and physiological traits across species, but only morphology and physiology had significantly more than expected. Two or three pairs of traits were significantly colocalized in three species (lake whitefish, coho salmon, and rainbow trout). Colocalization and fine-scale synteny suggest genetic linkage between traits within species and a conserved genetic basis across species. However, this pattern was weak overall, with colocalization and synteny being relatively rare. These findings advance our understanding of the role of genomic organization in the renowned ecological and phenotypic variability of salmonid fishes.
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Affiliation(s)
- Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
| | - Robyn Womack
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
| | - Mel Chen
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
- School of Mathematics and Statistics, College of Science and Engineering, University of Glasgow, G12 8QQ, UK
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, EH9 3FL, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
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Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin Y, Khalil K, Kocher T, Leeds T, Li N, Lindsey L, Liu S, Liu Z, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin G, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi H, Shoemaker C, Stiles S, Tan S, Tang KFJ, Thongda W, Tiersch T, Tomasso J, Prabowo WT, Vallejo R, van der Steen H, Vo K, Waldbieser G, Wang H, Wang X, Xiang J, Yang Y, Yant R, Yuan Z, Zeng Q, Zhou T. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 2017; 18:191. [PMID: 28219347 PMCID: PMC5319170 DOI: 10.1186/s12864-017-3557-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/06/2017] [Indexed: 12/31/2022] Open
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.
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Affiliation(s)
- Hisham Abdelrahman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mohamed ElHady
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | - Standish Allen
- Aquaculture Genetics & Breeding Technology Center, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Rafet Al-Tobasei
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Lisui Bao
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ben Beck
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Harvey Blackburn
- USDA-ARS-NL Wheat & Corn Collections at a Glance GRP, National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO, 80521-4500, USA
| | - Brian Bosworth
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - John Buchanan
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, Suite E, San Diego, CA, 92121, USA
| | - Jesse Chappell
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - William Daniels
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sheng Dong
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Evan Durland
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Ahmed Elaswad
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal & Veterinary Science, 134 Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Kamal Gosh
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Perry Hackett
- Department of Genetics, Cell Biology and Development, 5-108 MCB, 420 Washington Avenue SE, Minneapolis, MN, 55455, USA
| | - Terry Hanson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dennis Hedgecock
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Tiffany Howard
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Leigh Holland
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Molly Jackson
- Taylor Shellfish Farms, 130 SE Lynch RD, Shelton, WA, 98584, USA
| | - Yulin Jin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Karim Khalil
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Thomas Kocher
- Department of Biology, University of Maryland, 2132 Biosciences Research Building, College Park, MD, 20742, USA
| | - Tim Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Ning Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lauren Lindsey
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - Kyle Martin
- Troutlodge, 27090 Us Highway 12, Naches, WA, 98937, USA
| | - Romi Novriadi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ramjie Odin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dina Proestou
- USDA ARS NEA NCWMAC Shellfish Genetics at the University Rhode Island, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Guyu Qin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Benjamin Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695-7617, USA
| | - Caird Rexroad
- USDA ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD, 20705, USA
| | - Steven Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Mohamed Salem
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Andrew Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, 50011, USA
| | - Huitong Shi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Craig Shoemaker
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Sheila Stiles
- USDOC/NOAA, National Marine Fisheries Service, NEFSC, Milford Laboratory, Milford, Connectcut, 06460, USA
| | - Suxu Tan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Kathy F J Tang
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Wilawan Thongda
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Terrence Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, 70820, USA
| | - Joseph Tomasso
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Wendy Tri Prabowo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | | | - Khoi Vo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Geoff Waldbieser
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - Hanping Wang
- Aquaculture Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, OH, 45661, USA
| | - Xiaozhu Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yujia Yang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Yant
- Hybrid Catfish Company, 1233 Montgomery Drive, Inverness, MS, 38753, USA
| | - Zihao Yuan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qifan Zeng
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
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Phillis CC, Moore JW, Buoro M, Hayes SA, Garza JC, Pearse DE. Shifting Thresholds: Rapid Evolution of Migratory Life Histories in Steelhead/Rainbow Trout, Oncorhynchus mykiss. J Hered 2015; 107:51-60. [PMID: 26585381 DOI: 10.1093/jhered/esv085] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 10/07/2015] [Indexed: 11/13/2022] Open
Abstract
Expression of phenotypic plasticity depends on reaction norms adapted to historic selective regimes; anthropogenic changes in these selection regimes necessitate contemporary evolution or declines in productivity and possibly extinction. Adaptation of conditional strategies following a change in the selection regime requires evolution of either the environmentally influenced cue (e.g., size-at-age) or the state (e.g., size threshold) at which an individual switches between alternative tactics. Using a population of steelhead (Oncorhynchus mykiss) introduced above a barrier waterfall in 1910, we evaluate how the conditional strategy to migrate evolves in response to selection against migration. We created 9 families and 917 offspring from 14 parents collected from the above- and below-barrier populations. After 1 year of common garden-rearing above-barrier offspring were 11% smaller and 32% lighter than below-barrier offspring. Using a novel analytical approach, we estimate that the mean size at which above-barrier fish switch between the resident and migrant tactic is 43% larger than below-barrier fish. As a result, above-barrier fish were 26% less likely to express the migratory tactic. Our results demonstrate how rapid and opposing changes in size-at-age and threshold size contribute to the contemporary evolution of a conditional strategy and indicate that migratory barriers may elicit rapid evolution toward the resident life history on timescales relevant for conservation and management of conditionally migratory species.
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Affiliation(s)
- Corey C Phillis
- From the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060 (Phillis, Moore, and Pearse); Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada (Phillis and Moore); Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720 (Buoro); Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Rd., Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); Institute of Marine Sciences, University of California, Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); and Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA 98112 (Phillis).
| | - Jonathan W Moore
- From the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060 (Phillis, Moore, and Pearse); Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada (Phillis and Moore); Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720 (Buoro); Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Rd., Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); Institute of Marine Sciences, University of California, Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); and Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA 98112 (Phillis)
| | - Mathieu Buoro
- From the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060 (Phillis, Moore, and Pearse); Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada (Phillis and Moore); Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720 (Buoro); Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Rd., Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); Institute of Marine Sciences, University of California, Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); and Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA 98112 (Phillis)
| | - Sean A Hayes
- From the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060 (Phillis, Moore, and Pearse); Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada (Phillis and Moore); Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720 (Buoro); Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Rd., Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); Institute of Marine Sciences, University of California, Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); and Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA 98112 (Phillis)
| | - John Carlos Garza
- From the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060 (Phillis, Moore, and Pearse); Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada (Phillis and Moore); Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720 (Buoro); Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Rd., Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); Institute of Marine Sciences, University of California, Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); and Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA 98112 (Phillis)
| | - Devon E Pearse
- From the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060 (Phillis, Moore, and Pearse); Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada (Phillis and Moore); Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720 (Buoro); Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Rd., Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); Institute of Marine Sciences, University of California, Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); and Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA 98112 (Phillis)
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Genome-wide association study (GWAS) for growth rate and age at sexual maturation in Atlantic salmon (Salmo salar). PLoS One 2015; 10:e0119730. [PMID: 25757012 PMCID: PMC4355585 DOI: 10.1371/journal.pone.0119730] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/25/2015] [Indexed: 11/26/2022] Open
Abstract
Early sexual maturation is considered a serious drawback for Atlantic salmon aquaculture as it retards growth, increases production times and affects flesh quality. Although both growth and sexual maturation are thought to be complex processes controlled by several genetic and environmental factors, selection for these traits has been continuously accomplished since the beginning of Atlantic salmon selective breeding programs. In this genome-wide association study (GWAS) we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype ∼480 individuals from the Cermaq Canada broodstock program and search for SNPs associated with growth and age at sexual maturation. Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation. The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21. A lower level of association was detected with growth on Ssa13. Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation. However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.
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Richardson CJ, Bernier NJ, Danzmann RG, Ferguson MM. Phenotypic and QTL allelic associations among embryonic developmental rate, body size, and precocious maturation in male rainbow trout. Mar Genomics 2014; 18 Pt A:31-8. [PMID: 25023604 DOI: 10.1016/j.margen.2014.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/26/2014] [Accepted: 06/26/2014] [Indexed: 12/18/2022]
Abstract
We examined associations among embryonic developmental rate (EDR) as measured by hatching time, juvenile body weight (BW) and propensity for precocial sexual maturation (PM) at two years in two sets of diallel crosses of rainbow trout produced in two spawning seasons (September and December) at both the phenotypic and genotypic levels. Dams and sires had highly significant effects on the body weight of their male juvenile progeny on three measurement dates where parental effects remained consistent through time. Dams spawning earlier in the season produced a greater number of mature male progeny (56.7%) than did later spawning females (25.6%). The families from the December lot showed the expected associations among traits in that earlier hatching fish were significantly heavier on all three measurement dates than later hatching fish and were more likely to mature earlier when families were combined. Moreover, earlier maturing fish were significantly heavier on the third measurement date than those that did not mature. In the September lot, mature fish were significantly heavier as juveniles on all three measurement dates than immature fish as predicted but no significant associations were detected between EDR and BW or between PM and EDR. Significant QTL were detected for all three traits but the linkage group location varied depending on the trait and half-sib group analyzed (across dams and sires in each lot). A strong QTL for EDR with genome-wide effects was detected on linkage group RT-8 in all four half-sib analyses. None of the four linkage groups analyzed had QTL for all three traits. However, the phenotypic association between EDR and BW observed in the December lot was supported by the co-localization of QTL to linkage group RT-8 and a positive coupling of allelic effects. RT-8 marker alleles significantly associated with faster EDR were also associated with larger BW and this was observed in numerous families on all three measurement dates. Linkage group RT-24 had weaker QTL for all three traits in the September lot but these were not detected in the same half-sib group simultaneously. At the allelic level, marker alleles for faster EDR were also associated with BW but only at the third measurement date and the progeny of one male. Similarly, RT-30 had weaker QTL for EDR and PM in the December paternal half-sib analysis but no associations were evident at the allelic level. The detection of associations between life history traits and growth at both the phenotypic and genotypic levels has significant implications to aquaculture breeding programs where selection for a desirable trait may lead to unwanted alterations of other traits. Furthermore, the differences between spawning season lots emphasize the complex interaction between environment and genotype on economically important traits and the resulting challenges for aquaculture.
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Affiliation(s)
- Colin J Richardson
- Department of Integrative Biology, University of Guelph, Guelph N1G2W1, Canada
| | - Nicholas J Bernier
- Department of Integrative Biology, University of Guelph, Guelph N1G2W1, Canada
| | - Roy G Danzmann
- Department of Integrative Biology, University of Guelph, Guelph N1G2W1, Canada
| | - Moira M Ferguson
- Department of Integrative Biology, University of Guelph, Guelph N1G2W1, Canada.
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7
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Allen MS, Ferguson MM, Danzmann RG. Molecular markers for variation in spawning date in a hatchery population of rainbow trout (Oncorhynchus mykiss). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:289-298. [PMID: 24114565 DOI: 10.1007/s10126-013-9547-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 09/15/2013] [Indexed: 06/02/2023]
Abstract
We examined the distribution of alleles at 63 microsatellite loci distributed across 29 linkage groups in broodstock females from a commercial population of rainbow trout spawning on different dates throughout the season (August to January). A total of 368 females, 184 and 117 females from each of the tail-ends of the spawning distribution and a subsample of 67 females spawning in the middle, were used to detect marker-trait associations. Twenty-one loci in a subset of genomic regions (RT-5, 7, 8, 10, 12, 14, 15, 22, 23, 24, 25, 29, 30, and 31) were significantly associated with variation in spawning date. Many of these markers localize to regions with known spawning date quantitative trait loci based on previous studies. An individual assignment analysis was used to test how well the molecular data could be used to assign individuals to their correct spawning group, and markers were given a ranking reflecting their contribution to the accuracy of assignment. The top 15 ranked markers were successful at assigning the majority of females to the correct spawning group based on genotype with an average accuracy of 76 %. The most likely genes that could contribute to these differences in spawning date are discussed. Together, these data indicate that the loci could be incorporated into a selection index with phenotype data to increase the accuracy of selection for spawning date.
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Affiliation(s)
- M S Allen
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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8
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Hale MC, Colletti JA, Gahr SA, Scardina J, Thrower FP, Harmon M, Carter M, Phillips RB, Thorgaard GH, Rexroad CE, Nichols KM. Mapping and Expression of Candidate Genes for Development Rate in Rainbow Trout (Oncorhynchus mykiss). J Hered 2014; 105:506-520. [PMID: 24744432 DOI: 10.1093/jhered/esu018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 02/13/2014] [Indexed: 01/21/2023] Open
Abstract
Development rate has important implications for individual fitness and physiology. In salmonid fishes, development rate correlates with many traits later in life, including life-history diversity, growth, and age and size at sexual maturation. In rainbow trout (Oncorhynchus mykiss), a quantitative trait locus for embryonic development rate has been detected on chromosome 5 across populations. However, few candidate genes have been identified within this region. In this study, we use gene mapping, gene expression, and quantitative genetic methods to further identify the genetic basis of embryonic developmental rate in O. mykiss Among the genes located in the region of the major development rate quantitative trait locus (GHR1, Clock1a, Myd118-1, and their paralogs), all were expressed early in embryonic development (fertilization through hatch), but none were differentially expressed between individuals with the fast- or slow-developing alleles for a major embryonic development rate quantitative trait locus. In a follow-up study of migratory and resident rainbow trout from natural populations in Alaska, we found significant additive variation in development rate and, moreover, found associations between development rate and allelic variation in all 3 candidate genes within the quantitative trait locus for embryonic development. The mapping of these genes to this region and associations in multiple populations provide positional candidates for further study of their roles in growth, development, and life-history diversity in this model salmonid.
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Affiliation(s)
- Matthew C Hale
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - John A Colletti
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Scott A Gahr
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Julie Scardina
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Frank P Thrower
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Matthew Harmon
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Megan Carter
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Ruth B Phillips
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Gary H Thorgaard
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Caird E Rexroad
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Krista M Nichols
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols).
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Pearse DE, Miller MR, Abadía-Cardoso A, Garza JC. Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout. Proc Biol Sci 2014; 281:20140012. [PMID: 24671976 DOI: 10.1098/rspb.2014.0012] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.
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Affiliation(s)
- Devon E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, , 110 Shaffer Road, Santa Cruz, CA 95060, USA, Institute of Marine Sciences, University of California, , Santa Cruz, CA 95060, USA, Institute of Molecular Biology, University of Oregon, , Eugene, OR 97403, USA, Department of Animal Science, University of California, , One Shields Avenue, Davis, CA 95616, USA
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10
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Gutierrez AP, Lubieniecki KP, Fukui S, Withler RE, Swift B, Davidson WS. Detection of quantitative trait loci (QTL) related to grilsing and late sexual maturation in Atlantic salmon (Salmo salar). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:103-110. [PMID: 23912817 PMCID: PMC3896801 DOI: 10.1007/s10126-013-9530-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 07/15/2013] [Indexed: 06/02/2023]
Abstract
In Atlantic salmon aquaculture, early sexual maturation represents a major problem for producers. This is especially true for grilse, which mature after one sea winter before reaching a desirable harvest weight, rather than after two sea winters. Salmon maturing as grilse have a much lower market value than later maturing individuals. For this reason, most companies desire fish that grow fast and mature late. Marker-assisted selection has the potential to improve the efficiency of selection against early maturation and for late sexual maturation; however, studies identifying age of sexual maturation-related genetic markers are lacking for Atlantic salmon. Therefore, we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype five families from the Mainstream Canada broodstock program and search for SNPs associated with early (grilsing) or late sexual maturation. There were 529 SNP loci that were variable across all five families, and this was the set that was used for quantitative trait loci (QTL) analysis. GridQTL identified two chromosomes, Ssa10 and Ssa21, containing QTL related to grilsing. In contrast, only one QTL, on Ssa18, was found linked to late maturation in Atlantic salmon. Our previous work on these five families did not identify genome-wide significant growth-related QTL on Ssa10, Ssa21, or Ssa18. Therefore, taken together, these results suggest that both grilsing and late sexual maturation are controlled independently of one another and also from growth-related traits. The identification of genomic regions associated with grilsing or late sexual maturation provide an opportunity to incorporate this information into selective breeding programs that will enhance Atlantic salmon farming.
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Affiliation(s)
- Alejandro P. Gutierrez
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia Canada V5A 1S6
| | - Krzysztof P. Lubieniecki
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia Canada V5A 1S6
| | - Steve Fukui
- Mainstream Canada, 203-919 Island Highway, Campbell River, British Columbia Canada V9W 2C2
| | - Ruth E. Withler
- Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, British Columbia Canada V9T 6N7
| | - Bruce Swift
- TRI-GEN Fish Improvement Ltd., 2244 Wilson Road, Agassiz, British Columbia Canada V0M 1A0
| | - William S. Davidson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia Canada V5A 1S6
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11
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Sauvage C, Vagner M, Derôme N, Audet C, Bernatchez L. Coding Gene Single Nucleotide Polymorphism Mapping and Quantitative Trait Loci Detection for Physiological Reproductive Traits in Brook Charr, Salvelinus fontinalis. G3 (BETHESDA, MD.) 2012; 2:379-92. [PMID: 22413092 PMCID: PMC3291508 DOI: 10.1534/g3.111.001867] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 01/19/2012] [Indexed: 11/24/2022]
Abstract
A linkage map of 40 linkage groups (LGs) was developed for brook charr, Salvelinus fontinalis, using an F(2) interstrain hybrid progeny (n = 171) and 256 coding gene SNP developed specifically for brook charr and validated from a large (>1000) subset of putative SNP, as well as 81 microsatellite markers. To identify quantitative trait loci (QTL) related to reproduction functions, these fish were also phenotyped at six physiological traits, including spermatozoid head diameter, sperm concentration, plasma testosterone, plasma 11-keto-testosterone, egg diameter, and plasma 17β-estradiol. Five significant QTL were detected over four LGs for egg diameter and plasma 17β-estradiol concentration in females, and sperm concentration as well as spermatozoid head diameter in males. In females, two different QTLs located on LG 11 and LG 34 were associated with the egg number, whereas one QTL was associated with plasma 17β-estradiol concentration (LG 8). Their total percent variance explained (PVE) was 26.7% and 27.6%, respectively. In males, two QTL were also detected for the sperm concentration, and their PVE were estimated at 18.58% and 14.95%, respectively. The low QTL number, associated with the high PVE, suggests that the variance in these reproductive physiological traits was either under the control of one major gene or a small number of genes. The QTL associated with sperm concentration, plasma 17β-estradiol, and egg diameter appeared to be under a dominance effect, whereas the two others were under a negative additive effect. These results show that genes underlying the phenotypic variance of these traits are under different modes of action (additive vs. dominance) and may be used to predict an increase or a decrease in their phenotypic values in subsequent generations of selective breeding. Moreover, this newly developed panel of mapped SNP located in coding gene regions will be useful for screening wild populations, especially in the context of investigating the genetic impact of massive stocking of domestic brook charr to support the angling industry throughout eastern North America.
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Affiliation(s)
- Christopher Sauvage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec (Québec) Canada, G1V 0A6
- INRA, UR1052, Unité de Génétique et d’Amélioration des Fruits et Légumes, 84143 Montfavet, France
| | - Marie Vagner
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Rimouski (Québec) Canada, G5L 3A1
- Institut du Littoral et de l’Environnement, LIENSs UMR6250, 2 rue Olympe de Gouges, 17000 La Rochelle, France
| | - Nicolas Derôme
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec (Québec) Canada, G1V 0A6
| | - Céline Audet
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Rimouski (Québec) Canada, G5L 3A1
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec (Québec) Canada, G1V 0A6
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Küttner E, Moghadam HK, Skúlason S, Danzmann RG, Ferguson MM. Genetic architecture of body weight, condition factor and age of sexual maturation in Icelandic Arctic charr (Salvelinus alpinus). Mol Genet Genomics 2011; 286:67-79. [PMID: 21626198 DOI: 10.1007/s00438-011-0628-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 05/10/2011] [Indexed: 12/16/2022]
Abstract
The high commercial value from the aquaculture of salmonid fishes has prompted many studies into the genetic architecture of complex traits and the need to identify genomic regions that have repeatable associations with trait variation both within and among species. We searched for quantitative trait loci (QTL) for body weight (BW), condition factor (CF) and age of sexual maturation (MAT) in families of Arctic charr (Salvelinus alpinus) from an Icelandic breeding program. QTL with genome-wide significance were detected for each trait on multiple Arctic charr (AC) linkage groups (BW: AC-4, AC-20; CF: AC-7, AC-20, AC-23, AC-36; MAT: AC-13/34, AC-39). In addition to the genome-wide significant QTL for both BW and CF on AC-20, linkage groups AC-4, AC-7, AC-8, and AC-16 contain QTL for both BW and CF with chromosome-wide significance. These regions had effects (albeit weaker) on MAT with the exception of the region on AC-8. Comparisons with a North American cultured strain of Arctic charr, as well as North American populations of Atlantic salmon (Salmo salar), and rainbow trout (Oncorhynchus mykiss), reveal some conservation in QTL location and structure, particularly with respect to the joint associations of QTL influencing BW and CF. The detection of some differences in genetic architecture between the two aquaculture strains of Arctic charr may be reflective of the differential evolutionary histories experienced by these fishes, and illustrates the importance of including different strains to investigate genetic variation in a species where the intent is to use that variation in selective breeding programs.
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Affiliation(s)
- Eva Küttner
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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