Theoretical and Applied Genetics

, Volume 126, Issue 1, pp 1–11 | Cite as

Accessing complex crop genomes with next-generation sequencing

  • David Edwards
  • Jacqueline Batley
  • Rod J. Snowdon


Many important crop species have genomes originating from ancestral or recent polyploidisation events. Multiple homoeologous gene copies, chromosomal rearrangements and amplification of repetitive DNA within large and complex crop genomes can considerably complicate genome analysis and gene discovery by conventional, forward genetics approaches. On the other hand, ongoing technological advances in molecular genetics and genomics today offer unprecedented opportunities to analyse and access even more recalcitrant genomes. In this review, we describe next-generation sequencing and data analysis techniques that vastly improve our ability to dissect and mine genomes for causal genes underlying key traits and allelic variation of interest to breeders. We focus primarily on wheat and oilseed rape, two leading examples of major polyploid crop genomes whose size or complexity present different, significant challenges. In both cases, the latest DNA sequencing technologies, applied using quite different approaches, have enabled considerable progress towards unravelling the respective genomes. Our ability to discover the extent and distribution of genetic diversity in crop gene pools, and its relationship to yield and quality-related traits, is swiftly gathering momentum as DNA sequencing and the bioinformatic tools to deal with growing quantities of genomic data continue to develop. In the coming decade, genomic and transcriptomic sequencing, discovery and high-throughput screening of single nucleotide polymorphisms, presence–absence variations and other structural chromosomal variants in diverse germplasm collections will give detailed insight into the origins, domestication and available trait-relevant variation of polyploid crops, in the process facilitating novel approaches and possibilities for genomics-assisted breeding.


Double Haploid Oilseed Rape Genomic Selection General Combine Ability Tauschii Accession 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



DE and JB acknowledge funding support from the Grains Research and Development Corporation (Project DAN00117) and the Australian Research Council (Projects LP0882095, LP0883462, LP110100200 and DP0985953), along with further support from the Australian Genome Research Facility (AGRF) and the Queensland Cyber Infrastructure Foundation (QCIF). RS was supported by a fellowship from the OECD Cooperative Research Programme “Biological Resource Management for Sustainable Agricultural Systems” and by DFG grants SN14/11-1 and SN14/12-1.


  1. Allen AM, Barker GLA, Berry ST, Coghill JA, Gwilliam R, Kirby S, Robinson P, Brenchley RC, D’Amore R, McKenzie N, Waite D, Hall A, Bevan M, Hall N, Edwards KJ (2011) Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotech J (in press, 2012)Google Scholar
  2. Associated DNA (RAD) linkage map in barley. BMC Genomics 12:4Google Scholar
  3. Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu T et al (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:627–631PubMedCrossRefGoogle Scholar
  4. Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala B, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JDG, Varshney RK (2012) Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome. Am J Bot 99:186–192PubMedCrossRefGoogle Scholar
  5. Bagnato A, Rosati A (2012) From the editors—animal selection: the genomics revolution. Anim Front 12:1–2CrossRefGoogle Scholar
  6. Bancroft I, Stokes DR, Morgan CL, Fraser FP, O’Neill C (2009) Prediction of heterosis and other traits by transcriptome analysis. Patent application number 20090300781Google Scholar
  7. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51:910–918PubMedCrossRefGoogle Scholar
  8. Basunanda P, Radoev M, Ecke W, Friedt W, Becker HC, Snowdon RJ (2010) Comparative mapping of quantitative trait loci involved in heterosis for seedling and yield traits in oilseed rape (Brassica napus L.). Theor Appl Genet 120:271–281PubMedCrossRefGoogle Scholar
  9. Batley J, Edwards D (2007) SNP applications in plants. In: Oraguzie NC, Rikkerink EHA, Gardiner SE, De Silva HN (eds) Association mapping in plants. Springer, Berlin, pp 95–102Google Scholar
  10. Batley J, Edwards D (2009) Genome sequence data: management, storage, and visualization. Biotechniques 46:333–336PubMedCrossRefGoogle Scholar
  11. Beckmann JS, Soller M (1986) Restriction fragment length polymorphisms and genetic improvement of agricultural species. Euphytica 35:111–124CrossRefGoogle Scholar
  12. Berkman PJ, Skarshewski A, Lorenc MT, Lai K, 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 (2011a) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotech J 9:768–775CrossRefGoogle Scholar
  13. Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubalakova M, Simkova H, Batley J, Dolezel J, Hernandez P, Edwards D (2011b) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theor Appl Genet (in press)Google Scholar
  14. Berkman PJ, Lai K, Lorenc MT, Edwards D (2012) Next generation sequencing applications for wheat crop improvement. Am J Bot (in press)Google Scholar
  15. Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48:1649–1664CrossRefGoogle Scholar
  16. Breseghello F, Sorrells ME (2006) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46:1323–1330CrossRefGoogle Scholar
  17. Bundock PC, Casu RE, Henry RJ (2012) Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant. Plant Biotech J 10:657–667CrossRefGoogle Scholar
  18. Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P, Chalhoub B (2005) Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and aegilops). Plant Cell 17:1033–1045 Google Scholar
  19. Cheng F, Wu J, Fang L, Sun S, Liu B, Lin K, Bonnema G, Wang X (2012) Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. Plos One 7Google Scholar
  20. Chia J-M, Ware D (2011) Sequencing for the cream of the crop. Nat Biotech 29:138–139CrossRefGoogle Scholar
  21. Chutimanitsakun Y, Nipper R, Cuesta-Marcos A, Cistue L, Corey A, Filichkina T, Johnson E, Hayes P (2011) Construction and application for QTL analysis of a restriction siteGoogle Scholar
  22. 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 12:499–510PubMedCrossRefGoogle Scholar
  23. Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J, Edwards D (2009a) AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucl Acids Res 37:D951–D953PubMedCrossRefGoogle Scholar
  24. Duran C, Appleby N, Vardy M, Imelfort M, Edwards D, Batley J (2009b) Single nucleotide polymorphism discovery in barley using autoSNPdb. Plant Biotech J 7:326–333CrossRefGoogle Scholar
  25. Duran C, Appleby N, Edwards D, Batley J (2009c) Molecular genetic markers: discovery, applications, data storage and visualisation. Curr Bioinform 4:16–27CrossRefGoogle Scholar
  26. Duran C, Eales D, Marshall D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Appleby N, Batley J, Basford K, Edwards D (2010) Future tools for association mapping in crop plants. Genome 53:1017–1023PubMedCrossRefGoogle Scholar
  27. Eckardt NA (2001) A sense of self: the role of DNA sequence elimination in allopolyploidization. Plant Cell 13:1699–1704 PubMedGoogle Scholar
  28. Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotech J 7:1–8CrossRefGoogle Scholar
  29. Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Keeble-Gagnère G, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R, Fitzgerald A (2012) Bread matters: a national initiative to profile the genetic diversity of Australian wheat. Plant Biotech J 10:703–708CrossRefGoogle Scholar
  30. 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:e19379PubMedCrossRefGoogle Scholar
  31. Flavell RB, Rimpau J, Smith DB (1977) Repeated sequence DNA relationships in four cereal genomes. Chromosoma 63:205–222CrossRefGoogle Scholar
  32. Fleury D, Luo M-C, Dvorak J, Ramsay L, Gill BS, Anderson OD, You FM, Shoaei Z, Deal KR, Langridge P (2010) Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS. Bmc Genomics 11 Google Scholar
  33. Fu Y, Springer NM, Gerhardt DJ, Ying K, Yeh CT, 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 62:898–909PubMedCrossRefGoogle Scholar
  34. Gaeta RT, Pires JC (2010) Homoeologous recombination in allopolyploids: the polyploid ratchet. New Phytol 186:18–28PubMedCrossRefGoogle Scholar
  35. Gegas VC, Nazari A, Griffiths S, Simmonds J, Fish L, Orford S, Sayers L, Doonan JH, Snape JW (2010) A genetic framework for grain size and shape variation in wheat. Plant Cell 22:1046–1056PubMedCrossRefGoogle Scholar
  36. Gholami M, Bekele WA, Schondelmaier J, Snowdon RJ (2012) A tailed PCR procedure for cost-effective, two-order multiplex sequencing of candidate genes in polyploid plants. Plant Biotech J 10:635–645CrossRefGoogle Scholar
  37. Gill BS, Appels R, Botha-Oberholster A-M, Buell CR, Bennetzen JL, Chalhoub B, Chumley F, Dvorak J, Iwanaga M, Keller B, Li W, McCombie WR, Ogihara Y, Quetier F, Sasaki T (2004) A workshop report on wheat genome sequencing: international genome research on wheat consortium. Genetics 168:1087–1096Google Scholar
  38. Gore MQ, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JL, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES (2009) A first-generation haplotype map of maize. Science 326:1115–1117PubMedCrossRefGoogle Scholar
  39. Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME (2009) Genomic selection in dairy cattle: progress and challenges. J Dairy Sci 92:433–443PubMedCrossRefGoogle Scholar
  40. Hayward A, Dalton-Morgan J, Mason A, Zander M, Edwards D, Batley J (2012a) SNP discovery and applications in Brassica napus. J Plant Biotech 39:49–61CrossRefGoogle Scholar
  41. Hayward A, McLanders J, Campbell E, Edwards D, Batley J (2012b) Genomic advances will herald new insights into the Brassica:Leptosphaeria maculans pathosystem. Plant Biol 14:1–10PubMedCrossRefGoogle Scholar
  42. Hayward A, Vighnesh G, Delay C, Samian MR, Manoli S, Stiller J, McKenzie M, Edwards D, Batley J (2012c) Second-generation sequencing for gene discovery in the Brassicaceae. Plant Biotech J 10:750–759CrossRefGoogle Scholar
  43. Heffner EL, Sorrells ME, Jannink J-L (2009) Genomic selection for crop improvement. Crop Sci 49:1–12CrossRefGoogle Scholar
  44. Hernandez P, Martis M, Dorado G, Pfeifer M, Gálvez S, Schaaf S, Jouve N, Šimková H, Valárik M, Doležel J, Mayer KFX (2012) Next generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J 69:377–386PubMedCrossRefGoogle Scholar
  45. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967PubMedCrossRefGoogle Scholar
  46. Imelfort M, Edwards D (2009) De novo sequencing of plant genomes using second-generation technologies. Brief Bioinform 10:609–618PubMedCrossRefGoogle Scholar
  47. Imelfort M, Batley J, Grimmond S, Edwards D (2009a) Genome sequencing approaches and successes. In: Somers D, Langridge P, Gustafson J (eds) Plant genomics. Humana Press, New Jersey, pp 345–358CrossRefGoogle Scholar
  48. Imelfort M, Duran C, Batley J, Edwards D (2009b) Discovering genetic polymorphisms in next generation sequencing data. Plant Biotech J 7(4):312–317CrossRefGoogle Scholar
  49. Iñiguez Luy FL, Federico ML (2011) The genetics of Brassica napus L. In: Bancroft I, Schmidt R (eds) Genetics and genomics of the Brassicaceae. Springer, Dordrecht, pp 291–322CrossRefGoogle Scholar
  50. International Brachypodium Initiative (2010) The genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768CrossRefGoogle Scholar
  51. Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166–177PubMedCrossRefGoogle Scholar
  52. Kubalakova M, Lysak MA, Vrana J, Simkova H, Cihalikova J, Dolezel J (2000) Rapid identification and determination of purity of flow-sorted plant chromosomes using C-PRINS. Cytometry 41:102–108PubMedCrossRefGoogle Scholar
  53. Kubaláková M, Vrána J, Číhalíková J, Šimková H, Doležel J (2002) Flow karyotyping and chromosome sorting in bread wheat (Triticum aestivum L.). Theor Appl Genet 104:1362–1372PubMedCrossRefGoogle Scholar
  54. Kubalakova M, Valarik M, Bartos J, Vrana J, Cihalikova J, Molnar-Lang M, Dolezel J (2003) Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry. Genome 46:893–905PubMedCrossRefGoogle Scholar
  55. Laat AMMD, Blaas J (1984) Flow-cytometric characterization and sorting of plant chromosomes. Theor Appl Genet 67:463–467 CrossRefGoogle Scholar
  56. Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J, Edwards D (2011) an integrated database and portal for wheat genome information. Plant Cell Physiol 53:1–7Google Scholar
  57. Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden MJ, Forrest KL, Fleury D, Baumann U, Zander M, Mason AS, Batley J, Edwards D (2012a) Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotech J 10:743–749CrossRefGoogle Scholar
  58. Lai K, Lorenc MT, Edwards D (2012b) Genomic databases for crop improvement. Agronomy 2:62–73CrossRefGoogle Scholar
  59. Lee JH, Arumuganathan K (1999) Metaphase chromosome accumulation and flow karyotypes in rice (Oryza sativa L.) root tip meristem cells. Mol Cells 9:436–439 PubMedGoogle Scholar
  60. Lee H, Lai K, Lorenc MT, Imelfort M, Duran C, Edwards D (2012) Bioinformatics tools and databases for analysis of next generation sequence data. Brief Funct Genomics (in press)Google Scholar
  61. Leitch AR, Leitch IJ (2008) Genomic plasticity and the diversity of polyploid plants. Science 320:481–483PubMedCrossRefGoogle Scholar
  62. Li W, Zhang P, Fellers J, Friebe B, Gill B (2004) Sequence composition, organization, and evolution of the core Triticeae genome. Plant J 40:500–511 PubMedCrossRefGoogle Scholar
  63. Liu LZ, Wittkop B, Stein A, Sarvari P, Li JN, Dreyer F, Frauen M, Friedt W, Snowdon RJ (2012) A knockout mutation in the lignin biosynthesis gene CCR1 explains a major QTL for acid detergent lignin content in Brassica napus seeds. Theor Appl Genet 124:1573–1586PubMedCrossRefGoogle Scholar
  64. Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, Berkman PJ, Lai K, Batley J, Edwards D (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology (in press)Google Scholar
  65. Luo MC, Deal KR, Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo HY, Huo N, Lazo G, Ma Y, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J (2009) Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proc Natl Acad Sci USA 106:15780–15785Google Scholar
  66. Lysak MA, Koch MA, Pecinka A, Schubert I (2005) Chromosome triplication found across the tribe Brassiceae. Genome Res 15:516–525PubMedCrossRefGoogle Scholar
  67. Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J, Edwards D (2010) Targeted identification of genomic regions using TAGdb. Plant Methods 6:19PubMedCrossRefGoogle Scholar
  68. 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 151:496–505PubMedCrossRefGoogle Scholar
  69. Mayer KFX, Martis M, Hedley PE, Simkova H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubalakova M, Suchankova P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Dolezel J, Waugh R, Stein N (2011) Unlocking the Barley Genome by Chromosomal and Comparative Genomics. Plant Cell 23:1249–1263Google Scholar
  70. McKay JK, Leach JE (2011) Linkage illuminates a complex genome. Nat Biotech 29:717–718CrossRefGoogle Scholar
  71. McMullen MD, Kresovich S, Villeda HS, Bradbury PJ, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, Brown P, Browne C et al (2009) Genetic properties of the maize nested association mapping population. Science 325:737–740PubMedCrossRefGoogle Scholar
  72. Metzker M (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46PubMedCrossRefGoogle Scholar
  73. Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829PubMedGoogle Scholar
  74. Miller M, Dunham J, Amores A, Cresko W, Johnson E (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–248PubMedCrossRefGoogle Scholar
  75. Muers M (2011) Technology: getting Moore from DNA sequencing. Nat Rev Genet 12:586–587Google Scholar
  76. Nie X, Li B, Wang L, Liu P, Biradar SS, Li T, Dolezel J, Edwards D, Luo MC, Weining S (2012) Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology. Am J Bot (in press)Google Scholar
  77. Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456:720–723PubMedCrossRefGoogle Scholar
  78. Ozsolak F, Goren A, Gymrek MA, Guttman M, Regev A, Bernstein BE, Milos PM (2010) Digital transcriptome profiling from attomole-level RNA samples. Genome Res 20:519–525PubMedCrossRefGoogle Scholar
  79. Parkin IA, Gulden SM, Sharpe AG, Lukens L, Trick M, Osborn TC, Lydiate DJ (2005) Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171:765–781PubMedCrossRefGoogle Scholar
  80. Paux E, Roger D, Badaeva E, Gay G, Bernard M, Sourdille P, Feuillet C (2006) Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J 48:463–474PubMedCrossRefGoogle Scholar
  81. Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Berges H, Eversole K, Appels R, Safar J, Simkova H, Dolezel J, Bernard M, Feuillet C (2008) A physical map of the 1-gigabase bread wheat chromosome 3B. Science 322:101–104Google Scholar
  82. Pfender WF, Saha MC, Johnson EA, Slabaugh EA (2011) Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet 122:1467–1480PubMedCrossRefGoogle Scholar
  83. Pichon J-PD, Riviere N, Duarte J, Dugas O, Wilmer JA, Gerhardt DJ, Richmond T, Albert TJ, Jeddeloh JA (2010) Rapeseed (B. napus) SNP discovery using a dedicated sequence capture protocol and 454 sequencing. Plant and Animal Genome Conference 2010, San Diego, USAGoogle Scholar
  84. Rabinowicz PD, Citek R, Budiman MA, Nunberg A, Bedell JA, Lakey N, O'Shaughnessy AL, Nascimento LU, McCombie WR, Martienssen RA (2005) Differential methylation of genes and repeats in land plants. Genome Res 15:1431–1440PubMedCrossRefGoogle Scholar
  85. Raman H, Harsh R, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J, Luckett D, Wratten N, Dennis E (2012) Genetic and physical mapping of flowering time loci in oilseed rape (Brassica napus L.). Theor Appl Genet (in press) Google Scholar
  86. Riedelsheimer C, Czedik-Eysenberg A, Grieder C, Lisec J, Technow F, Sulpice R, Altmann T, Stitt M, Willmitzer L, Melchinger AE (2012) Genomic and metabolic prediction of complex heterotic traits in hybrid maize. Nat Genet. doi: 10.1038/ng.1033 PubMedGoogle Scholar
  87. 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 Y, 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 475:348–352Google Scholar
  88. Sabot F, Guyot R, Wicker T, Chantret N, Laubin B, Chalhoub B, Leroy P, Sourdille P, Bernard M (2005) Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations. Mol Genetics Genomics 274:119–130CrossRefGoogle Scholar
  89. Šafář J, Šimková H, Kubalákoá M, Číhalíková J, Suchánková P, Bartoš J, Doležel J (2010) Development of chromosome-specific BAC resources for genomics of bread wheat. Cytogenet Genome Res 129:211–223 PubMedCrossRefGoogle Scholar
  90. Saintenac C, Jiang D, Akhunov ED (2011) Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol 12:R88PubMedCrossRefGoogle Scholar
  91. Schmutz J, Cannon SB, Schlueter J, Ma JX, Mitros T, Nelson W, Hyten DL, Song QJ, Thelen JJ, Cheng JL, Xu D, Hellsten U et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183PubMedCrossRefGoogle Scholar
  92. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115PubMedCrossRefGoogle Scholar
  93. Schnable JC, Springer NM, Freeling M (2011) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Nat Acad Sci USA 108:4069–4074PubMedCrossRefGoogle Scholar
  94. Snowdon R, Iniguez Luy (2012) Breeding oilseed rape and canola in the genomics era. Plant Breed 131:351–360CrossRefGoogle Scholar
  95. Springer NM, Ying K, Fu Y, Ji T, Yeh C-T, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable PS (2009) Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet 5:e1000734PubMedCrossRefGoogle Scholar
  96. Stokes D, Fraser F, Morgan C, O’Neill CM, Dreos R, Magusin A, Szalma S, Bancroft I (2010) An association transcriptomics approach to the prediction of hybrid performance. Mol Breed 26:91–96CrossRefGoogle Scholar
  97. Szadkowski E, Eber F, Huteau V, Lodé M, Huneau C, Belcram H, Coriton O, Manzanares-Dauleux MJ, Delourme R, King GJ, Chalhoub B, Jenczewski E, Chèvre AM (2010) The first meiosis of resynthesized Brassica napus, a genome blender. New Phytol 186:102–112PubMedCrossRefGoogle Scholar
  98. Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Nat Biotech 7:257–264CrossRefGoogle Scholar
  99. The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195CrossRefGoogle Scholar
  100. Tollenaere R, Hayward A, Dalton-Morgan J, Campbell E, Lee JRM, Lorenc MT, Manoli S, Stiller J, Raman R, Raman H, Edwards D, Batley J (2012) Identification and characterization of candidate Rlm4 blackleg resistance genes in Brassica napus using next-generation sequencing. Plant Biotech J 10:709–715CrossRefGoogle Scholar
  101. Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, Hine EE, Althoff R, Arbogast TS, Tallon LJ, Vigouroux M, Trick M, Bancroft I (2006) Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18:1348–1359PubMedCrossRefGoogle Scholar
  102. Trick M, Long Y, Meng J, Bancroft I (2009) Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using solexa transcriptome sequencing. Plant Biotech J 7:334–346CrossRefGoogle Scholar
  103. Udall JA, Quijada PA, Osborn TC (2005) Detection of chromosomal rearrangements derived from homeologous recombination in four mapping populations of Brassica napus L. Genetics 169:967–979PubMedCrossRefGoogle Scholar
  104. Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522–530PubMedCrossRefGoogle Scholar
  105. Vlacilova K, Ohri D, Vrana J, Cihalikova J, Kubalakova M, Kahl G, Dolezel J (2002) Development of flow cytogenetics and physical genome mapping in chickpea (Cicer arietinum L.). Chromosom Res 10:695–706CrossRefGoogle Scholar
  106. Vrána J, Kubaláková M, Šimková H, Číhalíková J, Lysák MA, Doležel J (2000) Flow sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). Genetics 156:2033–2041PubMedGoogle Scholar
  107. Wang L, Li PH, Brutnell TP (2010) Exploring plant transcriptomes using ultra high-throughput sequencing. Brief Funct Genomics 9:118–128PubMedCrossRefGoogle Scholar
  108. Wang J, Lydiate IA, Parkin IAP, Falentin C, Delourme R, Carion PWC, King GJ (2011a) Integration of linkage maps for the amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa. BMC Genomics 12:101PubMedCrossRefGoogle Scholar
  109. Wang XW, Wang HZ, Wang J, Sun RF, Wu J, Liu SL, Bai YQ, Mun JH, Bancroft I, Cheng F, Huang SW, Li XX et al (2011b) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1040PubMedCrossRefGoogle Scholar
  110. Wanjugi H, Coleman-Derr D, Huo NX, Kianian SF, Luo MC, Wu JJ, Anderson O, Gu YQ (2009) Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome 52:576–587PubMedCrossRefGoogle Scholar
  111. Winfield MO, Wilkinson PA, Allen AM, Barker GLA, Coghill JA, Burridge A, Hall A, Brenchley RC, D’Amore R, Hall N, Bevan MW, Richmond T, Gerhardt DJ, Jeddeloh JA, Edwards KJ (2012) Targeted re-sequencing of the allohexaploid wheat exome. Plant Biotech J 10:733–742CrossRefGoogle Scholar
  112. Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407CrossRefGoogle Scholar
  113. You FM, Huo N, Deal KR, Gu YQ, Luo M-C, McGuire PE, Dvorak J, Anderson OD (2011) Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics 12:59PubMedCrossRefGoogle Scholar
  114. Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–551PubMedCrossRefGoogle Scholar
  115. Zou J, Zhu J, Huang S, Tian E, Xiao Y, Fu D, Tu J, Fu T, Meng J (2010) Broadening the avenue of intersubgenomic heterosis in oilseed Brassica. Theor Appl Genet 120:283–290PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • David Edwards
    • 1
  • Jacqueline Batley
    • 2
  • Rod J. Snowdon
    • 3
  1. 1.Australian Centre for Plant Functional Genomics, School of Agriculture and Food SciencesUniversity of QueenslandBrisbaneAustralia
  2. 2.Centre of Excellence for Integrative Legume Research, School of Agriculture and Food SciencesUniversity of QueenslandBrisbaneAustralia
  3. 3.Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany

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