Open Access
Review
Issue |
Aquat. Living Resour.
Volume 38, 2025
|
|
---|---|---|
Article Number | 11 | |
Number of page(s) | 24 | |
DOI | https://doi.org/10.1051/alr/2025006 | |
Published online | 23 June 2025 |
- Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao LS, 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 XM, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin YL, Khalil K, Kocher T, Leeds T, Li N, Lindsey L, Liu SK, Liu ZJ, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin GY, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi HT, Shoemaker C, Stiles S, Tan SX, Tang KFJ, Thongda W, Tiersch T, Tomasso J, Prabowo WT, Vallejo R, van der Steen F H, Vo K, Waldbieser G, Wang HP, Wang XZ, Xiang JH, Yang YJ, Yant R, Yuan ZH, Zeng QF, Zhou T, Bre AGG. 2017. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 18: 235. [CrossRef] [PubMed] [Google Scholar]
- Abdollahi-Arpanahi LR, Gianola D, Peñagaricano F. 2020. Deep learning versus parametric and ensemble methods for genomic prediction of complex phenotypes. Genet Sel Evol 52: 12. [CrossRef] [PubMed] [Google Scholar]
- Anderson JH, Pess GR, Carmichael RW, Ford MJ, Cooney TD, Baldwin CM, McClure MM. 2014. Planning Pacific salmon and steelhead reintroductions aimed at long-term viability and recovery. N Am J Fish Manage 34: 72–93. [CrossRef] [Google Scholar]
- Araki H, Cooper B, Blouin MS. 2007. Genetic effects of captive breeding cause a rapid, cumulative fitness decline in the wild. Science 318: 100–103. [CrossRef] [PubMed] [Google Scholar]
- Ashton DT, Hilario E, Jaksons P, Ritchie PA, Wellenreuther M. 2019. Genetic diversity and heritability of economically important traits in captive Australasian snapper (Chrysophrys auratus). Aquaculture 505: 190–198. [CrossRef] [Google Scholar]
- Attard CRM, Möller LM, Sasaki M, Hammer MP, Bice CM, Brauer CJ, Carvalho DC, Harris JO, Beheregaray LB. 2016. A novel holistic framework for genetic-based captive-breeding and reintroduction programs. Conserv Biol 30: 1060–1069. [CrossRef] [PubMed] [Google Scholar]
- Auld HL, Jacobson DP, Rhodes AC, Banks MA. 2021. Differences in mate pairings of hatchery- and natural-origin Coho salmon inferred from offspring genotypes. Integr Organism Biol 3: obab020. [CrossRef] [Google Scholar]
- Azodi CB, Bolger E, McCarren A, Roantree M, de los Campos G, Shiu SH. 2019. Benchmarking parametric and machine learning models for genomic prediction of complex traits. G3-Genes Genom Genet 9: 3691–3702. [Google Scholar]
- Baetscher DS, Clemento AJ, Ng TC, Anderson EC, Garza JC. 2018. Microhaplotypes provide increased power from short-read DNA sequences for relationship inference. Mol Ecol Resour 18: 296–305. [CrossRef] [PubMed] [Google Scholar]
- Balon EK. 2004. About the oldest domesticates among fishes. J Fish Biol 65(s1): 1–27. [Google Scholar]
- Barria A, Benzie JAH, Houston RD, De Koning DJ, de Verdal H. 2021. Genomic selection and genome-wide association study for feed-efficiency traits in a farmed Nile tilapia (Oreochromis niloticus) population. Front Genet 12: 737906. [CrossRef] [PubMed] [Google Scholar]
- Barson NJ, Aykanat T, Hindar K, Baranski M, Bolstad GH, Fiske P, Jacq C, Jensen AJ, Johnston SE, Karlsson S, Kent M, Oen TM, Niemelä E, Nome T, Næsje TF, Orell P, Romakkaniemi A, Sægrov H, Urdal K, Erkinaro J, Lien S, Primmer CR. 2015. Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon. Nature 528: 405–408. [CrossRef] [PubMed] [Google Scholar]
- Bay RA, Harrigan RJ, Underwood VL, Gibbs HL, Smith TB, Ruegg K. 2018. Genomic signals of selection predict climate-driven population declines in a migratory bird. Science 359: 83–86. [CrossRef] [PubMed] [Google Scholar]
- Bean TP, Tanguy A, Peñaloza C, Gundappa MK, Boutet I, Houston RD, Macqueen DJ, Boudry P. 2022. Two parallel chromosome-level reference genomes to support restoration and aquaculture of European flat oyster Ostrea edulis. Evol Appl 15: 1709–1712. [CrossRef] [PubMed] [Google Scholar]
- Bernatchez S, Xuereb A, Laporte M, Benestan L, Steeves R, Laflamme M, Bernatchez L, Mallet MA. 2019. Seascape genomics of eastern oyster (Crassostrea virginica) along the Atlantic coast of Canada. Evol Appl 12: 587–609. [CrossRef] [PubMed] [Google Scholar]
- Besnier F, Ayllon F, Skaala O, Solberg MF, Fjeldheim PT, Anderson K, Knutar S, Glover KA. 2022. Introgression of domesticated salmon changes life history and phenology of a wild salmon population. Evol Appl 15: 853–864. [CrossRef] [PubMed] [Google Scholar]
- Besson M, Allal F, Chatain B, Vergnet A, Clota F, Vandeputte M. 2019. Combining individual phenotypes of feed intake with genomic data to improve feed efficiency in sea bass. Front Genet 10: 219. [CrossRef] [PubMed] [Google Scholar]
- Besson M, Rombout N, Salou G, Vergnet A, Cariou S, Bruant JS, Izquierdo M, Bestin A, Clota F, Haffray P, Allal F, Vandeputte M. 2022. Potential for genomic selection on feed efficiency in gilthead sea bream (Sparus aurata), based on individual feed conversion ratio, carcass and lipid traits. Aquacult Rep 24: 101171. [Google Scholar]
- Bolstad GH, Hindar K, Robertsen G, Jonsson B, Sægrov H, Diserud OH, Fiske P, Jensen AJ, Urdal K, Næsje TF, Barlaup BT, Floro-Larsen B, Lo H, Niemelä E, Karlsson S. 2017. Gene flow from domesticated escapes alters the life history of wild Atlantic salmon. Nat Ecol Evol 1: 124. [CrossRef] [PubMed] [Google Scholar]
- Bolstad GH, Karlsson S, Hagen IJ, Fiske P, Urdal K, Sægrov H, Floro-Larsen B, Sollien VP, Ostborg G, Diserud OH, Jensen AJ, Hindar K. 2021. Introgression from farmed escapees affects the full life cycle of wild Atlantic salmon. Sci Adv 7: eabj3397. [CrossRef] [PubMed] [Google Scholar]
- Bootsma ML, Gruenthal KM, McKinney GJ, Simmons L, Miller L, Sass GG, Larson WA. 2020. A GT-seq panel for walleye (Sander vitreus) provides important insights for efficient development and implementation of amplicon panels in non-model organisms. Mol Ecol Resour 20: 1706–1722. [CrossRef] [PubMed] [Google Scholar]
- Bossu CM, Rodriguez M, Rayne C, Chromczak DA, Higgins PG, Trulio LA, Ruegg KC. 2023. Genomic approaches to mitigating genetic diversity loss in declining populations. Mol Ecol 32: 5228–5240. [CrossRef] [PubMed] [Google Scholar]
- Boudry P, Allal F, Aslam ML, Bargelloni L, Bean TP, Brard-Fudulea S, Brieuc MSO, Calboli FCF, Gilbey J, Haffray P, Lamy JB, Morvezen R, Purcell C, Prodohl PA, Vandeputte M, Waldbieser GC, Sonesson AK, Houston RD. 2021. Current status and potential of genomic selection to improve selective breeding in the main aquaculture species of International Council for the Exploration of the Sea (ICES) member countries. Aquacult Rep 20: 100700. [Google Scholar]
- Boutet I, Monteiro HJA, Baudry L, Takeuchi T, Bonnivard E, Billoud B, Farhat S, Gonzales-Araya R, Salaun B, Andersen AC, Toullec JY, Lallier FH, Flot JF, Guiglielmoni N, Guo XM, Li C, Allam B, Pales-Espinosa E, Hemmer-Hansen J, Moreau P, Marbouty M, Koszul R, Tanguy A. 2022. Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic resource for aquaculture. Evol Appl 15: 1730–1748. [CrossRef] [PubMed] [Google Scholar]
- Bradbury IR, Lehnert SJ, Kess T, Van Wyngaarden M, Duffy S, Messmer AM, Wringe B, Karoliussen S, Dempson JB, Fleming IA, Solberg MF, Glover KA, Bentzen P. 2022. Genomic evidence of recent European introgression into North American farmed and wild Atlantic salmon. Evol Appl 15: 1436–1448. [CrossRef] [PubMed] [Google Scholar]
- Bradbury IR, Wringe BF, Watson B, Paterson I, Horne J, Beiko R, Lehnert SJ, Clément M, Anderson EC, Jeffery NW, Duffy S, Sylvester E, Robertson M, Bentzen P. 2018. Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery. Evol Appl 11: 918–930. [CrossRef] [PubMed] [Google Scholar]
- Brieuc MSO, Waters CD, Drinan DP, Naish KA. 2018. A practical introduction to random forest for genetic association studies in ecology and evolution. Mol Ecol Resour 18: 755–766. [CrossRef] [PubMed] [Google Scholar]
- Capblancq T, Fitzpatrick MC, Bay RA, Exposito-Alonso M, Keller SR. 2020. Genomic prediction of (mal)adaptation across current and future climatic landscapes. Annu Rev Ecol Evol Syst 51: 245–269. [CrossRef] [Google Scholar]
- Casey J, Jardim E, Martinsohn JT. 2016. The role of genetics in fisheries management under the EU common fisheries policy. J Fish Biol 89: 2755–2767. [CrossRef] [PubMed] [Google Scholar]
- Catanach A, Ruigrok M, Bowatte D, Davy M, Storey R, Valenza-Troubat N, López-Girona E, Hilario E, Wylie MJ, Chagné D, Wellenreuther M. 2021. The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus. BMC Genomics 22: 302. [CrossRef] [PubMed] [Google Scholar]
- Chang SL, Ward HGM, Russello MA. 2021. Genotyping-in-thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales. PLoS One 16: e0261966. [CrossRef] [PubMed] [Google Scholar]
- Chen Z. 2020. Proof of concept: efficacy of cleaner fish, cultured juvenile cunner (Tautogolabrus adsperus), for sea lice (Lepeophtheirus salmonis) mitigation and control in Atlantic salmon (Salmo salar). PhD thesis, Memorial University of Newfoundland. Available at: http://research.library.mun.ca/id/eprint/15071 [Google Scholar]
- Chistiakov DA, Hellemans B, Volckaert FAM. 2006. Microsatellites and their genomic distribution, evolution, function and applications: a review with special reference to fish genetics. Aquaculture 255: 1–29. [CrossRef] [Google Scholar]
- Christie MR, French RA, Marine ML, Blouin MS. 2013. How much does inbreeding contribute to the reduced fitness of hatchery-born steelhead (Oncorhynchus mykiss) in the wild? J Hered 105: 111–119. [Google Scholar]
- Christie MR, Marine ML, French RA, Waples RS, Blouin MS. 2012. Effective size of a wild salmonid population is greatly reduced by hatchery supplementation. Heredity 109: 254–260. [CrossRef] [PubMed] [Google Scholar]
- Colihueque N. 2010. Genetics of salmonid skin pigmentation: clues and prospects for improving the external appearance of farmed salmonids. Rev Fish Biol Fish 20: 71–86. [CrossRef] [Google Scholar]
- Colihueque N, Araneda C. 2014. Appearance traits in fish farming: progress from classical genetics to genomics, providing insight into current and potential genetic improvement. Front Genet 5: 251. [CrossRef] [PubMed] [Google Scholar]
- Colsoul B, Boudry P, Pérez-Parallé ML, Bratoš Cetinić A, Hugh-Jones T, Arzul I, Mérou N, Wegner KM, Peter C, Merk V, Pogoda B. 2021. Sustainable large-scale production of European flat oyster (Ostrea edulis) seed for ecological restoration and aquaculture: a review. Rev Aquacult 13: 1423–1468. [CrossRef] [Google Scholar]
- Costa I, Hamoutene D, Murray H, Lush L, Burt K, Eaves A, Keng P. 2016. Documentation of cunner (Tautogolabrus adspersus) cleaning behaviour in tanks with Atlantic salmon (Salmo salar) smolts infested with sea lice (Lepeophtheirus salmonis). Can Tech Rep Fish Aquat Sci 3168: iv + 11 p. [Google Scholar]
- D'Agaro E, Favaro A, Matiussi S, Gibertoni PP, Esposito S. 2021. Genomic selection in salmonids: new discoveries and future perspectives. Aquacult Int 29: 2259–2289. [CrossRef] [Google Scholar]
- D'Ambrosio J, Phocas F, Haffray P, Bestin A, Brard-Fudulea S, Poncet C, Quillet E, Dechamp N, Fraslin C, Charles M, Dupont-Nivet M. 2019. Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding. Genet Sel Evol 51: 26. [CrossRef] [PubMed] [Google Scholar]
- Davidson WS, Birt TP, Green JM. 1989. A review of genetic variation in Atlantic salmon, Salmo salar L., and its importance for stock identification, enhancement programs and aquaculture. J Fish Biol 34: 547–560. [CrossRef] [Google Scholar]
- Devlin RH, Sundström LF, Leggatt RA. 2015. Assessing ecological and evolutionary consequences of growth-accelerated genetically engineered fishes. Bioscience 65: 685–700. [CrossRef] [Google Scholar]
- Devlin RH, Sundström LF, Muir WM. 2006. Interface of biotechnology and ecology for environmental risk assessments of transgenic fish. Trends Biotechnol 24: 89–97. [CrossRef] [PubMed] [Google Scholar]
- DFO. 2018. Environmental and indirect human health risk assessment of the Glofish® Electric Green® Tetra and the Glofish® Long-Fin Electric Green® Tetra (Gymnocorymbus ternetzi): a transgenic ornamental fish. DFO Can. Sci. Advis. Sec. Sci. Advis. Rep. 2018/027. [Google Scholar]
- DFO. 2018. Review of the science associated with the Inner Bay of Fundy Atlantic salmon Live Gene Bank and supplementation programs. DFO Can. Sci. Advis. Sec. Sci. Advis. Rep. 2018/041. [Google Scholar]
- DFO. 2019. Environmental and indirect human health risk assessment of the GloFish® Tetras (Gymnocorymbus ternetzi): five lines of transgenic ornamental fish. DFO Can. Sci. Advis. Sec. Sci. Advis. Rep. 2019/002. [Google Scholar]
- DFO. 2020. Environmental and indirect human health risk assessment of the GloFish® Cosmic Blue® and Galactic Purple® Danios (Danio rerio): transgenic ornamental fish. DFO Can. Sci. Advis. Sec. Sci. Advis. Rep. 2020/016. [Google Scholar]
- DFO. 2020. Environmental and indirect human health risk assessment of the GloFish® Sunburst Orange® Danio (Danio rerio): a transgenic ornamental fish. DFO Can. Sci. Advis. Sec. Sci. Advis. Rep. 2020/015. [Google Scholar]
- DFO. 2021. Environmental and indirect human health risk assessment of the GloFish® Bettas: three lines of transgenic ornamental fish. DFO Can. Sci. Advis. Sec. Sci. Advis. Rep. 2021/046. [Google Scholar]
- Diamond J. 2002. Evolution, consequences and future of plant and animal domestication. Nature 418: 700–707. [CrossRef] [PubMed] [Google Scholar]
- Dietrich C, Leggatt R, McGowan C. 2022. Environmental risk assessment of the GloFish® Starfire Red®, Electric Green®, Sunburst Orange®, and Galactic Purple® Barbs (Puntigrus tetrazona): transgenic ornamental fishes. DFO Can. Sci. Advis. Sec. Res. Doc. 2022/077: vii + 34 p. [Google Scholar]
- Divilov K, Merz N, Schoolfield B, Green TJ, Langdon C. 2023. Marker-assisted selection in a Pacific oyster population for an antiviral QTL conferring increased survival to OsHV-1 mortality events in Tomales Bay. Aquaculture 567: 739217. [Google Scholar]
- Doudna JA, Charpentier E. 2014. The new frontier of genome engineering with CRISPR-Cas9. Science 346: 1258096. [Google Scholar]
- Du SJ, Gong ZY, Fletcher GL, Shears MA, King MJ, Idler DR, Hew CL. 1992. Growth enhancement in transgenic Atlantic salmon by the use of an all fish chimeric growth-hormone gene construct. Bio-Technol 10: 176–181. [Google Scholar]
- Einfeldt AL, Kess T, Messmer A, Duffy S, Wringe BF, Fisher J, den Heyer C, Bradbury IR, Ruzzante DE, Bentzen P. 2021. Chromosome level reference of Atlantic halibut Hippoglossus hippoglossus provides insight into the evolution of sexual determination systems. Mol Ecol Resour 21: 1686–1696. [CrossRef] [PubMed] [Google Scholar]
- Enbody ED, Pettersson ME, Sprehn CG, Palm S, Wickström H, Andersson L. 2021. Ecological adaptation in European eels is based on phenotypic plasticity. Proc Natl Acad Sci USA 118: e2022620118. [CrossRef] [PubMed] [Google Scholar]
- Espiñeira M, Vieites JM. 2016. Genetic system for an integral traceability of European eel (Anguilla anguilla) in aquaculture and seafood products: authentication by fast real-time PCR. Eur Food Res Technol 242: 25–31. [CrossRef] [Google Scholar]
- Euclide PT, Larson WA, Bootsma M, Miller LM, Scribner KT, Stott W, Wilson CC, Latch EK. 2022. A new GTSeq resource to facilitate multijurisdictional research and management of walleye Sander vitreus. Ecol Evol 12: e9591. [CrossRef] [PubMed] [Google Scholar]
- Fernández Sánchez JL, Llorente I, Basurco B, Aguilera C. 2022. Assessing the economic impact of key operational factors on grow-out farms producing European sea bass under different scenarios of production. Aquacult Econ Manag 26: 232–250. [CrossRef] [Google Scholar]
- Frankham R. 2010. Challenges and opportunities of genetic approaches to biological conservation. Biol Conserv 143: 1919–1927. [CrossRef] [Google Scholar]
- Fuji K, Hasegawa O, Honda K, Kumasaka K, Sakamoto T, Okamoto N. 2007. Marker-assisted breeding of a lymphocystis disease-resistant Japanese flounder (Paralichthys olivaceus). Aquaculture 272: 291–295. [CrossRef] [Google Scholar]
- Gaj T, Gersbach CA, Barbas CF. 2013. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31: 397–405. [CrossRef] [PubMed] [Google Scholar]
- Gao GT, Waldbieser GC, Youngblood RC, Zhao DY, Pietrak MR, Allen MS, Stannard JA, Buchanan JT, Long RL, Milligan M, Burr G, Mejia-Guerra K, Sheehan MJ, Scheffler BE, Rexroad CE, Peterson BC, Palti Y. 2023. The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon. G3-Genes Genom Genet 13. [Google Scholar]
- Garcia ALS, Bosworth B, Waldbieser G, Misztal I, Tsuruta S, Lourenco DAL. 2018. Development of genomic predictions for harvest and carcass weight in channel catfish. Genet Sel Evol 50: 66. [CrossRef] [PubMed] [Google Scholar]
- Gautason E, Sahana G, Guldbrandtsen B, Berg P. 2022. Optimum contribution selection in a dairy cattle population with different relationship matrices. In: Proc 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Wageningen Academic Publishers, 2769–2772. [CrossRef] [Google Scholar]
- Gebregiwergis GT, Sorensen AC, Henryon M, Meuwissen T. 2020. Controlling coancestry and thereby future inbreeding by optimum-contribution selection using alternative genomic-relationship matrices. Front Genet 11: 345. [CrossRef] [PubMed] [Google Scholar]
- Ghildiyal K, Nayak SS, Rajawat D, Sharma A, Chhotaray S, Bhushan B, Dutt T, Panigrahi M. 2023. Genomic insights into the conservation of wild and domestic animal diversity: a review. Gene 886: 147719. [CrossRef] [PubMed] [Google Scholar]
- Ginson R, Walter RP, Mandrak NE, Beneteau CL, Heath DD. 2015. Hierarchical analysis of genetic structure in the habitat-specialist Eastern Sand Darter (Ammocrypta pellucida). Ecol Evol 5: 695–708. [CrossRef] [PubMed] [Google Scholar]
- Gjedrem T. 1985. Improvement of productivity through breeding schemes. GeoJournal 10: 233–241. [CrossRef] [Google Scholar]
- Gjedrem T, Gjoen HM, Gjerde B. 1991. Genetic origin of Norwegian farmed Atlantic salmon. Aquaculture 98: 41–50. [CrossRef] [Google Scholar]
- Gjedrem T, Robinson N, Rye M. 2012. The importance of selective breeding in aquaculture to meet future demands for animal protein: a review. Aquaculture 350: 117–129. [CrossRef] [Google Scholar]
- Gong J, Zhao J, Ke QZ, Li BJ, Zhou ZX, Wang JY, Zhou T, Zheng WQ, Xu P. 2022. First genomic prediction and genome-wide association for complex growth-related traits in Rock Bream (Oplegnathus fasciatus). Evol Appl 15: 523–536. [CrossRef] [PubMed] [Google Scholar]
- Gundappa MK, Peñaloza C, Regan T, Boutet I, Tanguy A, Houston RD, Bean TP, Macqueen DJ. 2022. Chromosome-level reference genome for European flat oyster (Ostrea edulis L.). Evol Appl 15: 1713–1729. [CrossRef] [PubMed] [Google Scholar]
- Gundappa MK, Robledo D, Hamilton A, Houston RD, Prendergast JGD, Macqueen DJ. 2023. High performance imputation of structural and single nucleotide variants in Atlantic salmon using low-coverage whole genome sequencing. bioRxiv, https://doi.org/10.1101/2023.03.05.531147. [Google Scholar]
- Güralp H, Skaftnesmo KO, Kjærner-Semb E, Straume AH, Kleppe L, Schulz RW, Edvardsen RB, Wargelius A. 2020. Rescue of germ cells in dnd crispant embryos opens the possibility to produce inherited sterility in Atlantic salmon. Sci Rep-UK 10: 18042. [CrossRef] [Google Scholar]
- Gutierrez AP, Matika O, Bean TP, Houston RD. 2018. Genomic selection for growth traits in Pacific oyster (Crassostrea gigas): potential of low-density marker panels for breeding value prediction. Front Genet 9: 391. [CrossRef] [PubMed] [Google Scholar]
- Gutierrez AP, Turner F, Gharbi K, Talbot R, Lowe NR, Peñaloza C, McCullough M, Prodöhl PA, Bean TP, Houston RD. 2017. Development of a medium density combined-species SNP array for Pacific and European oysters (Crassostrea gigas and Ostrea edulis). G3-Genes Genom Genet 7: 2209–2218. [CrossRef] [Google Scholar]
- Hagen IJ, Jensen AJ, Bolstad GH, Diserud OH, Hindar K, Lo H, Karlsson S. 2019. Supplementary stocking selects for domesticated genotypes. Nat Commun 10: 199. [CrossRef] [PubMed] [Google Scholar]
- Hagen IJ, Ugedal O, Jensen AJ, Lo H, Holthe E, Bjoru B, Floro-Larsen B, Sægrov H, Skoglund H, Karlsson S. 2021. Evaluation of genetic effects on wild salmon populations from stock enhancement. ICES J Mar Sci 78: 900–909. [CrossRef] [Google Scholar]
- Håstein T, Hill BJ, Berthe F, Lightner DV. 2001. Traceability of aquatic animals. Rev Sci Tech OIE 20: 564–583. [CrossRef] [PubMed] [Google Scholar]
- Herlin M, Delghandi M, Wesmajervi M, Taggart JB, McAndrew BJ, Penman DJ. 2008. Analysis of the parental contribution to a group of fry from a single day of spawning from a commercial Atlantic cod (Gadus morhua) breeding tank. Aquaculture 274: 218–224. [CrossRef] [Google Scholar]
- Herlin M, Taggart JB, McAndrew BJ, Penman DJ. 2007. Parentage allocation in a complex situation: a large commercial Atlantic cod (Gadus morhua) mass spawning tank. Aquaculture 272 (Suppl. 1): S195– S203. [CrossRef] [Google Scholar]
- Hess JE, Zendt JS, Matala AR, Narum SR. 2016. Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing. Proc R Soc B-Biol Sci 283: 20153064. [CrossRef] [PubMed] [Google Scholar]
- Hoban S, Kelley JL, Lotterhos KE, Antolin MF, Bradburd G, Lowry DB, Poss ML, Reed LK, Storfer A, Whitlock MC. 2016. Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions. Am Nat 188: 379–397. [CrossRef] [PubMed] [Google Scholar]
- Holborn MK, Ang KP, Elliott JAK, Powell F, Boulding EG. 2020. Genome wide analysis of infectious salmon anemia resistance in commercial Saint John River Atlantic salmon. Aquaculture 514. [Google Scholar]
- Holborn MK, Einfeldt AL, Kess T, Duffy SJ, Messmer AM, Langille BL, Brachmann MK, Gauthier J, Bentzen P, Knutsen TM, Kent M, Boyce D, Bradbury IR. 2022. Reference genome of lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway. Mol Ecol Resour 22: 1427–1439. [CrossRef] [PubMed] [Google Scholar]
- Holborn MK, Kess T, Nugent CM, Brodeur NN, Adesola J, Cronmiller E, Hamilton LC, Jones RA, Lenentine BL, Macdonnell A, Mcbride M, Messmer A, de Mestral L, Moreau DTR, Wilson T, Bradbury IR, Wringe BF. 2025. Improved estimation of aquaculture associated European introgression in a captive breeding program for endangered Atlantic salmon. Conserv Genet 26: 235–247. [Google Scholar]
- Holborn MK, Rochus CM, Ang KP, Elliott JAK, Leadbeater S, Powell F, Boulding EG. 2019. Family-based genome wide association analysis for salmon lice (Lepeophtheirus salmonis) resistance in North American Atlantic salmon using a 50K SNP array. Aquaculture 511: 734215. [CrossRef] [Google Scholar]
- Holman LE, de la Serrana DG, Onoufriou A, Hillestad B, Johnston IA. 2017. A workflow used to design low density SNP panels for parentage assignment and traceability in aquaculture species and its validation in Atlantic salmon. Aquaculture 476: 59–64. [CrossRef] [Google Scholar]
- Homburger JR, Neben CL, Mishne G, Zhou AY, Kathiresan S, Khera AV. 2019. Low coverage whole genome sequencing enables accurate assessment of common variants and calculation of genome-wide polygenic scores. Genome Med 11: 74. [CrossRef] [PubMed] [Google Scholar]
- Horn RL, Hess M, Harmon S, Hess J, Delomas TA, Campbell MR, Narum S. 2023. Multigeneration pedigrees to monitor hatchery broodstock composition and genetic variation of spring/summer Chinook salmon in the Columbia River Basin. N Am J Fish Manage 43: 794–820. [CrossRef] [Google Scholar]
- Horn RL, Kamphaus C, Murdoch K, Narum SR. 2020. Detecting genomic variation underlying phenotypic characteristics of reintroduced Coho salmon (Oncorhynchus kisutch). Conserv Genet 21: 1011–1021. [CrossRef] [Google Scholar]
- Horreo JL, Machado-Schiaffino G, Griffiths A, Bright D, Stevens J, Garcia-Vazquez E. 2008. Identification of differential broodstock contribution affecting genetic variability in hatchery stocks of Atlantic salmon (Salmo salar). Aquaculture 280: 89–93. [CrossRef] [Google Scholar]
- Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Jin YH, Jenkins TL, Selly SLC, Martin SAM, Stevens JR, Santos EM, Davie A, Robledo D. 2020. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet 21: 389–409. [CrossRef] [PubMed] [Google Scholar]
- Houston RD, Davey JW, Bishop SC, Lowe NR, Mota-Velasco JC, Hamilton A, Guy DR, Tinch AE, Thomson ML, Blaxter ML, Gharbi K, Bron JE, Taggart JB. 2012. Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon. BMC Genomics 13: 244. [CrossRef] [PubMed] [Google Scholar]
- Houston RD, Haley CS, Hamilton A, Guy DR, Mota-Velasco JC, Gheyas AA, Tinch AE, Taggart JB, Bron JE, Starkey WG, McAndrew BJ, Verner-Jeffreys DW, Paley RK, Rimmer GSE, Tew IJ, Bishop SC. 2010. The susceptibility of Atlantic salmon fry to freshwater infectious pancreatic necrosis is largely explained by a major QTL. Heredity 105: 318–327. [CrossRef] [PubMed] [Google Scholar]
- Hurt C, Harman A. 2017. Development of polymorphic microsatellite loci for the design of management and conservation strategies of the critically endangered Barrens topminnow (Fundulus julisia, Williams & Etnier, 1982). J Appl Ichthyol 33: 797–800. [CrossRef] [Google Scholar]
- Jackson TR, Martin-Robichaud DJ, Reith ME. 2003. Application of DNA markers to the management of Atlantic halibut (Hippoglossus hippoglossus) broodstock. Aquaculture 220: 245–259. [CrossRef] [Google Scholar]
- Janssen K, Saatkamp H, Komen H. 2018. Cost-benefit analysis of aquaculture breeding programs. Genet Sel Evol 50: 2. [CrossRef] [PubMed] [Google Scholar]
- Jansson E, Faust E, Bekkevold D, Quintela M, Durif C, Halvorsen KT, Dahle G, Pampoulie C, Kennedy J, Whittaker B, Unneland L, Post S, André C, Glover KA. 2023. Global, regional, and cryptic population structure in a high gene-flow transatlantic fish. PLOS One 18: e0283351. [CrossRef] [PubMed] [Google Scholar]
- Jeffery NW, Vercaemer B, Stanley RRE, Kess T, Dufresne F, Noisette F, O'Connor MI, Wong MC. 2024. Variation in genomic vulnerability to climate change across temperate populations of eelgrass (Zostera marina). Evol Appl 17: e13671. [CrossRef] [PubMed] [Google Scholar]
- Jeffery NW, Wringe BF, McBride MC, Hamilton LC, Stanley RRE, Bernatchez L, Kent M, Clément M, Gilbey J, Sheehan TF, Bentzen P, Bradbury IR. 2018. Range-wide regional assignment of Atlantic salmon (Salmo salar) using genome-wide single-nucleotide polymorphisms. Fish Res 206: 163–175. [CrossRef] [Google Scholar]
- Jerry DR, Jones DB, Lillehammer M, Massault C, Loughnan S, Cate HS, Harrison PJ, Strugnell JM, Zenger KR, Robinson NA. 2022. Predicted strong genetic gains from the application of genomic selection to improve growth related traits in barramundi. Aquaculture 549. [Google Scholar]
- Jones LF, Lou RN, Murray CS, Robert D, Bourne CM, Bouchard C, Kucka M, Chan YF, Carlon DB, Wiley DN, Therkildsen NO, Baumann H. 2023. Two distinct population clusters of northern sand lance (Ammodytes dubius) on the northwest Atlantic shelf revealed by whole genome sequencing. Ices J Mar Sci 80: 122–132. [CrossRef] [Google Scholar]
- Jónsdóttir ODB, Schregel J, Hagen SB, Tobiassen C, Aarnes SG, Imsland AKD. 2018. Population genetic structure of lumpfish along the Norwegian coast: aquaculture implications. Aquacult Int 26: 49–60. [CrossRef] [Google Scholar]
- Jorsboe E, Albrechtsen A. 2022. Efficient approaches for large-scale GWAS with genotype uncertainty. G3-Genes Genom Genet 12. [Google Scholar]
- Joshi R, Skaarud A, de Vera M, Alvarez AT, Ødegård J. 2020. Genomic prediction for commercial traits using univariate and multivariate approaches in Nile tilapia (Oreochromis niloticus). Aquaculture 516. [Google Scholar]
- Joung JK, Sander JD. 2013. INNOVATION TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Bio 14: 49–55. [CrossRef] [PubMed] [Google Scholar]
- Jourdan A, Morvezen R, Enez F, Haffray P, Lange A, Vétois E, Allal F, Phocas F, Bugeon J, Dégremont L, Boudry P. 2023. Potential of genomic selection for growth, meat content and colour traits in mixed-family breeding designs for the Pacific oyster Crassostrea gigas. Aquaculture 576: 739878. [CrossRef] [Google Scholar]
- Kankainen M, Setälä J, Kause A, Quinton C, Airaksinen S, Koskela J. 2016. Economic values of supply chain productivity and quality traits calculated for a farmed European whitefish breeding program. Aquacult Econ Manag 20: 131–164. [CrossRef] [Google Scholar]
- Karlsson S, Diserud OH, Fiske P, Hindar K. 2016. Widespread genetic introgression of escaped farmed Atlantic salmon in wild salmon populations. Ices J Mar Sci 73: 2488–2498. [CrossRef] [Google Scholar]
- Karlsson S, Diserud OH, Moen T, Hindar K. 2014. A standardized method for quantifying unidirectional genetic introgression. Ecol Evol 4: 3256–3263. [CrossRef] [PubMed] [Google Scholar]
- Karlsson S, Moen T, Lien S, Glover KA, Hindar K. 2011. Generic genetic differences between farmed and wild Atlantic salmon identified from a 7K SNP-chip. Mol Ecol Resour 11: 247–253. [CrossRef] [PubMed] [Google Scholar]
- Kause A, Quinton C, Airaksinen S, Ruohonen K, Koskela J. 2011. Quality and production trait genetics of farmed European whitefish, Coregonus lavaretus. J Anim Sci 89: 959–971. [CrossRef] [PubMed] [Google Scholar]
- Kause A, Ritola O, Paananen T. 2004. Breeding for improved appearance of large rainbow trout in two production environments. Aquac Res 35: 924–930. [CrossRef] [Google Scholar]
- Kause A, Ritola O, Paananen T, Mäntysaari E, Eskelinen U. 2003. Selection against early maturity in large rainbow trout Oncorhynchus mykiss: the quantitative genetics of sexual dimorphism and genotype-by-environment interactions. Aquaculture 228: 53–68. [CrossRef] [Google Scholar]
- Ke QZ, Wang JY, Bai YL, Zhao J, Gong J, Deng YC, Qu A, Suo N, Chen J, Zhou T, Xu P. 2022. GWAS and genomic prediction revealed potential for genetic improvement of large yellow croaker adapting to high plant protein diet. Aquaculture 553. [Google Scholar]
- Kess T, Bentzen P, Lehnert SJ, Sylvester EVA, Lien S, Kent MP, Sinclair-Waters M, Morris CJ, Regular P, Fairweather R, Bradbury IR. 2019. A migration-associated supergene reveals loss of biocomplexity in Atlantic cod. Sci Adv 5: eaav2461. [CrossRef] [PubMed] [Google Scholar]
- Kess T, Dempson JB, Lehnert SJ, Layton KKS, Einfeldt A, Bentzen P, Salisbury SJ, Messmer AM, Duffy S, Ruzzante DE, Nugent CM, Ferguson MM, Leong JS, Koop B, O'Connell MF, Bradbury IR. 2021. Genomic basis of deep-water adaptation in Arctic Charr (Salvelinus alpinus) morphs. Mol Ecol 30: 4415–4432. [CrossRef] [PubMed] [Google Scholar]
- Kess T, Lehnert SJ, Bentzen P, Duffy S, Messmer A, Dempson JB, Newport J, Whidden C, Robertson MJ, Chaput G, Breau C, April J, Gillis C-A., Kent M, Nugent CM, Bradbury IR. 2024. Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic salmon. Ecol Evol 14: e11068. [CrossRef] [PubMed] [Google Scholar]
- Kijas J, Elliot N, Kube P, Evans B, Botwright N, King H, Primmer CR, Verbyla K. 2017. Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon. Anim Genet 48: 237–241. [CrossRef] [PubMed] [Google Scholar]
- Kim SY, Lohmueller KE, Albrechtsen A, Li YR, Korneliussen T, Tian G, Grarup N, Jiang T, Andersen G, Witte D, Jorgensen T, Hansen T, Pedersen O, Wang J, Nielsen R. 2011. Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics 12: 231. [CrossRef] [PubMed] [Google Scholar]
- Kincaid HL. 1976. Effects of inbreeding on rainbow trout populations. T Am Fish Soc 105: 273–280. [CrossRef] [Google Scholar]
- Kishimoto K, Washio Y, Yoshiura Y, Toyoda A, Ueno T, Fukuyama H, Kato K, Kinoshita M. 2018. Production of a breed of red sea bream Pagrus major with an increase of skeletal muscle mass and reduced body length by genome editing with CRISPR/Cas9. Aquaculture 495: 415–427. [CrossRef] [Google Scholar]
- Kleppe L, Fjelldal PG, Andersson E, Hansen T, Sanden M, Bruvik A, Skaftnesmo KO, Furmanek T, Kjaerner-Semb E, Crespo D, Flavell S, Pedersen AO, Vogelsang P, Torsvik A, Kvestad KA, Olausson S, Norberg B, Schulz RW, Bogerd J, Santi N, Edvardsen RB, Wargelius A. 2022. Full production cycle performance of gene-edited, sterile Atlantic salmon: growth, smoltification, welfare indicators and fillet composition. Aquaculture 560. [Google Scholar]
- Klug A. 2010. The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annu Rev Biochem 79: 213–231. [CrossRef] [PubMed] [Google Scholar]
- Kovach RP, Leary RF, Bell DA, Painter S, Lodmell A, Whiteley AR. 2022. Genetic variation in westslope cutthroat trout reveals that widespread genetic rescue is warranted. Can J Fish Aquat Sci 79: 936–946. [CrossRef] [Google Scholar]
- Kozfkay CC, Campbell MR, Heindel JA, Baker DJ, Kline P, Powell MS, Flagg T. 2008. A genetic evaluation of relatedness for broodstock management of captive, endangered Snake River sockeye salmon, Oncorhynchus nerka. Conserv Genet 9: 1421–1430. [CrossRef] [Google Scholar]
- Kriaridou C, Tsairidou S, Fraslin C, Gorjanc G, Looseley ME, Johnston IA, Houston RD, Robledo D. 2023. Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species. Front Genet 14: 1194266. [CrossRef] [PubMed] [Google Scholar]
- Lacy RC. 2012. Extending pedigree analysis for uncertain parentage and diverse breeding systems. J Hered 103: 197–205. [CrossRef] [PubMed] [Google Scholar]
- Langille BL, Kess T, Brachmann M, Nugent CM, Messmer A, Duffy SJ, Holborn MK, Van Wyngaarden M, Knutsen TM, Kent M, Boyce D, Gregory RS, Gauthier J, Fairchild EA, Pietrak M, Eddy S, de Leaniz CG, Consuegra S, Whittaker B, Bentzen P, Bradbury IR. 2023. Fine-scale environmentally associated spatial structure of lumpfish (Cyclopterus lumpus) across the Northwest Atlantic. Evol Appl 16: 1619–1636. [CrossRef] [PubMed] [Google Scholar]
- Lapègue S, Harrang E, Heurtebise S, Flahauw E, Donnadieu C, Gayral P, Ballenghien M, Genestout L, Barbotte L, Mahla R, Haffray P, Klopp C. 2014. Development of SNP-genotyping arrays in two shellfish species. Mol Ecol Resour 14: 820–830. [CrossRef] [PubMed] [Google Scholar]
- Lapègue S, Reisser C, Harrang E, Heurtebise S, Bierne N. 2023. Genetic parallelism between European flat oyster populations at the edge of their natural range. Evol Appl 16: 393–407. [CrossRef] [PubMed] [Google Scholar]
- Layton KKS, Snelgrove PVR, Dempson JB, Kess T, Lehnert SJ, Bentzen P, Duffy SJ, Messmer AM, Stanley RRE, DiBacco C, Salisbury SJ, Ruzzante DE, Nugent CM, Ferguson MM, Leong JS, Koop BF, Bradbury IR. 2021. Genomic evidence of past and future climate-linked loss in a migratory Arctic fish. Nat Clim Change 11: 158–165. [CrossRef] [Google Scholar]
- Lehnert SJ, Bradbury IR, April J, Wringe BF, Van Wyngaarden M, Bentzen P. 2023. Pre-COSEWIC review of anadromous Atlantic salmon (Salmo salar) in Canada, Part 1: Designatable Units. DFO Can. Sci. Advis. Sec. Res. Doc. 2023/026. iv + 156 p. [Google Scholar]
- Lehnert SJ, Bradbury IR, Wringe BF, Van Wyngaarden M, Bentzen P. 2023. Multifaceted framework for defining conservation units: an example from Atlantic salmon (Salmo salar) in Canada. Evol Appl 16: 1568–1585. [CrossRef] [PubMed] [Google Scholar]
- Lehnert SJ, Kess T, Bentzen P, Kent MP, Lien S, Gilbey J, Clément M, Jeffery NW, Waples RS, Bradbury IR. 2019. Genomic signatures and correlates of widespread population declines in salmon. Nat Commun 10: 2996. [CrossRef] [PubMed] [Google Scholar]
- Lew RM, Finger AJ, Baerwald MR, Goodbla A, May B, Meek MH. 2015. Using next-generation sequencing to assist a conservation hatchery: a single-nucleotide polymorphism panel for the genetic management of endangered delta smelt. T Am Fish Soc 144: 767–779. [CrossRef] [Google Scholar]
- Lhorente JP, Araneda M, Neira R, Yáñez JM. 2019. Advances in genetic improvement for salmon and trout aquaculture: the Chilean situation and prospects. Rev Aquacult 11: 340–353. [CrossRef] [Google Scholar]
- Li XC, Bai YT, Dong Z, Xu CX, Liu SK, Yu H, Kong LF, Li Q. 2023. Chromosome-level genome assembly of the European flat oyster (Ostrea edulis) provides insights into its evolution and adaptation. Comp Biochem Phys D 45: 101045. [Google Scholar]
- Liu K, Feng XY, Ma HJ, Xie N. 2021. Development and characterisation of 13 microsatellite markers of Chanodichthys mongolicus (Cypriniformes: Cyprinidae) by RAD-s eq. J Appl Ichthyol 37: 975–979. [CrossRef] [Google Scholar]
- Liu L, Ang KP, Elliott JAK, Kent MP, Lien S, MacDonald D, Boulding EG. 2017. A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing colocalisation among outlier markers, candidate genes, and quantitative trait loci for production traits. Evol Appl 10: 276–296. [CrossRef] [MathSciNet] [PubMed] [Google Scholar]
- Liu SX, Palti Y, Gao GT, Rexroad CE. 2016. Development and validation of a SNP panel for parentage assignment in rainbow trout. Aquaculture 452: 178–182. [CrossRef] [Google Scholar]
- Lou RN, Jacobs A, Wilder AP, Therkildsen NO. 2021. A beginner's guide to low-coverage whole genome sequencing for population genomics. Mol Ecol 30: 5966–5993. [CrossRef] [PubMed] [Google Scholar]
- Marchini J, Howie B. 2010. Genotype imputation for genome-wide association studies. Nat Rev Genet 11: 499–511. [CrossRef] [PubMed] [Google Scholar]
- Marcy-Quay B, Wilson CC, Osborne CA, Marsden JE. 2023. Optimisation of an amplicon sequencing-based microsatellite panel and protocol for stock identification and kinship inference of lake trout (Salvelinus namaycush). Ecol Evol 13: e10020. [CrossRef] [PubMed] [Google Scholar]
- Marshall IR, Brauer CJ, Wedderburn SD, Whiterod NS, Hammer MP, Barnes TC, Attard CRM, Möller LM, Beheregaray LB. 2022. Longitudinal monitoring of neutral and adaptive genomic diversity in a reintroduction. Conserv Biol 36: e13889. [CrossRef] [PubMed] [Google Scholar]
- McKenzie JA, Paim U. 1969. Variations in the plasma proteins of Atlantic salmon (Salmo salar L.). Can J Zool 47: 759–761. [CrossRef] [PubMed] [Google Scholar]
- Mendes B, Sampaio T, Antunes MA, Magalhaes H, Silva FCE, Borges C, Simoes F, Usié A, Almeida MH, Ramos AM. 2022. Kinship analysis and pedigree reconstruction of a natural regenerated cork oak (Quercus suber) population. Forests 13. [Google Scholar]
- Meuwissen THE, Hayes BJ, Goddard ME. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819–1829. [CrossRef] [PubMed] [Google Scholar]
- Meuwissen THE, Sonesson AK. 2004. Genotype-assisted optimum contribution selection to maximise selection response over a specified time period. Genet Res 84: 109–116. [CrossRef] [Google Scholar]
- Miller J, McLachlan AD, Klug A. 1985. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. Embo J 4: 1609–1614. [CrossRef] [PubMed] [Google Scholar]
- Moen T, Baranski M, Sonesson AK, Kjoglum S. 2009. Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): population-level associations between markers and trait. BMC Genomics 10: 368. [CrossRef] [PubMed] [Google Scholar]
- Moghadam HK, Poissant J, Fotherby H, Haidle L, Ferguson MM, Danzmann RG. 2007. Quantitative trait loci for body weight, condition factor and age at sexual maturation in Arctic charr (Salvelinus alpinus): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar). Mol Genet Genomics 277: 647–661. [CrossRef] [PubMed] [Google Scholar]
- Moller D. 1970. Transferrin polymorphism in Atlantic salmon (Salmo salar). J Fish Res Board Can 27: 1617–1625. [CrossRef] [Google Scholar]
- Monk J, Boyce DL, Ang KP, George S, Tucker D, Jeannot K, Fry J, Gianasi B, Hickey S, O'Brien N. 2016. Cleaner fish research and production in Newfoundland. Bull Aquac Assoc Can 2016-2: 39–45. [Google Scholar]
- Morvezen R, Boudry P, Laroche J, Charrier G. 2016. Stock enhancement or sea ranching? Insights from monitoring the genetic diversity, relatedness and effective population size in a seeded great scallop population (Pecten maximus). Heredity 117: 142–148. [CrossRef] [PubMed] [Google Scholar]
- Murray K. 2005. Population genetic assessment of the endangered Atlantic whitefish, Coregonus huntsmani, and the lake whitefish, C. clupeaformis, in Atlantic Canada. MSc. thesis, Dept. of Biology, Dalhousie University, Halifax, NS. [Google Scholar]
- Narum SR, Di Genova A, Micheletti SJ, Maass A. 2018. Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon. P Roy Soc B-Biol Sci 285. [Google Scholar]
- Neira R, Díaz NF, Gall GAE, Gallardo JA, Lhorente JP, Manterola R. 2006. Genetic improvement in Coho salmon (Oncorhynchus kisutch). I: Selection response and inbreeding depression on harvest weight. Aquaculture 257: 9–17. [CrossRef] [Google Scholar]
- Nguyen NH. 2016. Genetic improvement for important farmed aquaculture species with a reference to carp, tilapia and prawns in Asia: achievements, lessons and challenges. Fish Fish 17: 483–506. [CrossRef] [Google Scholar]
- Nielsen ES, Henriques R, Beger M, von der Heyden S. 2021. Distinct interspecific and intraspecific vulnerability of coastal species to global change. Global Change Biol 27: 3415–3431. [CrossRef] [PubMed] [Google Scholar]
- Norris AT, Bradley DG, Cunningham EP. 2000. Parentage and relatedness determination in farmed Atlantic salmon (Salmo salar) using microsatellite markers. Aquaculture 182: 73–83. [CrossRef] [Google Scholar]
- Nugent CM, Kess T, Brachmann MK, Langille BL, Duffy SJ, Lehnert SJ, Wringe BF, Bentzen P, Bradbury IR. 2023. Whole-genome sequencing reveals fine-scale environment-associated divergence near the range limits of a temperate reef fish. Mol Ecol 32: 4742–4762. [CrossRef] [PubMed] [Google Scholar]
- Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi QM, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS. 2021. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell 184: 2503–2519. [CrossRef] [PubMed] [Google Scholar]
- O'Reilly P. 2006. Towards the identification of Conservation Units in Atlantic salmon from Eastern Canada. DFO Can. Sci. Advis. Sec. Res. Doc. 2006/012. [Google Scholar]
- O'Reilly P, Harvie CJ. 2010. Conservation of genetic variation in the Inner Bay of Fundy Atlantic salmon conservation breeding and rearing program. DFO Can. Sci. Advis. Sec. Res. Doc. 2009/095. [Google Scholar]
- Palaiokostas C, Bekaert M, Davie A, Cowan ME, Oral M, Taggart JB, Gharbi K, McAndrew BJ, Penman DJ, Migaud H. 2013. Mapping the sex determination locus in the Atlantic halibut (Hippoglossus hippoglossus) using RAD sequencing. BMC Genomics 14: 566. [CrossRef] [PubMed] [Google Scholar]
- Payne RH. 1974. Transferrin variation in North American populations of the Atlantic salmon, Salmo salar. J Fish Res Board Can 31: 1037–1041. [CrossRef] [Google Scholar]
- Peace CP. 2017. DNA-informed breeding of rosaceous crops: promises, progress and prospects. Hortic Res-England 4: 17006. [CrossRef] [Google Scholar]
- Peñaloza C, Barria A, Papadopoulou A, Hooper C, Preston J, Green M, Helmer L, Kean-Hammerson J, Nascimento-Schulze JC, Minardi D, Gundappa MK, Macqueen DJ, Hamilton J, Houston RD, Bean TP. 2022. Genome-wide association and genomic prediction of growth traits in the European flat oyster (Ostrea edulis). Front Genet 13: 926638. [CrossRef] [PubMed] [Google Scholar]
- Phelps MP, Seeb LW, Seeb JE. 2020. Transforming ecology and conservation biology through genome editing. Conserv Biol 34: 54–65. [CrossRef] [PubMed] [Google Scholar]
- Pouvreau S, Lapègue S, Arzul I, Boudry P. 2023. Fifty years of research to counter the decline of the European flat oyster (Ostrea edulis): a review of French achievements and prospects for the restoration of remaining beds and revival of aquaculture production. Aquat Living Resour 36. [Google Scholar]
- Prado P, Fernández M, Cordero D, Saavedra C, Carella F, Alcaraz C, Gairin I . 2022. Molecular identification, life cycle characterisation, and hatchery seed production of dwarf oysters from the Ebro Delta (Spain). Aquat Living Resour 35. [Google Scholar]
- Purcell CM, Seetharam AS, Snodgrass O, Ortega-García S, Hyde JR, Severin AJ. 2018. Insights into teleost sex determination from the Seriola dorsalis genome assembly. BMC Genomics 19: 31. [CrossRef] [PubMed] [Google Scholar]
- Qin W, Brown JL. 2006. Consumer opinions about genetically engineered salmon and information effect on opinions: a qualitative approach. Science Communication 28: 243–272. [CrossRef] [Google Scholar]
- Quinton CD, McMillan I, Glebe BD. 2005. Development of an Atlantic salmon (Salmo salar) genetic improvement program: genetic parameters of harvest body weight and carcass quality traits estimated with animal models. Aquaculture 247: 211–217. [CrossRef] [Google Scholar]
- Reid DP, Szanto A, Glebe B, Danzmann RG, Ferguson MM. 2005. QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus). Heredity 94: 166–172. [CrossRef] [PubMed] [Google Scholar]
- Rexroad C, Vallet J, Matukumalli LK, Reecy J, Bickhart D, Blackburn H, Boggess M, Cheng H, Clutter A, Cockett N, Ernst C, Fulton JE, Liu J, Lunney J, Neibergs H, Purcell C, Smith TPL, Sonstegard T, Taylor J, Telugu B, Van Eenennaam A, Van Tassell CP, Wells K, Martin A, Murdoch B, Sayre B, Keel B, Schmidt C, Hostetler C, Seabury C, Tuggle C, Elsik C, Gill C, Ciobanu D, Bailey D, Hamernik D, Grings E, Connor E, Rohrer G, Plastow G, Rosa G, Zhou HJ, Koltes J, Decker J, Weller J, Woodward-Greene J, Steibel J, Long J, Lee K, Kuehn L, Worku M, Salem M, McCue M, Serao N, Riggs P, Sponenberg P, Schnabel R, Brooks S, Fernando S, McKay S, Schmitz-Esser S, White S, Lamont S, Kurt T, Palti Y, AAG Community. 2019. Genome to phenome: improving animal health, production, and well-being − a new USDA blueprint for animal genome research 2018–2027. Front Genet 10: 327. [CrossRef] [PubMed] [Google Scholar]
- Robinson NA, Robledo D, Sveen L, Daniels RR, Krasnov A, Coates A, Jin YH, Barrett LT, Lillehammer M, Kettunen AH, Phillips BL, Dempster T, Doeschl-Wilson A, Samsing F, Difford G, Salisbury S, Gjerde B, Haugen JE, Burgerhout E, Dagnachew BS, Kurian D, Fast MD, Rye M, Salazar M, Bron JE, Monaghan SJ, Jacq C, Birkett M, Browman HI, Skiftesvik AB, Fields DM, Selander E, Bui S, Sonesson A, Skugor S, Ostbye TKK, Houston RD. 2023. Applying genetic technologies to combat infectious diseases in aquaculture. Rev Aquacult 15: 491–535. [CrossRef] [PubMed] [Google Scholar]
- Rollinson N, Keith DM, Houde ALS, Debes PV, McBride MC, Hutchings JA. 2014. Risk assessment of inbreeding and outbreeding depression in a captive-breeding program. Conserv Biol 28: 529–540. [Google Scholar]
- Roy S, Kumar V, Behera BK, Parhi J, Mohapatra S, Chakraborty T, Das BK. 2022. CRISPR/Cas genome editing − can it become a game changer in future fisheries sector? Front Mar Sci 9. [Google Scholar]
- Russello MA, Amato G. 2004. Ex situ population management in the absence of pedigree information. Mol Ecol 13: 2829–2840. [CrossRef] [PubMed] [Google Scholar]
- Ryman N, Laikre L. 1991. Effects of supportive breeding on the genetically effective population size. Conserv Biol 5: 325–329. [CrossRef] [Google Scholar]
- Saillant E, Adams N, Lemus JT, Franks JS, Zohar Y, Stubblefield J, Manley C. 2021. First data on aquaculture of the tripletail, Lobotes surinamensis, a promising candidate species for US marine aquaculture. J World Aquacult Soc 52: 582–594. [CrossRef] [Google Scholar]
- Sandoval-Castillo J, Beheregaray LB, Wellenreuther M. 2022. Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus). G3-Genes Genom Genet 12. [Google Scholar]
- Schaid DJ, Chen WN, Larson NB. 2018. From genome-wide associations to candidate causal variants by statistical fine-mapping. Nat Rev Genet 19: 491–504. [CrossRef] [PubMed] [Google Scholar]
- Schmidt E, Stuart K, Hyde J, Purcell C, Drawbridge M. 2021. Spawning dynamics and egg production characteristics of captive Seriola dorsalis assessed using parentage analyses. Aquac Res 52: 4050–4063. [CrossRef] [Google Scholar]
- Segelbacher G, Bosse M, Burger P, Galbusera P, Godoy JA, Helsen P, Hvilsom C, Iacolina L, Kahric A, Manfrin C, Nonic M, Thizy D, Tsvetkov I, Velickovic N, Vila C, Wisely SM, Buzan E. 2022. New developments in the field of genomic technologies and their relevance to conservation management. Conserv Genet 23: 217–242. [CrossRef] [Google Scholar]
- Serrao NR, Reid SM, Wilson CC. 2018. Conservation genetics of redside dace (Clinostomus elongatus): phylogeography and contemporary spatial structure. Conserv Genet 19: 409–424. [CrossRef] [Google Scholar]
- Simora RMC, Xing D, Bangs XR, Wang WW, Ma XL, Su BF, Khan MGQ, Qin ZK, Lu CY, Alston V, Hettiarachchi D, Johnson A, Li SJ, Coogan M, Gurbatow J, Terhune JS, Wang X, Dunham RA. 2020. CRISPR/Cas9-mediated knock-in of alligator cathelicidin gene in a non-coding region of channel catfish genome. Sci Rep-Uk 10: 22271. [CrossRef] [Google Scholar]
- Sinclair-Waters M, Odegård J, Korsvoll SA, Moen T, Lien S, Primmer CR, Barson NJ. 2020. Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon. Genet Sel Evol 52: 9. [CrossRef] [PubMed] [Google Scholar]
- Sirisha M, Sree Ramulu K, Pavan Kumar K, Ramya A, Shiva P, Krishna P, Rushinadha R. 2018. Identification of fish species using DNA barcode from Visakhapatnam, east coast of India. Pharma Innovation 7: 573–579. [Google Scholar]
- Song HL, Hu HX. 2022. Strategies to improve the accuracy and reduce costs of genomic prediction in aquaculture species. Evol Appl 15: 578–590. [CrossRef] [PubMed] [Google Scholar]
- Steele CA, Anderson EC, Ackerman MW, Hess MA, Campbell NR, Narum SR, Campbell MR. 2013. A validation of parentage-based tagging using hatchery steelhead in the Snake River basin. Can J Fish Aquat Sci 70: 1046–1054. [CrossRef] [Google Scholar]
- Stone NM, Kelly AM, Roy LA. 2016. A fish of weedy waters: golden shiner biology and culture. J World Aquacult Soc 47: 152–200. [CrossRef] [Google Scholar]
- Supple MA, Shapiro B. 2018. Conservation of biodiversity in the genomics era. Genome Biol 19: 131. [CrossRef] [PubMed] [Google Scholar]
- Szarmach SJ, Brelsford A, Witt CC, Toews DPL. 2021. Comparing divergence landscapes from reduced-representation and whole genome resequencing in the yellow-rumped warbler (Setophaga coronata) species complex. Mol Ecol 30: 5994–6005. [CrossRef] [PubMed] [Google Scholar]
- Taggart JB, Ferguson A. 1990. Hypervariable minisatellite DNA single locus probes for the Atlantic salmon, Salmo salar L. J Fish Biol 37: 991–993. [CrossRef] [Google Scholar]
- Therkildsen NO, Wilder AP, Conover DO, Munch SB, Baumann H, Palumbi SR. 2019. Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing. Science 365: 487–490. [CrossRef] [PubMed] [Google Scholar]
- Tringali MD, Bert TM. 1998. Risk to genetic effective population size should be an important consideration in fish stock-enhancement programs. B Mar Sci 62: 641–659. [Google Scholar]
- Tsai HY, Hamilton A, Tinch AE, Guy DR, Gharbi K, Stear MJ, Matika O, Bishop SC, Houston RD. 2015. Genome wide association and genomic prediction for growth traits in juvenile farmed Atlantic salmon using a high density SNP array. BMC Genomics 16: 969. [CrossRef] [PubMed] [Google Scholar]
- Tsai HY, Matika O, Edwards SM, Antolín-Sánchez R, Hamilton A, Guy DR, Tinch AE, Gharbi K, Stear MJ, Taggart JB, Bron JE, Hickey JM, Houston RD. 2017. Genotype imputation to improve the cost-efficiency of genomic selection in farmed Atlantic salmon. G3-Genes Genom Genet 7: 1377–1383. [Google Scholar]
- Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD. 2010. Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11: 636–646. [CrossRef] [PubMed] [Google Scholar]
- Valenza-Troubat N, Davy M, Storey R, Hilario E, Ritchie P, Wellenreuther M. 2022. Differential expression analyses reveal extensive transcriptional plasticity induced by temperature in New Zealand silver trevally (Pseudocaranx georgianus). Evol Appl 15: 237–248. [CrossRef] [PubMed] [Google Scholar]
- Valenza-Troubat N, Montanari S, Ritchie P, Wellenreuther M. 2022. Unravelling the complex genetic basis of growth in New Zealand silver trevally (Pseudocaranx georgianus). G3-Genes Genom Genet 12. [Google Scholar]
- Vallejo RL, Leeds TD, Gao GT, Parsons JE, Martin KE, Evenhuis JP, Fragomeni BO, Wiens GD, Palti Y. 2017. Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture. Genet Sel Evol 49. [PubMed] [Google Scholar]
- Vallejo RL, Silva RMO, Evenhuis JP, Gao GT, Liu SX, Parsons JE, Martin KE, Wiens GD, Lourenco DAL, Leeds TD, Palti Y. 2018. Accurate genomic predictions for BCWD resistance in rainbow trout are achieved using low-density SNP panels: evidence that long-range LD is a major contributing factor. J Anim Breed Genet 135: 263–274. [CrossRef] [Google Scholar]
- Vandeputte M, Haffray P. 2014. Parentage assignment with genomic markers: a major advance for understanding and exploiting genetic variation of quantitative traits in farmed aquatic animals. Front Genet 5: 432. [CrossRef] [PubMed] [Google Scholar]
- Vehviläinen H, Kause A, Koskinen H, Paananen T. 2010. Genetic architecture of rainbow trout survival from egg to adult. Genet Res 92: 1–11. [CrossRef] [PubMed] [Google Scholar]
- Vehviläinen H, Kause A, Kuukka-Anttila H, Koskinen H, Paananen T. 2012. Untangling the positive genetic correlation between rainbow trout growth and survival. Evol Appl 5: 732–745. [CrossRef] [PubMed] [Google Scholar]
- Vehviläinen H, Kause A, Quinton C, Koskinen H, Paananen T. 2008. Survival of the currently fittest: genetics of rainbow trout survival across time and space. Genetics 180: 507–516. [CrossRef] [PubMed] [Google Scholar]
- Vera M, Pardo BG, Cao A, Vilas R, Fernandez C, Blanco A, Gutierrez AP, Bean TP, Houston RD, Villalba A, Martinez P. 2019. Signatures of selection for bonamiosis resistance in European flat oyster (Ostrea edulis): new genomic tools for breeding programs and management of natural resources. Evol Appl 12: 1781–1796. [CrossRef] [PubMed] [Google Scholar]
- Verbyla KL, Kube PD, Evans BS. 2022. Commercial implementation of genomic selection in Tasmanian Atlantic salmon: scheme evolution and validation. Evol Appl 15: 631–644. [CrossRef] [PubMed] [Google Scholar]
- Vu SV, Knibb W, Gondro C, Subramanian S, Nguyen NTH, Alam M, Dove M, Gilmour AR, Vu IV, Bhyan S, Tearle R, Khuong L, Le TS, O'Connor W. 2021. Genomic prediction for whole weight, body shape, meat yield, and color traits in the Portuguese oyster Crassostrea angulata. Front Genet 12: 661276. [CrossRef] [PubMed] [Google Scholar]
- Wang JY, Chen L, Li BJ, Xu J, Feng JX, Dong CJ, Zhou T, Xu P. 2021. Performance of genome prediction for morphological and growth-related traits in Yellow River carp. Aquaculture 536. [Google Scholar]
- Wang QC, Yu Y, Yuan JB, Zhang XJ, Huang H, Li FH, Xiang JH. 2017. Effects of marker density and population structure on the genomic prediction accuracy for growth trait in Pacific white shrimp Litopenaeus vannamei. BMC Genet 18: 45. [CrossRef] [PubMed] [Google Scholar]
- Waples RS, Ford MJ, Nichols K, Kardos M, Myers J, Thompson TQ, Anderson EC, Koch IJ, McKinney G, Miller MR, Naish K, Narum SR, O'Malley KG, Pearse DE, Pess GR, Quinn TP, Seamons TR, Spidle A, Warheit K, Willis SC. 2022. Implications of large-effect loci for conservation: a review and case study with Pacific salmon. J Hered 113: 121–144. [CrossRef] [PubMed] [Google Scholar]
- Waples RS, Naish KA, Primmer CR. 2020. Conservation and management of salmon in the age of genomics. Annu Rev Anim Biosci 8: 117–143. [CrossRef] [PubMed] [Google Scholar]
- Wargelius A, Leininger S, Skaftnesmo KO, Kleppe L, Andersson E, Taranger GL, Schulz RW, Edvardsen RB. 2016. dnd knockout ablates germ cells and demonstrates germ cell independent sex differentiation in Atlantic salmon. Sci Rep-Uk 6: 21284. [CrossRef] [Google Scholar]
- Waters CD, Clemento A, Aykanat T, Garza JC, Naish KA, Narum S, Primmer CR. 2021. Heterogeneous genetic basis of age at maturity in salmonid fishes. Mol Ecol 30: 1435–1456. [CrossRef] [PubMed] [Google Scholar]
- Waters CD, Hard JJ, Brieuc MSO, Fast DE, Warheit KI, Knudsen CM, Bosch WJ, Naish KA. 2018. Genomewide association analyses of fitness traits in captive-reared Chinook salmon: applications in evaluating conservation strategies. Evol Appl 11: 853–868. [CrossRef] [PubMed] [Google Scholar]
- Waters CD, Hard JJ, Brieuc MSO, Fast DE, Warheit KI, Waples RS, Knudsen CM, Bosch WJ, Naish KA. 2015. Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding. Evol Appl 8: 956–971. [CrossRef] [PubMed] [Google Scholar]
- Waters CD, Hard JJ, Brieuc MSO, Fast DE, Warheit KI, Waples RS, Knudsen CM, Bosch WJ, Naish KA. 2016. What can genomics tell us about the success of enhancement programs in anadromous Chinook salmon? A comparative analysis across four generations. bioRxiv, 087973. [Google Scholar]
- Wellmann R, Bennewitz J, Meuwissen THE. 2014. A unified approach to characterise and conserve adaptive and neutral genetic diversity in subdivided populations. Genet Res 96: e16. [CrossRef] [PubMed] [Google Scholar]
- Wells ZRR, Bernos TA, Yates MC, Fraser DJ. 2019. Genetic rescue insights from population- and family-level hybridisation effects in brook trout. Conserv Genet 20: 851–863. [CrossRef] [Google Scholar]
- Weng ZY, Yang Y, Wang X, Wu LN, Hua SJ, Zhang HF, Meng ZN. 2021. Parentage analysis in giant grouper (Epinephelus lanceolatus) using microsatellite and SNP markers from genotyping-by-sequencing data. Genes-Basel 12(7). [Google Scholar]
- Wenne R. 2023. Single nucleotide polymorphism markers with applications in conservation and exploitation of aquatic natural populations. Animals-Basel 13. [Google Scholar]
- Wong TT, Zohar Y. 2015. Production of reproductively sterile fish: a mini-review of germ cell elimination technologies. Gen Comp Endocr 221: 3–8. [CrossRef] [Google Scholar]
- Wood G, Marzinelli EM, Campbell AH, Steinberg PD, Vergés A, Coleman MA. 2021. Genomic vulnerability of a dominant seaweed points to future-proofing pathways for Australia's underwater forests. Global Change Biol 27: 2200–2212. [CrossRef] [PubMed] [Google Scholar]
- Wringe BF, Devlin RH, Ferguson MM, Moghadam HK, Sakhrani D, Danzmann RG. 2010. Growth-related quantitative trait loci in domestic and wild rainbow trout (Oncorhynchus mykiss). BMC Genet 11. [PubMed] [Google Scholar]
- Xuereb A, Kimber CM, Curtis JMR, Bernatchez L, Fortin MJ. 2018. Putatively adaptive genetic variation in the giant California sea cucumber (Parastichopus californicus) as revealed by environmental association analysis of restriction-site associated DNA sequencing data. Mol Ecol 27: 5035–5048. [CrossRef] [PubMed] [Google Scholar]
- Yáñez JM, Xu P, Carvalheiro R, Hayes B. 2022. Genomics applied to livestock and aquaculture breeding. Evol Appl 15: 517–522. [CrossRef] [PubMed] [Google Scholar]
- Yoshida GM, Carvalheiro R, Lhorente JP, Correa K, Figueroa R, Houston RD, Yáñez JM. 2018. Accuracy of genotype imputation and genomic predictions in a two-generation farmed Atlantic salmon population using high-density and low-density SNP panels. Aquaculture 491: 147–154. [CrossRef] [Google Scholar]
- Yoshida GM, Lhorente JP, Correa K, Soto J, Salas D, Yáñez JM. 2019. Genome-wide association study and cost-efficient genomic predictions for growth and fillet yield in Nile tilapia (Oreochromis niloticus). G3-Genes Genom Genet 9: 2597–2607. [CrossRef] [Google Scholar]
- Zeng QF, Zhao BJ, Wang H, Wang MQ, Teng MX, Hu JJ, Bao ZM, Wang YF. 2022. Aquaculture molecular breeding platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture. Nucleic Acids Res 50(W1), W66– W74. [CrossRef] [PubMed] [Google Scholar]
- Zu Ermgassen PSE, Strand A, Bakker N, Blanco A, Bonacic K, Boudry P, Brundu G, Cameron TC, Connellan I, da Costa F, Debney A, Fabra M, Frankic A, Gamble C, Gray MW, Helmer L, Holbrook Z, Hugh-Jones T, Kamermans P, Magnesen T, Nielsen P, Preston J, Ranger CJ, Saurel C, Smyth D, Stechele B, Theodorou JA, Colsoul B 2023. Overcoming Ostrea edulis seed production limitations to meet ecosystem restoration demands in the UN decade on restoration. Aquat Living Resour 36. [Google Scholar]
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