Skip to main content
SpringerLink
Log in

Genotyping-by-sequencing: a promising tool for plant genetics research and breeding

  • Review
  • Published:
Horticulture, Environment, and Biotechnology Aims and scope Submit manuscript

Abstract

Plant genetics studies and breeding programs utilize the genetic variation caused by DNA polymorphisms. Molecular makers are used to detect these variations in the DNA. The advent of next-generation sequencing (NGS) technologies has conferred new opportunities for high-throughput genotyping in various plant species. Recent improvements in high-throughput sequencing have enabled sequences to be used to detect and score single nucleotide polymorphisms (SNPs) by bypassing the time-consuming process of marker development. With NGS, whole-genome sequencing data and millions of genome-wide SNPs for high-throughput genotyping have become available for a variety of genetic studies and breeding programs. SNP markers are powerful for analyses of integrated SNP sets in a species, although high costs hinder the wider use of SNPs. However, genotype-by-sequencing (GBS), a series of genetic analyses that includes molecular marker discovery and genotyping using NGS technologies, has opened new possibilities in plant breeding and plant genetics studies. It offers cost-effective genome-wide scanning and multiplexed sequencing platforms. The GBS method uses restriction enzymes coupled with DNA barcoded adapters to reduce complexity. GBS can simultaneously perform SNP discovery and genotyping with or without reference genome sequences. Therefore, GBS can be applied to various approaches for plant breeding and plant genetics studies, including linkage maps, genome-wide association studies, genomic selection, and genomic diversity studies. These features make GBS an ideal tool for studies ranging from single-gene markers to whole-genome profiling.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Literature Cited

  • Arruda MP, Lipka AE, Brown PJ, Krill AM, Thurber C, Brown-Guedira G, Dong Y, Foresman BJ, Kolb FL (2016) Comparing genomic selection and marker-assisted selection for Fusarium head blight resistance in wheat (Triticum aestivum). Mol Breed 36:1–11

    Article  CAS  Google Scholar 

  • Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376

    Article  PubMed  PubMed Central  Google Scholar 

  • Balsalobre TW, da Silva Pereira G, Margarido GR, Gazaffi R, Barreto FZ, Anoni CO, Cardoso-Silva CB, Costa EA, Mancini MC, Hoffmann HP, de Souza AP (2017) GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC Genomics 18:72

    Article  PubMed  PubMed Central  Google Scholar 

  • Bernatzky R, Tanksley SD (1986) Toward a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics 112:887–898

    CAS  PubMed  PubMed Central  Google Scholar 

  • Breiman L (2001) Random forests. Mach Learn 45:5–32

    Article  Google Scholar 

  • Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084–1097

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Crawford J, Brown PJ, Voigt T, Lee DK (2016) Linkage mapping in prairie cordgrass (Spartina pectinata Link) using genotyping-bysequencing. Mol Breed 36:1–12

    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 

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

    Article  PubMed  PubMed Central  Google Scholar 

  • Desmarais E, Lanneluc I, Lagnel J (1998) Direct amplification of length polymorphisms (DALP), or how to get and characterize new genetic markers in many species. Nucleic Acids Res 26:1458–1465

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dufresne F, Stift M, Vergilino R, Mable BK (2014) Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools. Mol Ecol 23:40–69

    Article  PubMed  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Escudero M, Eaton DA, Hahn M, Hipp AL (2014) Genotyping-bysequencing as a tool to infer phylogeny and ancestral hybridization: A case study in Carex (Cyperaceae). Mol Phylogenet Evol 79:359–367

    Article  CAS  PubMed  Google Scholar 

  • Fu Y-B, Cheng B, Peterson GW (2014) Genetic diversity analysis of yellow mustard (Sinapis alba L.) germplasm based on genotyping by sequencing. Genet Resour Crop Evol 61:579–594

    Article  CAS  Google Scholar 

  • Fu Y-B, Peterson GW (2011) Genetic diversity analysis with 454 pyrosequencing and genomic reduction confirmed the eastern and western division in the cultivated barley gene pool. Plant Genome 4:226–237

    Article  CAS  Google Scholar 

  • Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS ONE 9:e90346

    Article  PubMed  PubMed Central  Google Scholar 

  • Gore M, Bradbury P, Hogers R, Kirst M, Verstege E, van Oeveren J, Peleman J, Buckler E, van Eijk M (2007) Evaluation of target preparation methods for single-feature polymorphism detection in large complex plant genomes. Crop Sci 47:S–135–S–148

    Article  Google Scholar 

  • Gore MA, Chia J-M, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J (2009) A first-generation haplotype map of maize. Science 326:1115–1117

    Article  CAS  PubMed  Google Scholar 

  • He J, Zhao X, Laroche A, Lu Z-X, Liu H, Li Z (2014) Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 5:484

    Article  PubMed  PubMed Central  Google Scholar 

  • Heffner EL, Sorrells ME, Jannink J-L (2009) Genomic selection for crop improvement. Crop Sci 49:1–12

    Article  CAS  Google Scholar 

  • Hohenlohe PA, Day MD, Amish SJ, Miller MR, Kamps-Hughes N, Boyer MC, Muhlfeld CC, Allendorf FW, Johnson EA, Luikart G (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 

  • Howie BN, Donnelly P, Marchini J (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5:1000529

    Article  Google Scholar 

  • Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang Y-F, Poland JA, Wight CP, Jackson EW, Tinker NA (2014) Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat. PloS ONE 9:e102448

    Article  PubMed  PubMed Central  Google Scholar 

  • Jannink J-L, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166–177

    Article  CAS  PubMed  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 

  • Keller I, Wagner C, Greuter L, Mwaiko S, Selz O, Sivasundar A, Wittwer S, Seehausen O (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 

  • Kim C, Guo H, Kong W, Chandnani R, Shuang L-S, Paterson AH (2016) Application of genotyping by sequencing technology to a variety of crop breeding programs. Plant Sci 242:14–22

    Article  CAS  PubMed  Google Scholar 

  • Kim J, Ki, D-S, Lee ES, Ah, Y-K, Chae WB, Lee S-S. (2017) The Construction of a Chinese Cabbage Marker-assisted Backcrossing System Using High-throughput Genotyping Technology. Hortic Sci Technol 35:232–242

    Google Scholar 

  • Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403–410

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Willer C, Sanna S, Abecasis G (2009) Genotype imputation. Annu Rev Genomics Hum Genet 10:387

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Limborg MT, Seeb LW, Seeb JE (2016) Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing. Mol Ecol 25:2117–2129

    Article  CAS  PubMed  Google Scholar 

  • Lin M, Cai S, Wang S, Liu S, Zhang G, Bai G (2015) Genotypingby-sequencing (GBS) identified SNP tightly linked to QTL for pre-harvest sprouting resistance. Theor Appl Genet 128:1385–1395

    Article  CAS  PubMed  Google Scholar 

  • Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE (2013) Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 9:e1003215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S (2012) SNP markers and their impact on plant breeding. Int J Plant Genomics 2012:728398

    Article  PubMed  PubMed Central  Google Scholar 

  • Marchini J, Howie B, Myers S, McVean G, Donnelly P (2007) A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 39:906–913

    Article  CAS  PubMed  Google Scholar 

  • Marchini J, Howie B (2010) Genotype imputation for genome-wide association studies. Nature Rev Genet 11:499–511

    Article  CAS  PubMed  Google Scholar 

  • Mason AS (2015) Challenges of Genotyping Polyploid Species. Methods Mol Biol 1245:161–168

    Article  CAS  PubMed  Google Scholar 

  • McCaskie PA, Carter KW, McCaskie SR, Palmer LJ (2005) The effect of missing data on linkage disequilibrium mapping and haplotype association analysis in the GAW14 simulated datasets. BMC Genet 6:S151

    Article  PubMed  PubMed Central  Google Scholar 

  • Meuwissen TH, Hayes B, Goddard M (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829

    CAS  PubMed  PubMed Central  Google Scholar 

  • Moumouni KH, Kountche BA, Jean M, Hash CT, Vigouroux Y, Haussmann BIG, Belzile F (2015) Construction of a genetic map for pearl millet, Pennisetum glaucum (L.) R. Br., using a genotyping-by-sequencing (GBS) approach. Mol Breed 35:1–10

    CAS  Google Scholar 

  • Ogden R, Gharbi K, Mugue N, Martinsohn J, Senn H, Davey J, Pourkazemi M, McEwing R, Eland C, Vidotto M (2013) Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing. Mol Ecol 22:3112–3123

    Article  CAS  PubMed  Google Scholar 

  • Paran I, Michelmore RW (1993) Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet 85:985–993

    Article  CAS  PubMed  Google Scholar 

  • Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7:e37135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Phan NT, Sim S-C (2017) Genomic Tools and Their Implications for Vegetable Breeding. Hortic Sci Technol 35:149–164

    Google Scholar 

  • Poecke RM, Maccaferri M, Tang J, Truong HT, Janssen A, Orsouw NJ, Salvi S, Sanguineti MC, Tuberosa R, Vossen EA (2013) Sequence-based SNP genotyping in durum wheat. Plant Biotechnol J 11:809–817

    Article  PubMed  Google Scholar 

  • Poland JA, Endelman J, Dawson J, Rutkoski J, Wu S, Manes Y, Dreisigacker S, Crossa J, Sánchez-Villeda H, Sorrells M (2012a) Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome 5:103–113

    Article  CAS  Google Scholar 

  • Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012b) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7:e32253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Poland JA, Rife TW (2012) Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 5:92–102

    Article  CAS  Google Scholar 

  • Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–575

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roda F, Ambrose L, Walter GM, Liu HL, Schaul A, Lowe A, Pelser PB, Prentis P, Rieseberg LH, Ortiz-Barrientos D (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 

  • Saintenac C, Jiang D, Wang S, Akhunov E (2013) Sequence-based mapping of the polyploid wheat genome. G3 (Bethesda) 3:1105–1114

    Article  Google Scholar 

  • Salimath SS, Oliveira ACD, Bennetzen JL, Godwin ID (1995) As sessment of genome origins and genetic diversity in the genus Eleusine with DNA markers. Genome 38:757–763

    Article  CAS  PubMed  Google Scholar 

  • Sonah H, Bastien M, Iquira E, Tardivel A, Légaré G, Boyle B, Normandeau É, Laroche J, Larose S, Jean M (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE 8:e54603

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spindel J, Wright M, Chen C, Cobb, J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S (2013) Bridging the genotyping gp: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor Appl Genet 126:2699–2716

    Article  CAS  PubMed  Google Scholar 

  • Tester M, Langridge P (2010) Breeding technologies to increase crop production in a changing world. Science 327:818–822

    Article  CAS  PubMed  Google Scholar 

  • Uitdewilligen JG, Wolters A-MA, Bjorn B, Borm TJ, Visser RG, van Eck HJ (2013) A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS ONE 8:e62355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Varshney RK, Terauchi R, McCouch SR (2014) Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol 12:e1001883

    Article  PubMed  PubMed Central  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ward JA, Bhangoo J, Fernández-Fernández F, Moore P, Swanson JD, Viola R, Velasco R, Bassil N, Weber CA and Sargent DJ (2013) Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics 14:1–14

    Article  Google Scholar 

  • Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xie W, Feng Q, Yu H, Huang X, Zhao Q, Xing Y, Yu S, Han B, Zhang Q (2010) Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci USA 107:10578–10583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160

    Article  CAS  PubMed  Google Scholar 

  • Zheng P, Allen WB, Roesler K, Williams ME, Zhang S, Li J, Glassman K, Ranch J, Nubel D, Solawetz W (2008) A phenylalanine in DGAT is a key determinant of oil content and composition in maize. Nat Genet 40:367–372

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Author notes

  1. These authors equally contributed to this work.

Authors and Affiliations

  1. Dept. of Crop Science, College of Agriculture and Life Science, Chungnam National University, Daejeon, Republic of Korea

    Yong Suk Chung, Sang Chul Choi & Changsoo Kim

  2. Dept. of Plant bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea

    Tae-Hwan Jun

Authors
  1. Yong Suk Chung
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sang Chul Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tae-Hwan Jun
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Changsoo Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Changsoo Kim.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chung, Y.S., Choi, S.C., Jun, TH. et al. Genotyping-by-sequencing: a promising tool for plant genetics research and breeding. Hortic. Environ. Biotechnol. 58, 425–431 (2017). https://doi.org/10.1007/s13580-017-0297-8

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13580-017-0297-8

Additional key words

Search

Navigation