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Advances of genotyping-by-sequencing in fisheries and aquaculture

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Abstract

The use of genotyping has enabled the characterization and mapping of genes and the study of stock identification, population genetics, evolution, ecological speciation, and invasion, as well as genomic evaluation, sex control and sex determination, nutrition, biomarkers for disease, and quantitative trait loci mapping for marker-assisted selection in fisheries and aquaculture. High-throughput variant discovery has been made possible in multiple species by the recent advent of next-generation DNA sequencing technologies. New genotyping methods that are high-throughput, accurate, and inexpensive are urgently needed for gaining full access to the abundant genetic variation of organisms. This approach is known as genotyping-by-sequencing (GBS), which holds great promise as a research tool because of its ability to allow simultaneous marker discovery and genotyping at low cost and with a simple molecular biology workflow for fisheries and aquaculture studies. Since it was first developed for rice in 2009, GBS has been applied in over 50 species/studies by the end of 2014. It is also increasingly in use in fisheries and aquaculture and has been applied in nearly 40 species/studies from 2015 to present. This review summarizes the genotyping methodologies, recent advances in next-generation DNA sequencing technologies to achieve GBS, and the promises this approach holds as a genome-wide genotyping application in fisheries and aquaculture. Additionally, we discuss the potential of whole-genome sequencing (WGS) in GBS and present the advances of WGS in fisheries and aquaculture.

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References

  • Afman L, Muller M (2006) Nutrigenomics: from molecular nutrition to prevention of disease. J Am Diet Assoc 106:569–576

    Article  CAS  PubMed  Google Scholar 

  • Allendorf FW, Leary RF, Spruell P, Wenburg JK (2001) The problems with hybrids-setting conservation guidelines. Trends Ecol Evol 16:613–622

    Article  Google Scholar 

  • Allendorf FW, Hohenlohe PA, Luikart G (2010) Genomics and the future of conservation genetics. Nat Rev Genet 11:697–709

    Article  CAS  PubMed  Google Scholar 

  • Alligood KS, Lescak EA, Bassham SL, Catchen JM, Von Hippel FA, Cresko WA (2016) Linking phenotypic and genomic evolution in very young populations of threespine stickleback. Integr Comp Biol 56:E4

    Google Scholar 

  • Alwala S, Suman A, Arro JA, Veremis JC, Kimbeng CA (2006) Target region amplification polymorphism (TRAP) for assessing genetic diversity in sugarcane germplasm collections. Crop Sci 46:448

    Article  CAS  Google Scholar 

  • Amish SJ, Hohenlohe PA, Painter S et al (2012) RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays. Mol Ecol Resour 12:653–660

    Article  CAS  PubMed  Google Scholar 

  • Anderson JL, Rodriguez Mari A, Braasch I, Amores A, Hohenlohe P, Batzel P, Postlethwait JH (2012) Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics. PLoS ONE 7:e40701. doi:10.1371/journal.pone.0040701

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ao J, Li J, You X et al (2015) Construction of the high-density genetic linkage map and chromosome map of large yellow croaker (Larimichthys crocea). Int J Mol Sci 16:26237–26248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Araneda C (2015) Contrasting patterns of neutral and adaptive genetic variation of Chilean blue mussel (Mytilus chilensis) due to local adaptation and aquaculture. In: Plant and animal genome XXIII conference. Plant and animal genome

  • Araneda C, Angelica Larrain M, Hecht B, Narum S (2016) Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments. Ecol Evol 6:3632–3644

    Article  PubMed  PubMed Central  Google Scholar 

  • Baird NA, Etter PD, Atwood TS et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376. doi:10.1371/journal.pone.0003376

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Barnes S (2008) Nutritional genomics, polyphenols, diets, and their impact on dietetics. J Am Diet Assoc 108:1888–1895

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berthelot C, Brunet F, Chalopin D et al (2014) The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun 5:3657

    Article  PubMed  PubMed Central  Google Scholar 

  • Bohling J, Haffray P, Berrebi P (2016) Genetic diversity and population structure of domestic brown trout (Salmo trutta) in France. Aquaculture 462:1–9

    Article  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    CAS  PubMed  PubMed Central  Google Scholar 

  • Boussaha M, Guyomard R, Cabau C, Esquerr D, Quillet E (2012) Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout. BMC Genom 13(1):238

    Article  CAS  Google Scholar 

  • Bradbury IR, Hamilton LC, Dempson B, Robertson MJ, Bourret V, Bernatchez L, Verspoor E (2015) Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction-site associated DNA sequencing for the resolution of complex spatial structure. Mol Ecol 24:5130–5144

    Article  CAS  PubMed  Google Scholar 

  • Brawand D, Wagner CE, Li YI et al (2014) The genomic substrate for adaptive radiation in African cichlid fish. Nature 513:375–381

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brieuc MS, Waters CD, Seeb JE, Naish KA (2014) A dense linkage map for Chinook salmon (Oncorhynchus tshawytscha) reveals variable chromosomal divergence after an ancestral whole genome duplication event. G3 (Bethesda) 4:447–460

    Article  CAS  Google Scholar 

  • Brown JK, Taggart JB, Bekaert M, Wehner S, Palaiokostas C, Setiawan AN, Symonds JE, Penman DJ (2016) Mapping the sex determination locus in the hapuku (Polyprion oxygeneios) using ddRAD sequencing. BMC Genom 17:448

    Article  Google Scholar 

  • Bruneaux M, Johnston SE, Herczeg G, Merila J, Primmer CR, Vasemagi A (2013) Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach. Mol Ecol 22:565–582

    Article  CAS  PubMed  Google Scholar 

  • Buermans HP, den Dunnen JT (2014) Next generation sequencing technology: advances and applications. Biochim Biophys Acta 1842(10):1932–1941

    Article  CAS  PubMed  Google Scholar 

  • Buerstmayr H, Ban T, Anderson JA (2009) QTL mapping and marker-assisted selection for Fusarium head blight resistance. Plant Breed 128:1–26

    Article  CAS  Google Scholar 

  • Candy JR, Campbell NR, Grinnell MH, Beacham TD, Larson WA, Narum SR (2015) Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt. Mol Ecol Resour. doi:10.1111/1755-0998.12400

    PubMed  Google Scholar 

  • Carlson BM, Onusko SW, Gross JB (2015) A high-density linkage map for astyanax mexicanus using genotyping-by-sequencing technology. G3-Genes Genom Genet 5:241–251

    CAS  Google Scholar 

  • Chen L, Zhao E (2013) Advances of nutrigenomics: concept, content, technology and development. J Exp Biol Agric Sci 1(3):152–158

    CAS  Google Scholar 

  • Chen S, Zhang G, Shao C et al (2014) Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nat Genet 46:253–260

    Article  CAS  PubMed  Google Scholar 

  • Ciosi M, Miller NJ, Kim KS, Giordano R, Estoup A, Guillemaud T (2008) Invasion of Europe by the western corn rootworm, Diabrotica virgifera virgifera: multiple transatlantic introductions with various reductions of genetic diversity. Mol Ecol 17:3614–3627

    Article  CAS  PubMed  Google Scholar 

  • Clark SA, Hickey JM, van der Werf JH (2011) Different models of genetic variation and their effect on genomic evaluation. Genet Sel Evol 43:18

    Article  PubMed  PubMed Central  Google Scholar 

  • Corander J, Majander KK, Cheng L, Merila J (2013) High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus. Mol Ecol 22:2931–2940

    Article  CAS  PubMed  Google Scholar 

  • Cortés AJ, Chavarro MC, Blair MW (2011) SNP marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 123:827–845

    Article  PubMed  Google Scholar 

  • Craig DW, Pearson JV, Szelinger S et al (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 5:887–893

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36:e122

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cutter AD (2013) Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory. Mol Phylogenet Evol 69:1172–1185

    Article  CAS  PubMed  Google Scholar 

  • Daniel H (2007) Genomics and proteomics: importance for the future of nutrition research. Br J Nutr 87:S305

    Article  CAS  Google Scholar 

  • Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510

    Article  CAS  PubMed  Google Scholar 

  • Dayan DI, Crawford DL, Oleksiak MF (2015) Population genomics of rapid adaptation in Fundulus heteroclitus exposed to power station thermal effluents. Integr Comp Biol 55:E42

    Google Scholar 

  • De Donato M, Peters SO, Mitchell SE, Hussain T, Imumorin IG (2013) Genotyping-by-sequencing (GBS): a novel, efficient and cost-effective genotyping method for cattle using next-generation sequencing. PLoS ONE 8:e62137. doi:10.1371/journal.pone.0062137

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • DellaPenna D (1999) Nutritional genomics: manipulating plant micronutrients to improve human health. Science 285:375–379

    Article  CAS  PubMed  Google Scholar 

  • Deschamps S, Llaca V, May GD (2012) Genotyping-by-sequencing in plants. Biology (Basel) 1:460–483

    Google Scholar 

  • Dodds KG, McEwan JC, Brauning R, Anderson RM, van Stijn TC, Kristjansson T, Clarke SM (2015) Construction of relatedness matrices using genotyping-by-sequencing data. BMC Genom 16(1):1047

    Article  CAS  Google Scholar 

  • Dominik S, Henshall JM, Kube PD et al (2010) Evaluation of an Atlantic salmon SNP chip as a genomic tool for the application in a Tasmanian Atlantic salmon (Salmo salar) breeding population. Aquaculture 308:S56–S61

    Article  CAS  Google Scholar 

  • Dong L, Xiao S, Wang Q, Wang Z (2016) Comparative analysis of the GBLUP, emBayesB, and GWAS algorithms to predict genetic values in large yellow croaker (Larimichthys crocea). BMC Genom 17:460

    Article  Google Scholar 

  • Doubleday ZA, Semmens JM, Smolenski AJ, Shaw PW (2009) Microsatellite DNA markers and morphometrics reveal a complex population structure in a merobenthic octopus species (Octopus maorum) in south-east Australia and New Zealand. Mar Biol 156:1183–1192

    Article  CAS  Google Scholar 

  • Du X, Oleksiak MF, Crawford DL (2015) A genotyping by sequencing study of natural populations of Fundulus heteroclitus inhabiting a strong pollution cline. Integr Comp Biol 55:E49

    Google Scholar 

  • Ekblom R, Wolf JBW (2014) A field guide to whole-genome sequencing, assembly and annotation. Evol Appl. doi:10.1111/eva.12178

    PubMed  PubMed Central  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379. doi:10.1371/journal.pone.0019379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Emahazion T, Feuk L, Jobs M et al (2001) SNP association studies in Alzheimer’s disease highlight problems for complex disease analysis. Trends Genet 17:407–413

    Article  CAS  PubMed  Google Scholar 

  • Erickson PA, Glazer AM, Killingbeck EE, Agoglia RM, Baek J, Carsanaro SM, Lee AM, Cleves PA, Schluter D, Miller CT (2016) Partially repeatable genetic basis of benthic adaptation in threespine sticklebacks. Evol Int J Org Evol 70:887–902

    Article  Google Scholar 

  • Etter P, Bassham S, Hohenlohe P, Johnson E, Cresko W (2011a) SNP discovery and genotyping for evolutionary genetics using RAD sequencing. Methods Mol Biol 772:157–178

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA (2011b) Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS ONE 6:e18561. doi:10.1371/journal.pone.0018561

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet 104:399–407

    Article  CAS  PubMed  Google Scholar 

  • Evans DM, Cardon LR, Morris AP (2004) Genotype prediction using a dense map of SNPs. Genet Epidemiol 27:375–384

    Article  PubMed  Google Scholar 

  • Everett MV, Seeb JE (2014) Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing. Evol Appl 7:480–492

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Faria R, Renaut S, Galindo J et al (2014) Advances in ecological speciation: an integrative approach. Mol Ecol Notes 23:513–521

    Article  Google Scholar 

  • Ferchaud AL, Pedersen SH, Bekkevold D, Jian J, Niu Y, Hansen MM (2014) A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus). BMC Genom 15:867. doi:10.1186/1471-2164-15-867

    Article  Google Scholar 

  • Franchini P, Fruciano C, Spreitzer ML et al (2014) Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes. Mol Ecol 23:1828–1845

    Article  PubMed  Google Scholar 

  • Fraser BA, Kunstner A, Reznick DN, Dreyer C, Weigel D (2015) Population genomics of natural and experimental populations of guppies (Poecilia reticulata). Mol Ecol 24:389–408

    Article  PubMed  Google Scholar 

  • Futuyma DJ, Moreno G (1988) The evolution of ecological specialization. Annu Rev Ecol Evol Syst 19:207–233

    Article  Google Scholar 

  • Gagnaire PA, Normandeau E, Pavey SA, Bernatchez L (2013) Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis). Mol Ecol 22:3036–3048

    Article  CAS  PubMed  Google Scholar 

  • Gamble T (2016) Using RAD-seq to recognize sex-specific markers and sex chromosome systems. Mol Ecol 25:2114–2116

    Article  CAS  PubMed  Google Scholar 

  • Glazer AM, Killingbeck EE, Mitros T, Rokhsar DS, Miller CT (2015) Genome assembly improvement and mapping convergently evolved skeletal traits in sticklebacks with genotyping-by-sequencing. G3-Genes Genomes Genet 5:1463–1472

    Google Scholar 

  • Goddard ME, Hayes BJ (2009) Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat Rev Genet 10:381–391

    Article  CAS  PubMed  Google Scholar 

  • Goddard ME, Hayes BJ, Meuwissen TH (2010) Genomic selection in livestock populations. Genet Res (Camb) 92:413–421

    Article  CAS  Google Scholar 

  • Gonen S, Lowe NR, Cezard T, Gharbi K, Bishop SC, Houston RD (2014) Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing. BMC Genom 15:166. doi:10.1186/1471-2164-15-166

    Article  CAS  Google Scholar 

  • Gonen S, Bishop SC, Houston RD (2015) Exploring the utility of cross-laboratory RAD-sequencing datasets for phylogenetic analysis. BMC Res Notes 8:299

    Article  PubMed  PubMed Central  Google Scholar 

  • Gunderson KL, Kuhn KM, Steemers FJ, Ng P, Murray SS, Shen R (2006) Whole-genome genotyping of haplotype tag single nucleotide polymorphisms. Pharmacogenomics 7:641–648

    Article  CAS  PubMed  Google Scholar 

  • Guo B, DeFaveri J, Sotelo G, Nair A, Merila J (2015) Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks. BMC Biol 13(1):1–18

    Article  Google Scholar 

  • Guo B, Li Z, Merila J (2016) Population genomic evidence for adaptive differentiation in the Baltic Sea herring. Mol Ecol 25:2833–2852

    Article  CAS  PubMed  Google Scholar 

  • Gupta PK, Rustgi S (2004) Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genom 4:139–162

    Article  CAS  Google Scholar 

  • Gut IG (2001) Automation in genotyping of single nucleotide polymorphisms. Hum Mutat 17:475–492

    Article  CAS  PubMed  Google Scholar 

  • Hand BK, Tyler DH, Kovach RP et al (2015) Genomics and introgression: discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing. Curr Zool 61(1):146–154

    Article  Google Scholar 

  • Handley LJL, Estoup A, Evans DM et al (2011) Ecological genetics of invasive alien species. Biocontrol 56:409–428

    Article  Google Scholar 

  • Hauser L, Seeb JE (2008) Advances in molecular technology and their impact on fisheries genetics. Fish Fish 9:473–486

    Article  Google Scholar 

  • Haussmann BI, Mahalakshmi V, Reddy BV, Seetharama N, Hash CT, Geiger HH (2002) QTL mapping of stay-green in two sorghum recombinant inbred populations. Theor Appl Genet 106:133–142

    Article  CAS  PubMed  Google Scholar 

  • Hawthorne DJ, Via S (2001) Genetic linkage of ecological specialization and reproductive isolation in pea aphids. Nature 412:904–907

    Article  CAS  PubMed  Google Scholar 

  • He S, Liang XF, Sun J et al (2013) Insights into food preference in hybrid F1 of Siniperca chuatsi (♀) × Siniperca scherzeri (♂) mandarin fish through transcriptome analysis. BMC Genom 14:601. doi:10.1186/1471-2164-14-601

    Article  CAS  Google Scholar 

  • Hecht BC, Thrower FP, Hale MC, Miller, Nichols KM (2012) Genetic architecture of migration-related traits in rainbow and steelhead trout, Oncorhynchus mykiss. G3 (Bethesda) 2:1113–1127

    Article  CAS  Google Scholar 

  • Hecht BC, Campbell NR, Holecek DE, Narum SR (2013) Genome-wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout. Mol Ecol 22:3061–3076

    Article  CAS  PubMed  Google Scholar 

  • Heller MJ (2002) DNA microarray technology: devices, systems, and applications. Annu Rev Biomed Eng 4:129–153

    Article  CAS  PubMed  Google Scholar 

  • Henning F, Meyer A (2014) The evolutionary genomics of cichlid fishes: explosive speciation and adaptation in the postgenomic era. Annu Rev Genom Hum Genet 15:417–441

    Article  CAS  Google Scholar 

  • Henning F, Lee HJ, Franchini P, Meyer A (2014) Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using RAD markers for dense linkage mapping. Mol Ecol. doi:10.1111/mec.12860

    Google Scholar 

  • Hess JE, Campbell NR, Close DA, Docker MF, Narum SR (2013) Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species. Mol Ecol 22:2898–2916

    Article  CAS  PubMed  Google Scholar 

  • Hess JE, Campbell NR, Docker MF et al (2015) Use of genotyping by sequencing data to develop a high-throughput and multifunctional SNP panel for conservation applications in Pacific lamprey. Mol Ecol Resour 15:187–202

    Article  CAS  PubMed  Google Scholar 

  • Hickey JM, Kinghorn BP, Tier B, van der Werf JH, Cleveland MA (2012) A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation. Genet Sel Evol 44:9. doi:10.1186/1297-9686-44-9

    Article  PubMed  PubMed Central  Google Scholar 

  • Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA (2010) Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet 6:e1000862. doi:10.1371/journal.pgen.1000862

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hohenlohe PA, Amish SJ, Catchen JM, Allendorf FW, Luikart G (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Mol Ecol Resour 11(Suppl 1):117–122

    Article  PubMed  Google Scholar 

  • Hohenlohe PA, Day MD, Amish SJ et al (2013) Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Mol Ecol 22:3002–3013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Houston RD (2015) Application of genomics to selective breeding of Atlantic salmon. In: Plant and animal genome XXIII conference. Plant and animal genome

  • Houston RD, Davey JW, Bishop SC et al (2012) Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon. BMC Genom 13:244. doi:10.1186/1471-2164-13-244

    Article  CAS  Google Scholar 

  • Houston RD, Taggart JB, Cézard T et al (2014) Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar). BMC Genom 15:90. doi:10.1186/1471-2164-15-90

    Article  CAS  Google Scholar 

  • Howe K, Clark MD, Torroja CF et al (2013) The zebrafish reference genome sequence and its relationship to the human genome. Nature 496:498–503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu J, Vick BA (2003) Target region amplified polymorphism: a novel marker technique for plant genotyping. Plant Mol Biol Report 21:289–294

    Article  CAS  Google Scholar 

  • Huang X, Feng Q, Qian Q et al (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hunter DJ (2005) Gene-environment interactions in human diseases. Nat Rev Genet 6:287–298

    Article  CAS  PubMed  Google Scholar 

  • Jaillon O, Aury JM, Brunet F et al (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946–957

    Article  PubMed  Google Scholar 

  • Jenkins S, Gibson N (2002) High-throughput SNP genotyping. Comp Funct Genomics 3:57–66

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiao W, Fu X, Dou J et al (2014) High-resolution linkage and quantitative trait locus mapping aided by genome survey sequencing: building up an integrative genomic framework for a bivalve mollusc. DNA Res 21:85–101

    Article  CAS  PubMed  Google Scholar 

  • Jones FC, Grabherr MG, Chan YF et al (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484:55–61

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jones JC, Fan S, Franchini P, Schartl M, Meyer A (2013) The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing. Mol Ecol 22:2986–3001

    Article  CAS  PubMed  Google Scholar 

  • Jones DB, Jerry DR, Khatkar MS et al (2014) Determining genetic contributions to host oyster shell growth: quantitative trait loci and genetic association analysis for the silver-lipped pearl oyster, Pinctada maxima. Aquaculture 434:367–375

    Article  CAS  Google Scholar 

  • Judson R, Salisbury B, Schneider J, Windemuth A, Stephens JC (2002) How many SNPs does a genome-wide haplotype map require? Pharmacogenomics 3:279–391

    Article  Google Scholar 

  • Kakioka R, Kokita T, Kumada H, Watanabe K, Okuda N (2015) Genomic architecture of habitat-related divergence and signature of directional selection in the body shapes of Gnathopogon fishes. Mol Ecol 24:4159–4174

    Article  CAS  PubMed  Google Scholar 

  • Kanamori A, Sugita Y, Yuasa Y, Suzuki T, Kawamura K, Uno Y, Kamimura K, Matsuda Y, Wilson CA, Amores A, Postlethwait JH, Suga K, Sakakura Y (2016) A genetic map for the only self-fertilizing vertebrate. G3-Genes Genomes Genet 6:1095–1106

    Google Scholar 

  • Kasahara M, Naruse K, Sasaki S et al (2007) The medaka draft genome and insights into vertebrate genome evolution. Nature 447:714–719

    Article  CAS  PubMed  Google Scholar 

  • Keller I, Wagner CE, Greuter L et al (2013) Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes. Mol Ecol 22:2848–2863

    Article  CAS  PubMed  Google Scholar 

  • Khamnamtong B, Klinbunga S, Menasveta P (2009) Genetic diversity and geographic differentiation of the giant tiger shrimp (Penaeus monodon) in Thailand analyzed by mitochondrial COI sequences. Biochem Genet 47:42–55

    Article  CAS  PubMed  Google Scholar 

  • Kim S, Misra A (2007) SNP genotyping: technologies and biomedical applications. Annu Rev Biomed Eng 9:289–320

    Article  CAS  PubMed  Google Scholar 

  • Kothiyal P, Cox S, Ebert J, Aronow BJ, Greinwald JH, Rehm HL (2009) An overview of custom array sequencing. Current protocols in human genetics, Chapter 7: Unit 7.17. doi: 10.1002/0471142905.hg0717s61

  • Kumar S, Banks TW, Cloutier S (2012) SNP discovery through next-generation sequencing and its applications. Int J Plant Genomics 2012:831460

    PubMed  PubMed Central  Google Scholar 

  • Kwok PY (2001) Methods for genotyping single nucleotide polymorphisms. Annu Rev Genomics Hum Genet 2:235–258

    Article  CAS  PubMed  Google Scholar 

  • Kwok PY, Gu Z (1999) Single nucleotide polymorphism libraries: Why and how are we building them? Mol Med Today 5:538–543

    Article  CAS  PubMed  Google Scholar 

  • Kwok PY, Xiao M (2004) Single-molecule analysis for molecular haplotyping. Hum Mutat 23:442–446

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lah L, Benke H, Berggren P et al (2014) Investigating harbor porpoise (Phocoena phocoena) population differentiation using RAD-tag genotyping by sequencing. IWC Meeting Portal, Scientific Committee Annual Meeting 2014 (SC65B), https://events.iwc.int/index.php/scientific/SC65B/paper/view/825

  • Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199

    CAS  PubMed  PubMed Central  Google Scholar 

  • Laporte M, Pavey SA, Rougeux C, Pierron F, Lauzent M, Budzinski H, Labadie P, Geneste E, Couture P, Baudrimont M, Bernatchez L (2016) RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels. Mol Ecol 25:219–237

    Article  CAS  PubMed  Google Scholar 

  • Larson WA, Seeb JE, Pascal CE, Templin WD, Seeb LW, Taylor E (2014a) Single-nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing improve genetic stock identification of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Can J Fish Aquat Sci 71:698–708

    Article  CAS  Google Scholar 

  • Larson WA, Seeb LW, Everett MV, Waples RK, Templin WD, Seeb JE (2014b) Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha). Evol Appl 7:355–369

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee CE (2002) Evolutionary genetics of invasive species. Trends Ecol Evol 17:386–391

    Article  Google Scholar 

  • Lemay MA, Russello MA (2015) Genetic evidence for ecological divergence in kokanee salmon. Mol Ecol 24:798–811

    Article  CAS  PubMed  Google Scholar 

  • Lescak EA, Bassham SL, Catchen J, Gelmond O, Sherbick ML, von Hippel FA, Cresko WA (2015) Evolution of stickleback in 50 years on earthquake-uplifted islands. Proc Natl Acad Sci USA 112:E7204–E7212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP et al (2007) The diploid genome sequence of an individual human. PLoS Biol 5(10):e254. doi:10.1371/journal.pbio.0050254

    Article  PubMed  PubMed Central  CAS  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. Trans Am Fish Soc 144:767–779

    Article  Google Scholar 

  • Li Y, Guo X, Cao X, Deng W, Luo W, Wang W (2012) Population genetic structure and post-establishment dispersal patterns of the red swamp crayfish Procambarus clarkii in China. PLoS ONE 7:e40652. doi:10.1371/journal.pone.0040652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li C, Waldbieser G, Bosworth B, Beck BH, Thongda W, Peatman E (2014) SNP discovery in wild and domesticated populations of blue catfish, Ictalurus furcatus, using genotyping-by-sequencing and subsequent SNP validation. Mol Ecol Resour. doi:10.1111/1755-0998.12272

    Google Scholar 

  • Limborg MT, Waples RK, Seeb JE, Seeb LW (2014) Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation. J Hered. doi:10.1093/jhered/esu063

    PubMed  Google Scholar 

  • Liu S, Vallejo RL, Gao G, Palti Y, Weber GM, Hernandez A, Rexroad CE III (2015a) Identification of single-nucleotide polymorphism markers associated with cortisol response to crowding in rainbow trout. Mar Biotechnol 17:328–337

    Article  CAS  PubMed  Google Scholar 

  • Liu S, Vallejo RL, Palti Y, Gao G, Marancik DP, Hernandez AG, Wiens GD (2015b) Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout. Front Genet 6:298

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Liu-Stratton Y, Roy S, Sen CK (2004) DNA microarray technology in nutraceutical and food safety. Toxicol Lett 150:29–42

    Article  CAS  PubMed  Google Scholar 

  • Longo G, Bernardi G (2015) The evolutionary history of the embiotocid surfperch radiation based on genome-wide RAD sequence data. Mol Phylogenet Evol 88:55–63

    Article  PubMed  Google Scholar 

  • Luikart G, England PR, Tallmon D, Jordan S, Taberlet P (2003) The power and promise of population genomics: from genotyping to genome typing. Nat Rev Genet 4:981–994

    Article  CAS  PubMed  Google Scholar 

  • Lynch M, Milligan BG (1994) Analysis of population genetic structure with RAPD markers. Mol Ecol 3:91–99

    Article  CAS  PubMed  Google Scholar 

  • Majewski J, Schwartzentruber J, Lalonde E, Montpetit A, Jabado N (2011) What can exome sequencing do for you? J Med Genet 48:580–589

    Article  CAS  PubMed  Google Scholar 

  • Mandeville EG, Parchman TL, McDonald DB, Buerkle CA (2015) Highly variable reproductive isolation among pairs of Catostomus species. Mol Ecol. doi:10.1111/mec.13118

    PubMed  PubMed Central  Google Scholar 

  • Manousaki T, Tsakogiannis A, Taggart JB, Palaiokostas C, Tsaparis D, Lagnel J, Chatziplis D, Magoulas A, Papandroulakis N, Mylonas CC, Tsigenopoulos CS (2016) Exploring a nonmodel teleost genome through RAD sequencing-linkage mapping in common pandora, Pagellus erythrinus and comparative genomic analysis. G3-Genes Genomes Genet 6:509–519

    Google Scholar 

  • Martin CH, Feinstein LC (2014) Novel trophic niches drive variable progress towards ecological speciation within an adaptive radiation of pupfishes. Mol Ecol 23:1846–1862

    Article  PubMed  Google Scholar 

  • Mascher M, Wu S, Amand PS, Stein N, Poland J (2013) Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS ONE 8:e76925. doi:10.1371/journal.pone.0076925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mastretta-Yanes A, Arrigo N, Alvarez N, Jorgensen TH, Pinero D, Emerson BC (2015) Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference. Mol Ecol Resour 15:28–41

    Article  CAS  PubMed  Google Scholar 

  • McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT (2013) Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol 66:526–538

    Article  CAS  PubMed  Google Scholar 

  • McPherson JD (2009) Next-generation gap. Nat Methods 6:S2–S5

    Article  CAS  PubMed  Google Scholar 

  • Messer PW, Ellner SP, Hairston NG Jr (2016) Can population genetics adapt to rapid evolution? Trends Genet 32(7):408–418

    Article  CAS  PubMed  Google Scholar 

  • Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Milner JA (2004) Molecular targets for bioactive food components. J Nutr 134:2492S–2498S

    CAS  PubMed  Google Scholar 

  • Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Tree 14:389–394

    CAS  PubMed  Google Scholar 

  • Nakamura Y, Mori K, Saitoh K et al (2013) Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna. Proc Natl Acad Sci 110:11061–11066

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA (2013a) Genotyping-by-sequencing in ecological and conservation genomics. Mol Ecol 22:2841–2847

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Narum SR, Campbell NR, Meyer KA, Miller MR, Hardy RW (2013b) Thermal adaptation and acclimation of ectotherms from differing aquatic climates. Mol Ecol 22:3090–3097

    Article  PubMed  Google Scholar 

  • Norrell AE, Crawley D, Jones KL, Saillant EA (2014) Development and characterization of eighty-four microsatellite markers for the red snapper (Lutjanus campechanus) using illumina paired-end sequencing. Aquaculture 430:128–132

    Article  CAS  Google Scholar 

  • Nunez JCB, Seale TP, Fraser MA, Burton TL, Fortson TN, Hoover D, Travis J, Oleksiak MF, Crawford DL (2015) Population Genomics of the Euryhaline Teleost Poecilia latipinna. PLoS ONE. doi:10.1371/journal.pone.0137077

    Google Scholar 

  • Ogden R, Gharbi K, Mugue N et al (2013) Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing. Mol Ecol 22:3112–3123

    Article  CAS  PubMed  Google Scholar 

  • Oliphant A, Barker DL, Stuelpnagel JR, Chee MS (2002) BeadArray technology-enabling an accurate. Biotechniques 32:S56–S61

    Google Scholar 

  • O’Quin KE, Schulte JE, Patel Z et al (2012) Evolution of cichlid vision via trans-regulatory divergence. BMC Evol Biol 12:251. doi:10.1186/1471-2148-12-251

    Article  PubMed  PubMed Central  Google Scholar 

  • O’Quin KE, Yoshizawa M, Doshi P, Jeffery WR (2013) Quantitative genetic analysis of retinal degeneration in the blind cavefish Astyanax mexicanus. PLoS ONE 8:e57281. doi:10.1371/journal.pone.0057281

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Palaiokostas C, Bekaert M, Davie A et al (2013a) Mapping the sex determination locus in the Atlantic halibut (Hippoglossus hippoglossus) using RAD sequencing. BMC Genom 14:566. doi:10.1186/1471-2164-14-566

    Article  CAS  Google Scholar 

  • Palaiokostas C, Bekaert M, Khan MG et al (2013b) Mapping and validation of the major sex-determining region in Nile tilapia (Oreochromis niloticus L.) using RAD sequencing. PLoS ONE 8:e68389. doi:10.1371/journal.pone.0068389

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Palti Y, Gao G, Miller MR et al (2014) A resource of single-nucleotide polymorphisms for rainbow trout generated by restriction-site associated DNA sequencing of doubled haploids. Mol Ecol Resour 14:588–596

    Article  CAS  PubMed  Google Scholar 

  • Piferrer F, Ribas L, Diaz N (2012) Genomic approaches to study genetic and environmental influences on fish sex determination and differentiation. Mar Biotechnol (NY) 14:591–604

    Article  CAS  Google Scholar 

  • Poland JA, Rife TW (2012) Genotyping-by-sequencing for plant breeding and genetics. Plant Genome J 5:92

    Article  CAS  Google Scholar 

  • Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7:e32253. doi:10.1371/journal.pone.0032253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Powell W, Machray GC, Provan J (1996a) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222

    Article  Google Scholar 

  • Powell W, Morgante M, Andre C et al (1996b) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Puebla O, Bermingham E, McMillan WO (2014) Genomic atolls of differentiation in coral reef fishes (Hypoplectrus spp., Serranidae). Mol Ecol doi: 10.1111/mec.12926

  • Pujolar JM, Jacobsen MW, Frydenberg J et al (2013) A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel. Mol Ecol Resour 13:706–714

    Article  CAS  PubMed  Google Scholar 

  • Pukk L, Ahmad F, Hasan S, Kisand V, Gross R, Vasemagi A (2015) Less is more: extreme genome complexity reduction with ddRAD using ion torrent semiconductor technology. Mol Ecol Resour. doi:10.1111/1755-0998.12392

    PubMed  Google Scholar 

  • Pyšek P, Richardson DM (2010) Invasive species, environmental change and management, and health. Annu Rev Environ Resour 35:25–55

    Article  Google Scholar 

  • Reinhardt F, Liu Z, Seefried F, Thaller G (2009) Implementation of genomic evaluation in German Holsteins. Interbull Bull 40:219–226

    Google Scholar 

  • Reitzel AM, Herrera S, Layden MJ, Martindale MQ, Shank TM (2013) Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics. Mol Ecol 22:2953–2970

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reznick DN, Ghalambor CK (2001) The population ecology of contemporary adaptations: what empirical studies reveal about the conditions that promote adaptive evolution. Genetica 112–113:183–198

    Article  PubMed  Google Scholar 

  • Roberts MA, Mutch DM, German JB (2001) Genomics: food and nutrition. Curr Opin Biotechnol 12:516–522

    Article  CAS  PubMed  Google Scholar 

  • Roda F, Ambrose L, Walter GM et al (2013) Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex. Mol Ecol 22:2941–2952

    Article  CAS  PubMed  Google Scholar 

  • Roesti M, Moser D, Berner D (2013) Recombination in the threespine stickleback genome—patterns and consequences. Mol Ecol 22:3014–3027

    Article  CAS  PubMed  Google Scholar 

  • Rondeau EB, Messmer AM, Sanderson DS et al (2013) Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene. BMC Genom 14:452. doi:10.1186/1471-2164-14-452

    Article  CAS  Google Scholar 

  • Sansaloni C, Petroli C, Jaccoud D et al (2011) Diversity arrays technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. BMC Proc 5:P54

    Article  PubMed Central  Google Scholar 

  • Sax DF, Stachowicz JJ, Brown JH et al (2007) Ecological and evolutionary insights from species invasions. Trends Ecol Evol 22:465–471

    Article  PubMed  Google Scholar 

  • Schartl M, Walter RB, Shen Y et al (2013) The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nat Genet 45:567–572

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schlötterer C (2004) The evolution of molecular markers—Just a matter of fashion? Nat Rev Genet 5(1):63–69

    Article  PubMed  CAS  Google Scholar 

  • Schorka N, Fallina D, Lanchburyd J (2000) Single nucleotide polymorphisms and the future of genetic epidemiology. Clin Genet 58:250–264

    Article  Google Scholar 

  • Schunter C, Garza JC, Macpherson E, Pascual M (2014) SNP development from RNA-seq data in a nonmodel fish: How many individuals are needed for accurate allele frequency prediction? Mol Ecol Resour 14:157–165

    Article  CAS  PubMed  Google Scholar 

  • Seeb LW, Waples RK, Limborg MT, Warheit KI, Pascal CE, Seeb JE (2014) Parallel signatures of selection in temporally isolated lineages of pink salmon. Mol Ecol 23:2473–2485

    Article  CAS  PubMed  Google Scholar 

  • Shao C, Niu Y, Rastas P, Liu Y, Xie Z, Li H, Wang L, Jiang Y, Tai S, Tian Y, Sakamoto T, Chen S (2015) Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis. DNA Res 22:161–170

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shi Y, Wang S, Gu Z et al (2014) High-density single nucleotide polymorphisms linkage and quantitative trait locus mapping of the pearl oyster, Pinctada fucata martensii Dunker. Aquaculture 434:376–384

    Article  Google Scholar 

  • Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation sequencing technologies for environmental DNA research. Mol Ecol 21:1794–1805

    Article  CAS  PubMed  Google Scholar 

  • Skovrind M, Olsen MT, Vieira FG, Pacheco G, Carl H, Gilbert MTP, Moller PR (2016) Genomic population structure of freshwater-resident and anadromous ide (Leuciscus idus) in north-western Europe. Ecol Evol 6:1064–1074

    Article  PubMed  PubMed Central  Google Scholar 

  • Sreeparvathy M (2013) Nutritional genomics. Int J Biol Biol Sci 2:150–153

    Google Scholar 

  • Stapley J, Reger J, Feulner PG et al (2010) Adaptation genomics: the next generation. Trends Ecol Evol 25:705–712

    Article  PubMed  Google Scholar 

  • Star B, Nederbragt AJ, Jentoft S et al (2011) The genome sequence of Atlantic cod reveals a unique immune system. Nature 477:207–210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Steemers FJ, Gunderson KL (2007) Whole genome genotyping technologies on the BeadArray platform. Biotechnology 2(1):41–49

    CAS  Google Scholar 

  • Storer CG, Pascal CE, Roberts SB, Templin WD, Seeb LW, Seeb JE (2012) Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism. PLoS ONE 7:e49018. doi:10.1371/journal.pone.0049018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stranden I, Christensen OF (2011) Allele coding in genomic evaluation. Genet Sel Evol 43:25

    Article  PubMed  PubMed Central  Google Scholar 

  • Syvänen AC (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2:930–942

    Article  PubMed  CAS  Google Scholar 

  • Syvanen AC (2005) Toward genome-wide SNP genotyping. Nat Genet 37(Suppl):S5–S10

    Article  PubMed  CAS  Google Scholar 

  • Takahashi T, Sota T, Hori M (2013) Genetic basis of male colour dimorphism in a Lake Tanganyika cichlid fish. Mol Ecol 22:3049–3060

    Article  CAS  PubMed  Google Scholar 

  • Tang K, Fu DJ, Julien D, Braun A, Cantor CR, Köster H (1999) Chip-based genotyping by mass spectrometry. Proc Natl Acad Sci 96:10016–10020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Templin WD, Seeb JE, Jasper JR, Barclay AW, Seeb LW (2011) Genetic differentiation of Alaska Chinook salmon: the missing link for migratory studies. Mol Ecol Resour 11(Suppl 1):226–246

    Article  PubMed  Google Scholar 

  • Tost J, Gut IG (2005) Genotyping single nucleotide polymorphisms by MALDI mass spectrometry in clinical applications. Clin Biochem 38:335–350

    Article  CAS  PubMed  Google Scholar 

  • Trujillo E, Davis C, Milner J (2006) Nutrigenomics, proteomics, metabolomics, and the practice of dietetics. J Am Diet Assoc 106:403–413

    Article  CAS  PubMed  Google Scholar 

  • Underwood ZE, Mandeville EG, Walters AW (2016) Population connectivity and genetic structure of burbot (Lota lota) populations in the Wind River Basin, Wyoming. Hydrobiologia 765:329–342

    Article  Google Scholar 

  • Vamosi JC, Armbruster WS, Renner SS (2014) Evolutionary ecology of specialization: insights from phylogenetic analysis. Proc R Soc B Biol Sci. doi:10.1098/rspb.2014.2004

    Google Scholar 

  • Van Bers NE, Crooijmans RP, Groenen MA, Dibbits BW, Komen J (2012) SNP marker detection and genotyping in tilapia. Mol Ecol Resour 12:932–941

    Article  PubMed  Google Scholar 

  • van Der WMJ, Schuren FHJ, Bijlsma S, Tas AC, van Omen B (2001) Nutrigenomics: application of genomics technologies in nutritional sciences and food technology. J Food Sci 66:772–780

    Article  Google Scholar 

  • van Orsouw NJ, Hogers RC, Janssen A et al (2007) Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS ONE 2:e1172. doi:10.1371/journal.pone.0001172

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vera M, Alvarez-Dios JA, Fernandez C, Bouza C, Vilas R, Martinez P (2013) Development and validation of single nucleotide polymorphisms (SNPs) markers from two transcriptome 454-runs of turbot (Scophthalmus maximus) using high-throughput genotyping. Int J Mol Sci 14:5694–5711

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Viricel A, Pante E, Dabin W, Simon-Bouhet B (2014) Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans. Mol Ecol Resour 14:597–605

    Article  CAS  PubMed  Google Scholar 

  • Vos P, Hogers R, Bleeker M et al (1995) AFLP-a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wagner CE, Keller I, Wittwer S et al (2013) Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Mol Ecol 22:787–798

    Article  CAS  PubMed  Google Scholar 

  • Walker WA, Blackburn G (2004) Symposium introduction: nutrition and gene regulation. J Nutr 134:2434S–2436S

    CAS  PubMed  Google Scholar 

  • Wang S (2015) Genotyping-by-sequencing (GBS) using a semiconductor sequencing platform. In: Plant and animal genome XXIII conference. Plant and animal genome

  • Wang Z, Pascual-Anaya J, Zadissa A et al (2013) The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet 45:701–706

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang W, Hu Y, Ma Y, Xu L, Guan J, Kong J (2015) High-density genetic linkage mapping in turbot (Scophthalmus maximus L.) based on SNP markers and major sex- and growth-related regions detection. PLoS ONE. doi:10.1371/journal.pone.0120410

    Google Scholar 

  • Wiggans GR, Sonstegard TS, VanRaden PM et al (2009) Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada. J Dairy Sci 92:3431–3436

    Article  CAS  PubMed  Google Scholar 

  • Wiggans GR, VanRaden PM, Bacheller LR et al (2010) Selection and management of DNA markers for use in genomic evaluation. J Dairy Sci 93:2287–2292

    Article  CAS  PubMed  Google Scholar 

  • Willing EM, Hoffmann M, Klein JD, Weigel D, Dreyer C (2011) Paired-end RAD-seq for de novo assembly and marker design without available reference. Bioinformatics 27:2187–2193

    Article  CAS  PubMed  Google Scholar 

  • Xu J, Zhao Z, Zhang X et al (2014a) Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio). BMC Genom 15:307 http://www.biomedcentral.com/1471-2164/1415/1307

  • Xu P, Zhang X, Wang X et al (2014b) Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nat Genet. doi:10.1038/ng.3098

    Google Scholar 

  • Yim HS, Cho YS, Guang X et al (2014) Minke whale genome and aquatic adaptation in cetaceans. Nat Genet 46:88–92

    Article  CAS  PubMed  Google Scholar 

  • Yoshizawa M, Robinson BG, Duboué ER et al (2015) Distinct genetic architecture underlies the emergence of sleep loss and prey-seeking behavior in the Mexican cavefish. BMC Biol 13:15. doi:10.1186/s12915-015-0119-3

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang B-D, Xue D-X, Wang J, Li Y-L, Liu B-J, Liu J-X (2016) Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis). Mol Ecol Resour 16:755–768

    Article  CAS  PubMed  Google Scholar 

  • Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequenc repeat (SSR)-achored polymerase chain reaction amplification. Genomics 20:176–183

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This study was supported by the National Institute of Food and Agriculture (NIFA), U.S. Department of Agriculture, under Agreement No. 2010-38,879-20946. Salaries and research support were provided by state and federal funds appropriated to The Ohio State University, Ohio Agricultural Research and Development Center, and Huazhong Agricultural University. We thank Joy Bauman for her comments on the manuscript.

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  1. Fish Genetics and Breeding Laboratory, The Ohio State University South Centers, 1864 Shyville Road, Piketon, OH, 45661, USA

    Yan-He Li & Han-Ping Wang

  2. College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China

    Yan-He Li

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Li, YH., Wang, HP. Advances of genotyping-by-sequencing in fisheries and aquaculture. Rev Fish Biol Fisheries 27, 535–559 (2017). https://doi.org/10.1007/s11160-017-9473-2

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