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Allele Re-sequencing Technologies

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Diagnostics in Plant Breeding

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Abstract

The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large and complex genomes. Recent developments in strategies for target-enrichment, transcriptome re-sequencing, and partial genome re-sequencing allows for enrichment for regions of interest at a scale that is matched to the throughput of next-generation sequencing platforms, and has emerged as a promising alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information.

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References

  • Adessi C, Matton G, Ayala G, Turcatti G, Mermod JJ, Mayer P, Kawashima E (2000) Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic Acids Res 28(20):E87. doi:10.1093/nar/28.20.e87

    Article  PubMed  CAS  Google Scholar 

  • Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J (2010) Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinformatics 11. doi:10.1186/1471-2105-11-s12-s4

  • Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, Richmond TA, Middle CM, Rodesch MJ, Packard CJ, Weinstock GM, Gibbs RA (2007) Direct selection of human genomic loci by microarray hybridization. Nat Methods 4(11):903–905. doi:http://www.nature.com/nmeth/journal/v4/n11/suppinfo/nmeth1111_S1.html

    Google Scholar 

  • Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM, Al-Azwani EK, Chaluvadi S, Pontaroli AC, DeBarry J, Arondel V, Ohlrogge J, Saie IJ, Suliman-Elmeer KM, Bennetzen JL, Kruegger RR, Malek JA (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol 29(6):521–U584. doi:10.1038/nbt.1860

    Article  PubMed  CAS  Google Scholar 

  • Altshuler DL, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Collins FS, De la Vega FM, Donnelly P, Egholm M, Flicek P, Gabriel SB, Gibbs RA, Knoppers BM, Lander ES, Lehrach H, Mardis ER, McVean GA, Nickerson D, Peltonen L, Schafer AJ, Sherry ST, Wang J, Wilson RK, Deiros D, Metzker M, Muzny D, Reid J, Wheeler D, Li JX, Jian M, Li G, Li RQ, Liang HQ, Tian G, Wang B, Wang W, Yang HM, Zhang XQ, Zheng HS, Ambrogio L, Bloom T, Cibulskis K, Fennell TJ, Jaffe DB, Shefler E, Sougnez CL, Gormley N, Humphray S, Kingsbury Z, Koko-Gonzales P, Stone J, McKernan KJ, Costa GL, Ichikawa JK, Lee CC, Sudbrak R, Borodina TA, Dahl A, Davydov AN, Marquardt P, Mertes F, Nietfeld W, Rosenstiel P, Schreiber S, Soldatov AV, Timmermann B, Tolzmann M, Affourtit J, Ashworth D, Attiya S, Bachorski M, Buglione E, Burke A, Caprio A, Celone C, Clark S, Conners D, Desany B, Gu L, Guccione L, Kao K, Kebbel A, Knowlton J, Labrecque M, McDade L, Mealmaker C, Minderman M, Nawrocki A, Niazi F, Pareja K, Ramenani R, Riches D, Song W, Turcotte C, Wang S, Dooling D, Fulton L, Fulton R, Weinstock G, Burton J, Carter DM, Churcher C, Coffey A, Cox A, Palotie A, Quail M, Skelly T, Stalker J, Swerdlow HP, Turner D, De Witte A, Giles S, Bainbridge M, Challis D, Sabo A, Yu F, Yu J, Fang XD, Guo XS, Li YR, Luo RB, Tai S, Wu HL, Zheng HC, Zheng XL, Zhou Y, Marth GT, Garrison EP, Huang W, Indap A, Kural D, Lee WP, Leong WF, Huang WC, Quinlan AR, Stewart C, Stromberg MP, Ward AN, Wu JT, Lee C, Mills RE, Shi XH, Daly MJ, DePristo MA, Ball AD, Banks E, Browning BL, Garimella KV, Grossman SR, Handsaker RE, Hanna M, Hartl C, Kernytsky AM, Korn JM, Li H, Maguire JR, McCarroll SA, McKenna A, Nemesh JC, Philippakis AA, Poplin RE, Price A, Rivas MA, Sabeti PC, Schaffner SF, Shlyakhter IA, Cooper DN, Ball EV, Mort M, Phillips AD, Stenson PD, Sebat J, Makarov V, Ye K, Yoon SC, Bustamante CD, Boyko A, Degenhardt J, Gravel S, Gutenkunst RN, Kaganovich M, Keinan A, Lacroute P, Ma X, Reynolds A, Clarke L, Cunningham F, Herrero J, Keenen S, Kulesha E, Leinonen R, McLaren W, Radhakrishnan R, Smith RE, Zalunin V, Zheng-Bradley XQ, Korbel JO, Stutz AM, Bauer M, Cheetham RK, Cox T, Eberle M, James T, Kahn S, Murray L, Fu YT, Hyland FCL, Manning JM, McLaughlin SF, Peckham HE, Sakarya O, Sun YA, Tsung EF, Batzer MA, Konkel MK, Walker JA, Albrecht MW, Amstislavskiy VS, Herwig R, Parkhomchuk DV, Agarwala R, Khouri H, Morgulis AO, Paschall JE, Phan LD, Rotmistrovsky KE, Sanders RD, Shumway MF, Xiao CL, Auton A, Iqbal Z, Lunter G, Marchini JL, Moutsianas L, Myers S, Tumian A, Knight J, Winer R, Craig DW, Beckstrom-Sternberg SM, Christoforides A, Kurdoglu AA, Pearson J, Sinari SA, Tembe WD, Haussler D, Hinrichs AS, Katzman SJ, Kern A, Kuhn RM, Przeworski M, Hernandez RD, Howie B, Kelley JL, Melton SC, Li Y, Anderson P, Blackwell T, Chen W, Cookson WO, Ding J, Kang HM, Lathrop M, Liang LM, Moffatt MF, Scheet P, Sidore C, Snyder M, Zhan XW, Zollner S, Awadalla P, Casals F, Idaghdour Y, Keebler J, Stone EA, Zilversmit M, Jorde L, Xing JC, Eichler EE, Aksay G, Alkan C, Hajirasouliha I, Hormozdiari F, Kidd JM, Sahinalp SC, Sudmant PH, Chen K, Chinwalla A, Ding L, Koboldt DC, McLellan MD, Wallis JW, Wendl MC, Zhang QY, Albers CA, Ayub Q, Balasubramaniam S, Barrett JC, Chen YA, Conrad DF, Danecek P, Dermitzakis ET, Hu M, Huang N, Hurles ME, Jin HJ, Jostins L, Keane TM, Le SQ, Lindsay S, Long QA, MacArthur DG, Montgomery SB, Parts L, Tyler-Smith C, Walter K, Zhang YJ, Gerstein MB, Abyzov A, Balasubramanian S, Bjornson R, Du JA, Grubert F, Habegger L, Haraksingh R, Jee J, Khurana E, Lam HYK, Leng J, Mu XJ, Urban AE, Zhang ZD, Coafra C, Dinh H, Kovar C, Lee S, Nazareth L, Yu FL, Wilkinson J, Khouri HM, Scott C, Gharani N, Kaye JS, Kent A, Li T, McGuire AL, Ossorio PN, Rotimi CN, Su YY, Toji LH, Brooks LD, Felsenfeld AL, McEwen JE, Abdallah A, Christopher R, Clemm NC, Duncanson A, Green ED, Guyer MS, Peterson JL, Genomes Project C (2010) A map of human genome variation from population-scale sequencing. Nature 467(7319):1061–1073. doi:10.1038/nature09534

    Article  PubMed  Google Scholar 

  • Anselmetti D (2012) NANOPORES tiny holes with great promise. Nat Nanotechnol 7:81–82

    Article  PubMed  CAS  Google Scholar 

  • Arabidopsis Genome I (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796–815

    Article  Google Scholar 

  • Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JSS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Berard A, Viot C, Boccara M, Risterucci AM, Guignon V, Sabau X, Axtell MJ, Ma ZR, Zhang YF, Brown S, Bourge M, Golser W, Song XA, Clement D, Rivallan R, Tahi M, Akaza JM, Pitollat B, Gramacho K, D’Hont A, Brunel D, Infante D, Kebe I, Costet P, Wing R, McCombie WR, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C (2011) The genome of Theobroma cacao. Nat Genet 43(2):101–108. doi:10.1038/ng.736

    Article  PubMed  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(10). doi:doi:10.1371/journal.pone.0003376

  • Baker M (2010) Next-generation sequencing: adjusting to data overload. Nat Methods 7(7):495–499

    Article  CAS  Google Scholar 

  • Bancroft I, Morgan C, Fraser F, Higgins J, Wells R, Clissold L, Baker D, Long Y, Meng JL, Wang XW, Liu SY, Trick M (2011) Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat Biotechnol 29(8):762–766. doi:10.1038/nbt.1926

    Article  PubMed  CAS  Google Scholar 

  • Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51(5):910–918. doi:10.1111/j.1365-313X.2007.03193.x

    Article  PubMed  CAS  Google Scholar 

  • Bau S, Schracke N, Kränzle M, Wu H, Stähler P, Hoheisel J, Beier M, Summerer D (2009) Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays. Anal Bioanal Chem 393(1):171–175. doi:10.1007/s00216-008-2460-7

    Article  PubMed  CAS  Google Scholar 

  • Berkman PJ, Skarshewski A, Lorenc MT, Lai KT, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubalakova M, Simkova H, Batley J, Fleury D, Dolezel J, Edwards D (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol J 9(7):768–775. doi:10.1111/j.1467-7652.2010.00587.x

    Article  PubMed  CAS  Google Scholar 

  • Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, Di Ventra M, Garaj S, Hibbs A, Huang X, Jovanovich SB, Krstic PS, Lindsay S, Ling XS, Mastrangelo CH, Meller A, Oliver JS, Pershin YV, Ramsey JM, Riehn R, Soni GV, Tabard-Cossa V, Wanunu M, Wiggin M, Schloss JA (2008) The potential and challenges of nanopore sequencing. Nat Biotechnol 26(10):1146–1153. doi:10.1038/nbt.1495

    Article  PubMed  CAS  Google Scholar 

  • Braslavsky I, Hebert B, Kartalov E, Quake SR (2003) Sequence information can be obtained from single DNA molecules. Proc Natl Acad Sci USA 100(7):3960–3964. doi:10.1073/pnas.0230489100

    Article  PubMed  CAS  Google Scholar 

  • Callaway E (2011) Genome giant offers data service. Nature 475(7357):435–437

    Article  PubMed  CAS  Google Scholar 

  • Canovas A, Rincon G, Islas-Trejo A, Wickramasinghe S, Medrano JF (2010) SNP discovery in the bovine milk transcriptome using RNA-Seq technology. Mamm Genome 21(11–12):592–598. doi:10.1007/s00335-010-9297-z

    Article  PubMed  CAS  Google Scholar 

  • Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Muller J, Alonso-Blanco C, Borgwardt K, Schmid KJ, Weigel D (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43(10):956–U960. doi:10.1038/ng.911

    Article  PubMed  CAS  Google Scholar 

  • Chain PSG, Grafham DV, Fulton RS, FitzGerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A, Detter JC, Genomic Stand C, Human Microbiome Project J (2009) Genome project standards in a new era of sequencing. Science 326(5950):236–237. doi:10.1126/science.1180614

    Article  PubMed  CAS  Google Scholar 

  • Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistue L, Corey A, Filichkina T, Johnson EA, Hayes PM (2011) Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics 12. doi:10.1186/1471-2164-12-4

  • Clarke J, Wu H-C, Jayasinghe L, Patel A, Reid S, Bayley H (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4(4):265–270. doi:10.1038/nnano.2009.12

    Article  PubMed  CAS  Google Scholar 

  • Cyranoski D (2010) The sequence factory. Nature 464(7285):22–24. doi:10.1038/464022a

    Article  PubMed  CAS  Google Scholar 

  • Dahl F, Gullberg M, Stenberg J, Landegren U, Nilsson M (2005) Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments. Nucleic Acids Res 33(8):e71. doi:10.1093/nar/gni070

    Article  PubMed  Google Scholar 

  • Dahl F, Stenberg J, Fredriksson S, Welch K, Zhang M, Nilsson M, Bicknell D, Bodmer WF, Davis RW, Ji H (2007) Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc Natl Acad Sci USA 104(22):9387–9392. doi:10.1073/pnas.0702165104

    Article  PubMed  CAS  Google Scholar 

  • Dolezel J, Kubalakova M, Paux E, Bartos J, Feuillet C (2007) Chromosome-based genomics in the cereals. Chromosome Res 15(1):51–66. doi:10.1007/s10577-006-1106-x

    Article  PubMed  CAS  Google Scholar 

  • Dressman D, Yan H, Traverso G, Kinzler KW, Vogelstein B (2003) Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci USA 100(15):8817–8822. doi:10.1073/pnas.1133470100

    Article  PubMed  CAS  Google Scholar 

  • Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, deWinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S (2009) Real-time DNA sequencing from single polymerase molecules. Science 323(5910):133–138. doi:10.1126/science.1162986

    Article  PubMed  CAS  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(5). doi:doi:10.1371/journal.pone.0019379

  • Feuillet C, Leach JE, Rogers J, Schnable PS, Eversole K (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci 16(2):77–88. doi:10.1016/j.tplants.2010.10.005

    Article  PubMed  CAS  Google Scholar 

  • Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, Korlach J, Turner SW (2010) Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 7(6):461–U472. doi:10.1038/nmeth.1459

    Article  PubMed  CAS  Google Scholar 

  • Fu Y, Springer NM, Gerhardt DJ, Ying K, Yeh C-T, Wu W, Swanson-Wagner R, D’Ascenzo M, Millard T, Freeberg L, Aoyama N, Kitzman J, Burgess D, Richmond T, Albert TJ, Barbazuk WB, Jeddeloh JA, Schnable PS (2010) Repeat subtraction-mediated sequence capture from a complex genome. Plant J 62(5):898–909. doi:10.1111/j.1365-313X.2010.04196.x

    Article  PubMed  CAS  Google Scholar 

  • Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang XH, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC, Vezenov DV (2009) The challenges of sequencing by synthesis. Nat Biotechnol 27(11):1013–1023. doi:10.1038/nbt.1585

    Article  PubMed  CAS  Google Scholar 

  • Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao YJ, Tam A, Wang SC, Friedmann M, Birol I, Jones SJM, Cronk QCB, Douglas CJ (2011) SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour 11:81–92. doiDOI 10.1111/j.1755-0998.2010.02960.x

    Article  PubMed  CAS  Google Scholar 

  • Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15(10):1451–1455. doi:10.1101/gr.4086505

    Article  PubMed  CAS  Google Scholar 

  • Glenn TC (2011) Field guide to next-generation DNA sequencers. Mol Ecol Resour 11(5):759–769. doi:10.1111/j.1755-0998.2011.03024.x

    Article  PubMed  CAS  Google Scholar 

  • Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27(2):182–189. doi:http://www.nature.com/nbt/journal/v27/n2/suppinfo/nbt.1523_S1.html

    Google Scholar 

  • Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES (2009) A first-generation haplotype map of maize. Science 326(5956):1115–1117. doi:10.1126/science.1177837

    Article  PubMed  CAS  Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng QD, Chen ZH, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652. doi:10.1038/nbt.1883

    Article  PubMed  CAS  Google Scholar 

  • Hamilton JP, Hansey CN, Whitty BR, Stoffel K, Massa AN, Van Deynze A, De Jong WS, Douches DS, Buell CR (2011) Single nucleotide polymorphism discovery in elite north american potato germplasm. BMC Genomics 12. doi:10.1186/1471-2164-12-302

  • Hardin S, Gao X, Briggs J, Willson R, Tu S-C (2008) Methods for real-time single molecule sequence determination. Official Gazette of the United States Patent and Trademark Office Patents

    Google Scholar 

  • Harismendy O, Frazer KA (2009) Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology. Biotechniques 46(3):229–231

    Article  PubMed  CAS  Google Scholar 

  • Haseneyer G, Schmutzer T, Seidel M, Zhou RN, Mascher M, Schon CC, Taudien S, Scholz U, Stein N, Mayer KFX, Bauer E (2011) From RNA-seq to large-scale genotyping – genomics resources for rye (Secale cereale L.). BMC Plant Biol 11:131. doi:10.1186/1471-2229-11-131

    Article  PubMed  CAS  Google Scholar 

  • Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia GF, Springer NM, Vance CP, Stupar RM (2011) The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol 155(2):645–655. doi:10.1104/pp. 110.166736

    Article  PubMed  CAS  Google Scholar 

  • Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, McCombie WR (2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet 39(12):1522–1527. doi:http://www.nature.com/ng/journal/v39/n12/suppinfo/ng.2007.42_S1.html

    Google Scholar 

  • Huse SM, Huber JA, Morrison HG, Sogin ML, Mark Welch D (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8(7):R143. doi:doi:10.1186/gb-2007-8-7-r143

    Article  PubMed  Google Scholar 

  • Information Technolgies Pvt Ltd (2011) Application note: performance, Spring 2011 [Online]. Available: http://www.iontorrent.com/lib/images/PDFs/performance_overview_application_note_041211.pdf

  • Johansson H, Isaksson M, Falk Sörqvist E, Roos F, Stenberg J, Sjöblom T, Botling J, Micke P, Edlund K, Fredriksson S, Göransson Kultima H, Ericsson O, Nilsson M (2010) Targeted resequencing of candidate genes using selector probes. Nucleic Acids Res. doi:10.1093/nar/gkq1005

  • Ju J, Kim DH, Bi L, Meng Q, Bai X, Li Z, Li X, Marma MS, Shi S, Wu J, Edwards JR, Romu A, Turro NJ (2006) Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci USA 103(52):19635–19640. doi:10.1073/pnas.0609513103

    Article  PubMed  CAS  Google Scholar 

  • Kahn SD (2011) On the future of genomic data. Science 331(6018):728–729. doi:10.1126/science.1197891

    Article  PubMed  CAS  Google Scholar 

  • Kahvejian A, Quackenbush J, Thompson JF (2008) What would you do if you could sequence everything? Nat Biotechnol 26(10):1125–1133

    Article  PubMed  CAS  Google Scholar 

  • Kasianowicz JJ, Brandin E, Branton D, Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 93(24):13770–13773. doi:10.1073/pnas.93.24.13770

    Article  PubMed  CAS  Google Scholar 

  • Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, Belcher AR, Oropeza-Rosas MA, Zwonitzer JC, Kresovich S, McMullen MD, Ware D, Balint-Kurti PJ, Holland JB (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43(2):163–168. doi:10.1038/ng.747

    Article  PubMed  CAS  Google Scholar 

  • Lam HM, Xu X, Liu X, Chen WB, Yang GH, Wong FL, Li MW, He WM, Qin N, Wang B, Li J, Jian M, Wang JA, Shao GH, Wang J, Sun SSM, Zhang GY (2011) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection (vol 42, pg 1053, 2010). Nat Genet 43(4):387–387. doi:10.1038/ng0411-387

    Article  CAS  Google Scholar 

  • Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL (2009) Searching for SNPs with cloud computing. Genome Biol 10(11). doi:doi:10.1186/gb-2009-10-11-r134

  • Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW (2003) Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299(5607):682–686. doi:10.1126/science.1079700

    Article  PubMed  CAS  Google Scholar 

  • Lin S, Wang W, Palm C, Davis R, Juneau K (2010) A molecular inversion probe assay for detecting alternative splicing. BMC Genomics 11(1):712

    Article  PubMed  CAS  Google Scholar 

  • Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ (2010) Target-enrichment strategies for next-generation sequencing. Nat Methods 7(2):111–118. doi:http://www.nature.com/nmeth/journal/v7/n2/suppinfo/nmeth.1419_S1.html

    Google Scholar 

  • Mardis ER (2008a) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141

    Article  PubMed  CAS  Google Scholar 

  • Mardis ER (2008b) Next-generation DNA sequencing methods. Annu Rev Gen Hum Genet 9:387–402

    Article  CAS  Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu PG, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380. doi:10.1038/nature03959

    PubMed  CAS  Google Scholar 

  • Mayer KFX, Taudien S, Martis M, Simkova H, Suchankova P, Gundlach H, Wicker T, Petzold A, Felder M, Steuernagel B, Scholz U, Graner A, Platzer M, Dolezel J, Stein N (2009) Gene content and virtual gene order of barley chromosome 1H. Plant Physiol 151(2):496–505. doi:10.1104/pp. 109.142612

    Article  PubMed  CAS  Google Scholar 

  • McCarthy A (2010) Third generation DNA sequencing: Pacific biosciences’ single molecule real time technology. Chem Biol 17:675–676

    Article  PubMed  CAS  Google Scholar 

  • McCourt P, Benning C (2010) Arabidopsis: a rich harvest 10 years after completion of the genome sequence. Plant J 61(6):905–908. doi:10.1111/j.1365-313X.2010.04176.x

    Article  PubMed  CAS  Google Scholar 

  • Metzker ML (2010) Applications of next-generation sequencing. Sequencing technologies – the next generation. Nat Rev Genet 11(1):31–46. doi:10.1038/nrg2626

    Article  PubMed  CAS  Google Scholar 

  • Mitra RD, Church GM (1999) In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res 27(24):e34. doi:doi:10.1093/nar/27.24.e34

    Article  PubMed  CAS  Google Scholar 

  • Mondal K, Shetty AC, Patel V, Cutler DJ, Zwick ME (2011) Targeted sequencing of the human X chromosome exome. Genomics 98(4):260–265. doi:10.1016/j.ygeno.2011.04.004

    Article  PubMed  CAS  Google Scholar 

  • Myles S, Chia JM, Hurwitz B, Simon C, Zhong GY, Buckler E, Ware D (2010) Rapid genomic characterization of the genus vitis. PLoS One 5(1). doi:doi:10.1371/journal.pone.0008219

  • Niedringhaus TP, Milanova D, Kerby MB, Snyder MP, Barron AE (2011) Landscape of next-generation sequencing technologies. Anal Chem 83(12):4327–4341. doi:10.1021/ac2010857

    Article  PubMed  CAS  Google Scholar 

  • Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME (2007) Microarray-based genomic selection for high-throughput resequencing. Nat Methods 4(11):907–909. doi:http://www.nature.com/nmeth/journal/v4/n11/suppinfo/nmeth1109_S1.html

    Google Scholar 

  • Ozsolak F (2012) Third-generation sequencing techniques and applications to drug discovery. Expert Opin Drug Dis 7:231–243

    Article  CAS  Google Scholar 

  • Pareek CS, Smoczynski R, Tretyn A (2011) Sequencing technologies and genome sequencing. J Appl Genet 52(4):413–435. doi:10.1007/s13353-011-0057-x

    Article  PubMed  CAS  Google Scholar 

  • Pennisi E (2010) GENOMICS semiconductors inspire new sequencing technologies. Science 327(5970):1190

    Article  PubMed  CAS  Google Scholar 

  • Pennisi E (2011) Will computers crash genomics? Science 331(6018):666–668. doi:10.1126/science.331.6018.666

    Article  PubMed  CAS  Google Scholar 

  • Pfender WF, Saha MC, Johnson EA, Slabaugh MB (2011) Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet 122(8):1467–1480. doi:10.1007/s00122-011-1546-3

    Article  PubMed  CAS  Google Scholar 

  • Poland JA, Bradbury PJ, Buckler ES, Nelson RJ (2011) Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci USA 108(17):6893–6898. doi:10.1073/pnas.1010894108

    Article  PubMed  CAS  Google Scholar 

  • Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, Shendure J (2007) Multiplex amplification of large sets of human exons. Nat Methods 4(11):931–936. doi:http://www.nature.com/nmeth/journal/v4/n11/suppinfo/nmeth1110_S1.html

    Google Scholar 

  • Pushkarev D, Neff NF, Quake SR (2009) Single-molecule sequencing of an individual human genome. Nat Biotechnol 27(9):847–850. doi:10.1038/nbt.1561

    Article  PubMed  CAS  Google Scholar 

  • Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao YJ, Moore RA, Hirst M, Marra MA, Jones SJM, Hoodless PA, Birol I (2010) De novo assembly and analysis of RNA-seq data. Nat Methods 7(11):909–U962. doi:10.1038/nmeth.1517

    Article  PubMed  CAS  Google Scholar 

  • Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 242(1):84–89. doi:10.1006/abio.1996.0432

    Article  PubMed  CAS  Google Scholar 

  • Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu YT, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475(7356):348–352. doi:10.1038/nature10242

    Article  PubMed  CAS  Google Scholar 

  • Schatz MC, Delcher AL, Salzberg SL (2010) Assembly of large genomes using second-generation sequencing. Genome Res 20(9):1165–1173. doi:10.1101/gr.101360.109

    Article  PubMed  CAS  Google Scholar 

  • Service RF (2006) Gene sequencing - the race for the $1000 genome. Science 311:1544–1546

    Article  PubMed  Google Scholar 

  • Shendure J, Porreca GJ, Reppas NB, Lin XX, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309(5741):1728–1732. doi:10.1126/science.1117389

    Article  PubMed  CAS  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  PubMed  CAS  Google Scholar 

  • Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJG, Williams KP, Holt SH, Rojas JJR, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Girona EL, Zdepski A, Wang WQ, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43(2):109–U151. doi:10.1038/ng.740

    Article  PubMed  CAS  Google Scholar 

  • Stein LD (2010) The case for cloud computing in genome informatics. Genome Biol 11(5). doi:doi:10.1186/gb-2010-11-5-207

  • Su Z, Ning B, Fang H, Hong H, Perkins R, Tong W, Shi L (2011) Next-generation sequencing and its applications in molecular diagnostics. Expert Rev Mol Diagn 11(3):333–343. doi:10.1586/erm.11.3

    PubMed  Google Scholar 

  • Summerer D, Wu H, Haase B, Cheng Y, Schracke N, Stähler CF, Chee MS, Stähler PF, Beier M (2009) Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing. Genome Res 19(9):1616–1621. doi:10.1101/gr.091942.109

    Article  PubMed  CAS  Google Scholar 

  • Tanaka H, Kawai T (2009) Partial sequencing of a single DNA molecule with a scanning tunnelling microscope. Nat Nanotechnol 4:518–522

    Article  PubMed  CAS  Google Scholar 

  • Teer JK, Mullikin JC (2010) Exome sequencing: the sweet spot before whole genomes. Hum Mol Genet 19(R2):R145–R151. doi:10.1093/hmg/ddq333

    Article  PubMed  CAS  Google Scholar 

  • Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, Kotsopoulos SK, Samuels ML, Hutchison JB, Larson JW, Topol EJ, Weiner MP, Harismendy O, Olson J, Link DR, Frazer KA (2009) Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol 27(11):1025–1031. doi:http://www.nature.com/nbt/journal/v27/n11/suppinfo/nbt.1583_S1.html

    Google Scholar 

  • Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43(2):159–162. doi:10.1038/ng.746

    Article  PubMed  CAS  Google Scholar 

  • Treffer R, Deckert V (2010) Recent advances in single-molecule sequencing. Curr Opin Biotechnol 21(1):4–11. doi:10.1016/j.copbio.2010.02.009

    Article  PubMed  CAS  Google Scholar 

  • Turcatti G, Romieu A, Fedurco M, Tairi A-P (2008) A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res 36(4):e25. doi:doi:10.1093/nar/gkn021

    Article  PubMed  Google Scholar 

  • Turner EH, Lee C, Ng SB, Nickerson DA, Shendure J (2009a) Massively parallel exon capture and library-free resequencing across 16 genomes. Nat Methods 6(5):315–316. doi:http://www.nature.com/nmeth/journal/v6/n5/suppinfo/nmeth.f.248_S1.html

    Google Scholar 

  • Turner EH, Ng SB, Nickerson DA, Shendure J (2009b) Methods for genomic partitioning. Annu Rev Genomics Hum Genet 10(1):263–284. doi:doi:10.1146/annurev-genom-082908-150112

    Article  PubMed  CAS  Google Scholar 

  • Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5(3):247–252. doi:10.1038/nmeth.1185

    Article  PubMed  Google Scholar 

  • Wang XW, Wang HZ, Wang J, Sun RF, Wu J, Liu SY, Bai YQ, Mun JH, Bancroft I, Cheng F, Huang SW, Li XX, Hua W, Wang JY, Wang XY, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu BH, Li B, Liu B, Tong CB, Song C, Duran C, Peng CF, Geng CY, Koh CS, Lin CY, Edwards D, Mu DS, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang HB, Wang HP, Belcram H, Zhou HL, Hirakawa H, Abe H, Guo H, Wang H, Jin HZ, Parkin IAP, Batley J, Kim JS, Just J, Li JW, Xu JH, Deng J, Kim JA, Li JP, Yu JY, Meng JL, Wang JP, Min JM, Poulain J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao MX, Jin MN, Ramchiary N, Drou N, Berkman PJ, Cai QL, Huang QF, Li RQ, Tabata S, Cheng SF, Zhang S, Zhang SJ, Huang SM, Sato S, Sun SL, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li YR, Du YC, Liao YC, Lim Y, Narusaka Y, Wang YP, Wang ZY, Li ZY, Wang ZW, Xiong ZY, Zhang ZH (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43(10):1035–U1157. doi:10.1038/ng.919

    Article  PubMed  CAS  Google Scholar 

  • Wu XL, Ren CW, Joshi T, Vuong T, Xu D, Nguyen HT (2010) SNP discovery by high-throughput sequencing in soybean. BMC Genomics 11. doi:10.1186/1471-2164-11-469

  • Xu X, Pan SK, Cheng SF, Zhang B, Mu DS, Ni PX, Zhang GY, Yang S, Li RQ, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DMA, Li GC, Yang Y, Kuang HH, Hu Q, Xiong XY, Bishop GJ, Sagredo B, Mejia N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang SW, Zhang ZH, Liang CB, He J, Li Y, He Y, Xu JF, Zhang YJ, Xie BY, Du YC, Qu DY, Bonierbale M, Ghislain M, Herrera MD, Giuliano G, Pietrella M, Perrotta G, Facella P, O’Brien K, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin HN, Massa A, Geoffroy M, Lundback S, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ, Destefanis M, Nagy I, Milbourne D, Thomson SJ, Fiers M, Jacobs JME, Nielsen KL, Sonderkaer M, Iovene M, Torres GA, Jiang JM, Veilleux RE, Bachem CWB, de Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert BTL, Goverse A, van Ham R, Visser RGF, Potato Genome Sequencing C (2011) Genome sequence and analysis of the tuber crop potato. Nature 475(7355):189–U194. doi:10.1038/nature10158

    Article  PubMed  CAS  Google Scholar 

  • Zhang J, Chiodini R, Badr A, Zhang GF (2011) The impact of next-generation sequencing on genomics. J Genet Genomics 38(3):95–109. doi:10.1016/j.jgg.2011.02.003

    Article  PubMed  Google Scholar 

  • Zhou X, Ren L, Li Y, Zhang M, Yu Y, Yu J (2010) The next-generation sequencing technology: a technology review and future perspective. Sci China Life Sci 53(1):44–57. doi:10.1007/s11427-010-0023-6

    Article  PubMed  CAS  Google Scholar 

  • Zhulidov PA, Bogdanova EA, Shcheglov AS, Vagner LL, Khaspekov GL, Kozhemyako VB, Matz MV, Meleshkevitch E, Moroz LL, Lukyanov SA, Shagin DA (2004) Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Res 32(3). doi:doi:10.1093/nar/gnh031

    Google Scholar 

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  1. Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark

    Stephen Byrne, Jacqueline D. Farrell & Torben Asp

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  2. Jacqueline D. Farrell
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  1. Dept. Agronomy, Iowa State University, Agronomy Hall 1204, Ames, 50011, Iowa, USA

    Thomas Lübberstedt

  2. ICRISAT, Centre of Excellence in Genomics (CEG), Patancheru, 502 324, Andra Pradesh, India

    Rajeev K. Varshney

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Byrne, S., Farrell, J.D., Asp, T. (2013). Allele Re-sequencing Technologies. In: Lübberstedt, T., Varshney, R. (eds) Diagnostics in Plant Breeding. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5687-8_5

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