Harnessing genomics to fast-track genetic improvement in aquaculture

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 21(7), P. 389 - 409

Published: April 16, 2020

Language: Английский

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The crucial role of genome-wide genetic variation in conservation

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(48)

Published: Nov. 12, 2021

The unprecedented rate of extinction calls for efficient use genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field conservation biology has placed too much focus on conserving genome-wide genetic variation, should instead managing subset functional variation is thought affect fitness. Here, we critically evaluate feasibility likely benefits this approach in conservation. We find population theory empirical results show generally best prevent inbreeding depression loss adaptive potential from driving populations toward extinction. Focusing efforts presumably will only be feasible occasionally, often misleading, counterproductive when prioritized over variation. Given increasing habitat other environmental changes, failure recognize detrimental effects lost long-term viability worsen biodiversity crisis.

Language: Английский

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Genomics advances the study of inbreeding depression in the wild

Evolutionary Applications, Journal Year: 2016, Volume and Issue: 9(10), P. 1205 - 1218

Published: Aug. 17, 2016

Abstract Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus ecology, evolution, and conservation biology. Despite decades research, we still have limited understanding the strength, underlying genetic mechanisms, demographic consequences inbreeding in wild. Studying natural populations hampered by inability to precisely measure individual inbreeding. Fortunately, rapidly increasing availability high‐throughput sequencing data means it is now feasible any high precision. Here, review how genomic are advancing our Recent results show that can be measured more than via traditional pedigree analysis. Additionally, made possible pinpoint loci large effects contributing wild populations, although this will continue challenging task many study systems due low statistical power. Now reliably measuring no longer limitation, future studies should accurately quantify on population growth viability.

Language: Английский

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rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure

Molecular Ecology Resources, Journal Year: 2016, Volume and Issue: 17(1), P. 78 - 90

Published: Nov. 14, 2016

Abstract Identifying genomic regions with unusually high local haplotype homozygosity represents a powerful strategy to characterize candidate genes responding natural or artificial positive selection. To that end, statistics measuring the extent of within (e.g. EHH , iHS ) and between (Rsb XP ‐ populations have been proposed in literature. The rehh package for r was previously developed facilitate genome‐wide scans selection, based on analysis long‐range haplotypes. However, its performance not sufficient cope growing size available data sets. Here, we propose major upgrade package, which includes an improved processing input files, faster algorithm enumerate haplotypes, as well multithreading. As illustrated large human sets, these improvements decrease computation time by more than one order magnitude. This new version will thus allow performing ‐, Rsb‐ ‐based 2.0 is from CRAN repository ( http://cran.r-project.org/web/packages/rehh/index.html together help files detailed manual.

Language: Английский

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Harnessing genomic information for livestock improvement

Nature Reviews Genetics, Journal Year: 2018, Volume and Issue: 20(3), P. 135 - 156

Published: Dec. 4, 2018

Language: Английский

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Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions

Fish and Fisheries, Journal Year: 2017, Volume and Issue: 18(5), P. 890 - 927

Published: March 10, 2017

Abstract Atlantic salmon ( Salmo salar ) is one of the best researched fishes, and its aquaculture plays a global role in blue revolution. However, since 1970s, tens millions farmed have escaped into wild. We review current knowledge genetic interactions identify unanswered questions. Native populations are typically genetically distinct from each other potentially locally adapted. Farmed represent limited number wild source that been exposed to ≥12 generations domestication. Consequently, differ many traits including molecular‐genetic polymorphisms, growth, morphology, life history, behaviour, physiology gene transcription. Field experiments demonstrated offspring display lower lifetime fitness than following introgression, there reduced production and, potentially, total production. It formidable task estimate introgression where they not exotic. New methods revealed half ~150 Norwegian populations, with point estimates as high 47%, an unweighted average 6.4% across 109 populations. Outside Norway, remains unquantified, all regions, biological changes mechanisms driving population‐specific impacts remain poorly documented. Nevertheless, existing shows long‐term consequences expected lead life‐history traits, population productivity decreased resilience future challenges. Only major reduction escapees and/or sterility can eliminate further impacts.

Language: Английский

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Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

Molecular Ecology, Journal Year: 2017, Volume and Issue: 26(20), P. 5369 - 5406

Published: July 26, 2017

Abstract Whole‐genome resequencing ( WGR ) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. includes four approaches: the sequencing of individuals to high depth coverage with either unresolved or haplotypes, population genomes by mixing equimolar amounts unlabelled‐individual DNA (Pool‐seq) and multiple from low (lc ). These techniques require availability reference genome. This, along still cost shotgun large demand computing resources storage, has limited their implementation in nonmodel species scarce genomic fields such as conservation biology. Our goal here describe various methods, pros cons potential applications offers an unprecedented marker density surveys wide diversity genetic variations single nucleotide polymorphisms (e.g., structural variants mutations regulatory elements), increasing power detection signatures selection local adaptation well identification basis phenotypic traits diseases. Currently, though, no approach fulfils all requirements genetics, each its own limitations sources bias. We discuss proposed ways minimize biases. envision distant future where analysis whole becomes routine task many including

Language: Английский

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Sex-dependent dominance maintains migration supergene in rainbow trout

Nature Ecology & Evolution, Journal Year: 2019, Volume and Issue: 3(12), P. 1731 - 1742

Published: Nov. 25, 2019

Abstract Males and females often differ in their fitness optima for shared traits that have a genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how is resolved species lack largely unknown. Here we present chromosome-anchored genome assembly rainbow trout ( Oncorhynchus mykiss ) characterize 55-Mb double-inversion supergene mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism resolving The double inversion contains key photosensory, circadian rhythm, adiposity sex-related genes displays latitudinal frequency cline, indicating environmentally dependent selection. Our results show reversal across large autosomal supergene, resolution capable of protecting variation while avoiding the homozygous lethality mutations associated with typical heteromorphic chromosomes.

Language: Английский

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The role of sex in the genomics of human complex traits

Nature Reviews Genetics, Journal Year: 2018, Volume and Issue: 20(3), P. 173 - 190

Published: Dec. 23, 2018

Language: Английский

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Harnessing the Power of Genomics to Secure the Future of Seafood

Trends in Ecology & Evolution, Journal Year: 2017, Volume and Issue: 32(9), P. 665 - 680

Published: Aug. 14, 2017

Advancements of genetic technologies now allow the collection genome-wide data in nonmodel species a cost -effective manner. These genomic-informed addressing comprehensive spectrum needs and applications relevant to fisheries, aquaculture , biosecurity. Genomics tools also improve our understanding how aquatic organisms adapt respond environment, ability monitor environmental variation exploited species. Genomic approaches are rapidly replacing traditional markers, but their application fisheries management has stagnated when compared agriculture where they have long been used for improved production. There is no reason further delay genomic Best use scientific knowledge required maintain fundamental role seafood human nutrition. While it acknowledged that genomic-based methods powerful data, value inform management, biosecurity remains underestimated. We review relevance sustainable resources, illustrate benefits of, identify barriers integration. conclude information towards securing future does not need be demonstrated. Instead, we immediate efforts remove structural roadblocks focus on ways support integration into production practices. propose solutions pave way forward. Seafood plays meeting current food [1Béné C. et al.Contribution security poverty reduction: assessing evidence.World Dev. 2016; 79: 177-196Crossref Scopus (409) Google Scholar]. Capture only remaining wild animal protein source, fastest growing sector world. Together provide 4.5 billion people with at least 15% [2Béné Small-scale fisheries: contribution rural livelihoods developing countries.FAO Fisheries Circular. FAO, 2006Google Scholar, 3McIntyre P.B. al.Linking freshwater fishery global biodiversity conservation.Proc. Nat. Acad. Sci. U. S. A. 113: 12880-12885Crossref (139) The population may exceed 9 by 2050, so pressing question whether can help alleviate issues [3McIntyre answer this unknown. some developed countries longer sustained from local fish stocks increasingly supplemented elsewhere [4Pauly D. Zeller Catch reconstructions reveal marine catches higher than reported declining.Nat. Commun. 7: 10244Crossref PubMed (707) This trend will probably remain or increase over time, as several near above limits [5Hilborn R. Stokes K. Defining overfished stocks: lost plot?.Fisheries. 2010; 35: 113-120Crossref (61) 6Rose G.A. Rowe Northern cod comeback.Can. J. Fish. Aquat. 2015; 72: 1789-1798Crossref (69) Scholar], many overexploited collapse 7Worm B. al.Rebuilding fisheries.Science. 2009; 325: 578-585Crossref (1578) 8Osio G.C. al.Assessing vulnerability Mediterranean demersal predicting exploitation status un-assessed stocks.Fish. Res. 171: 110-121Crossref (35) For example, 95% Black Seas overharvested [8Osio being severely affected worldwide cumulative effects habitat degradation, climate change,and diseases [39Bhattacharya M. al.DNA barcoding fishes: directions.Mitochondrial DNA Part 27: 2744-2752PubMed finfish reached volume [10Béné al.Feeding 2050–Putting back menu.Food Secur. 261-274Crossref (424) growth expected decelerate response shortage, lack suitable locations, increasing feed costs [11Food Agriculture Organization State World Aquaculture 2016. Contributing nutrition all.STECF: Scientific, Technical Economic Committee Fisheries. Publications Office European Union, 2016Google Moreover, other industries (e.g., shellfish) suffering setbacks due disease outbreaks ocean acidification [12S al.An Updated Synthesis Impacts Ocean Acidification Marine Biodiversity. Secretariat Convention Biological Diversity, 2014Google Careful strategies industry, making critical best informs decision-making 4Pauly 13Melnychuk M.C. al.Fisheries impacts target status.Proc. 2017; 114: 178-183Crossref (100) Traditional relies stock assessment models predict variability stock–recruitment relationships determine catch [7Worm 14Myers R.A. Stock recruitment: generalizations about maximum reproductive rate, density dependence, using meta-analytic approaches.ICES Mar. 2001; 58: 937-951Crossref (208) 15Beddington J.R. al.Current problems 2007; 316: 1713-1716Crossref (457) Genetic [16Waples R.S. al.Integrating resources: do better?.Fish 2008; 9: 423-449Crossref (235) however, (Box 1). Consequently, despite demonstrated delineate populations accurately (see section below), units predominantly based administrative units, which often closely connected biology 17Borja al.Overview integrative systems: ecosystem approach practice.Front. 3: 20Crossref (180) contradicts basis science whereby Maximum Sustainable Yield (MSY) achieved efficient distinct 16Waples 18Utter F.M. Biochemical genetics management: an historical perspective.J. Fish Biol. 1991; 39: 1-20Crossref (147) Scholar].Box 1Why Data Has Seldom Been Incorporated Management, What Do itThe explosion began 1980 s propelled allelic interpretation electrophoretic mobility proteins accelerated genomics revolution 9Snapper9 [49Ryman N. Utter F. Genetics past, present future.in: Ryman Population management. University Washington, 1987: 1-20Google Sadly, exclamations practical conservation largely fallen deaf ears. Despite trouble-shooting experts 50Hauser L. Carvalho G.R. Paradigm shifts genetics: ugly hypotheses slain beautiful facts.Fish 333-362Crossref (449) impediments downstream still remain.To systematically address this, three user groups were consulted one-to-one structured interviews [51Dichmont, C.M. al. (2012) Scoping tools, limitations Final Report. Australian Research & Development Corporation Project 2011/035.Google scientists (n = 26), managers 24), fishing industry representatives 12) Australia, Europe, North South America, Western Pacific, Africa New Zealand. purpose was qualitatively assess attitudes perceptions context if there uptake might improved. Over 90% interviewees familiar structure (Theme II [52Ovenden al.Ocean's eleven: evaluation population, evolutionary molecular fisheries.Fish 16: 125-159Crossref (113) Scholar]). awareness ten themes poor moderate. Industry viewed more positively scientists. positive recognition general usefulness genetics, particular defining spatial populations. Where negative perception interviewees, reasons provided:•A potential information,•A studies expensive,•A results 'oversold',•A consistency interpretations geneticists,•The importance far outweighed inputs decisions.All agreed effectiveness could suggestions grouped two categories: communication technical. Improvements (around 70% suggestions) considered essential. Specific included: across plain language; greater among scientists, geneticists, industry; utility groups; accessibility research geneticists. improvement included reducing projects; robust reliable techniques; sampling designs.Unhappily, challenges roadblock wake-up call those involved security. glimmers hope changing. survey showed most understand its power sympathetic, knowledgeable, genetics. Thus, judicious likely well received, carefully tailored policy (Ovenden Moore, S11). onus geneticists end-users reach mutual (Figure I), else perceived sustained. remain. To decisions. All designs. Unhappily, Novel better biosecurity, [19Willette al.So, you want next-generation sequencing systems? Insight Pan-Pacific Advanced Studies Institute.Bull. 2014; 90: 79-122Crossref (45) 20da Fonseca R.R. al.Next-generation biology: analysis non-model organisms.Mar. Genom. 30: 3-13Crossref (97) markers microsatellite DNA), little policies refers relating complete genome organism [21Pearse Saving spandrels? Adaptive management.J. 89: 2697-2716Crossref (37) In term typically shorthand describe applying large datasets; typical, yet arbitrary, threshold >1000s versus 10s–100s distinguish between studies, respectively. decades, low-resolution available pertaining aquaculture. Indeed first sequence key published 2011 [22Star al.The Atlantic reveals unique immune system.Nature. 2011; 477: 207-210Crossref (570) limited incorporation new problem makes situation different. because time development cost-effective traceability supply chain [23Kelley J.L. life aquatic: advances vertebrate genomics.Nat. Rev. Genet. 4: 523-534Crossref (52) Scholar] Specifically defines quantifies extent adaptive divergence connectivity them, allows performing mixed-stock substantially increased resolution. advance means selection resistance, identifying greatest domestication [24Yáñez J.M. al.Genomics accelerate progress.Front. 6https://doi.org/10.3389/fgene.2015.00128Crossref (76) escapees farms. A small moderate number sometimes sufficient hand 25Ovenden (31) necessary step set subsequent surveys. Tools derived environments community level, biological species, instance, provided exponential (eDNA) metabarcoding [26Rees H.C. al.REVIEW: detection – eDNA tool ecology.J. Appl. Ecol. 51: 1450-1459Crossref (596) following outlines representative examples direct aquaculture, quality safety purposes. Details each these case presented 14 short papers (S1–S14) Supplementary Material summarise presentations invited speakers during symposium entitled: "Genomics conservation: promises fulfilled?" Accurate identification mandatory enable proactive Bernatchez (S6) thousands single nucleotide polymorphism (SNP) allowed refinement American lobster, documenting degree overlap while providing evidence adaptation. Regional patterns recruitment eel imposed shown recur every generation dispersal spawning area (Bernatchez, S6). finding influence both restoration strategies. Species practices aided approaches. Lee (S7) neutral considerable discriminate cryptic sympatric fishes Korean peninsula. Similarly, Araneda Larraín (S1) 2).Box 2Genomic Approaches TraceabilityTraceability aquacultured products like shellfish throughout ('from fork ') high certainty origin identity crucial utilisation, prevent fraud [53Stawitz C.C. al.Financial Ecological Implications Global Mislabeling.Conserv. Lett. https://doi.org/10.1111/conl.12328Crossref (28) general, identified external traits; phenotypic tracing becomes unusable once entered processing. resources reproducibility reliability, products; easily combined reference materials [54Martinshohn al.Tracing advanced technologies. Woodhead Publishing, 2011Google authenticity verify labelling information. Traceability applied broad levels: individual identification. Hitherto, levels explored either methods.Two objectives level include preventing substitution valuable lower marketing potentially harmful consumer protected [55Abbadi al.Species bivalve molluscs pyrosequencing.J. Food Agr. Discipl. 97: 512-519Crossref (19) 56Wong E.H.-K. Hanner R.H. detects market seafood.Food Int. 41: 828-837Crossref (351) 57Miller al.Seafood mislabelling: comparisons western assist influencing factors, mechanisms motives.Fish 2012; 13: 345-358Crossref (68) 58Filonzi al.Molecular mislabelling commercial Italy.Food 43: 1383-1388Crossref (151) Many detected through cytochrome oxidase I gene (COI) comparing database (FISH-BOL) [59Ward R.D. campaign barcode all fishes, FISH-BOL.J. 74: 329-356Crossref (656) 60Becker al.Five years FISH-BOL: brief report.Mitochondrial DNA. 22: 3-9Crossref (98) 61Oliveira al.Assembling auditing library fishes.J. 2741-2754Crossref (21) less requires different mitochondrial nuclear SNP panels [62Zbawicka al.Identification validation novel Mytilus mussels.Mar. 159: 1347-1362Crossref (43) depending taxa [63Kijewski T. al.Distribution coastal areas inferred markers.J. Sea 65: 224-234Crossref (53) Examples include, separation mussel, common blue Baltic mussel Chilean accuracy panel 49 SNPs (Larraín preparation) mussels subpanel 19 (Araneda Larraín, S1).The second (population) sale illegal, unreported unregulated protecting consumers collected threats public health (for algal blooms). Assignments non-neutral successful differentiating (Atlantic cod, herring, sole, hake) geographical Europe [31Nielsen E.E. al.Gene-associated tackling illegal false eco-certification.Nat. 851Crossref (178) differentiate [64Araneda al.Adaptive distinguishes (Mytilus chilensis) environments.Ecol. Evol. 6: 3632-3644Crossref (38) red tide 2016, thus permitting physical (records, labels). Such informative usually perform

Language: Английский

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