Accessing complex crop genomes with next-generation sequencing

Theoretical and Applied Genetics

Volumn 126, Issue 1, 2013, Pages 1-11

  Edwards, David ^a   Batley, Jacqueline ^a   Snowdon, Rod J ^b  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELIC VARIATION; BIOINFORMATIC TOOLS; CHROMOSOMAL REARRANGEMENT; CROP GENE POOLS; DATA ANALYSIS TECHNIQUES; DNA SEQUENCING; GENE DISCOVERY; GENETIC DIVERSITY; GENOME ANALYSIS; GENOMIC DATA; GENOMICS; GERMPLASM COLLECTIONS; HIGH-THROUGHPUT SCREENING; HOMOEOLOGOUS GENES; MOLECULAR GENETICS; OIL SEED RAPE; POLYPLOIDISATION; PRESENCE-ABSENCE; SINGLE NUCLEOTIDE POLYMORPHISMS; TECHNOLOGICAL ADVANCES;

BIOINFORMATICS; CROPS; DNA SEQUENCES; MOLECULAR BIOLOGY;

GENES;

TRANSCRIPTOME;

ALLELE; BIOLOGICAL MODEL; BRASSICA; CROP; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; GENETICS; GENOME; GENOMICS; GENOTYPE; METHODOLOGY; PLANT GENOME; PLOIDY; POLYPLOIDY; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; WHEAT;

ALLELES; BRASSICA; CROPS, AGRICULTURAL; GENE EXPRESSION PROFILING; GENETIC VARIATION; GENOME; GENOME, PLANT; GENOMICS; GENOTYPE; MODELS, GENETIC; PLOIDIES; POLYMORPHISM, SINGLE NUCLEOTIDE; POLYPLOIDY; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME; TRITICUM;

BRASSICA NAPUS; TRITICUM AESTIVUM;

EID: 84871906959     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-012-1964-x     Document Type: Review

References (115)

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).
2. Associated DNA (RAD) linkage map in barley. BMC Genomics 12: 4.
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: 627-631.
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: 186-192.
5. Bagnato A, Rosati A (2012) From the editors-animal selection: the genomics revolution. Anim Front 12: 1-2.
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 20090300781.
7. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51: 910-918.
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: 271-281.
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 95-102.
10. Batley J, Edwards D (2009) Genome sequence data: management, storage, and visualization. Biotechniques 46: 333-336.
11. Beckmann JS, Soller M (1986) Restriction fragment length polymorphisms and genetic improvement of agricultural species. Euphytica 35: 111-124.
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: 768-775.
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).
14. Berkman PJ, Lai K, Lorenc MT, Edwards D (2012) Next generation sequencing applications for wheat crop improvement. Am J Bot (in press).
15. Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48: 1649-1664.
16. Breseghello F, Sorrells ME (2006) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46: 1323-1330.
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: 657-667.
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.
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 7.
20. Chia J-M, Ware D (2011) Sequencing for the cream of the crop. Nat Biotech 29: 138-139.
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 site.
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: 499-510.
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-D953.
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: 326-333.
25. Duran C, Appleby N, Edwards D, Batley J (2009c) Molecular genetic markers: discovery, applications, data storage and visualisation. Curr Bioinform 4: 16-27.
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: 1017-1023.
27. Eckardt NA (2001) A sense of self: the role of DNA sequence elimination in allopolyploidization. Plant Cell 13: 1699-1704.
28. Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotech J 7: 1-8.
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: 703-708.
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: e19379.
31. Flavell RB, Rimpau J, Smith DB (1977) Repeated sequence DNA relationships in four cereal genomes. Chromosoma 63: 205-222.
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.
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: 898-909.
34. Gaeta RT, Pires JC (2010) Homoeologous recombination in allopolyploids: the polyploid ratchet. New Phytol 186: 18-28.
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: 1046-1056.
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: 635-645.
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: 1087-1096.
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: 1115-1117.
39. Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME (2009) Genomic selection in dairy cattle: progress and challenges. J Dairy Sci 92: 433-443.
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: 49-61.
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: 1-10.
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: 750-759.
43. Heffner EL, Sorrells ME, Jannink J-L (2009) Genomic selection for crop improvement. Crop Sci 49: 1-12.
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: 377-386.
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: 961-967.
46. Imelfort M, Edwards D (2009) De novo sequencing of plant genomes using second-generation technologies. Brief Bioinform 10: 609-618.
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 345-358.
48. Imelfort M, Duran C, Batley J, Edwards D (2009b) Discovering genetic polymorphisms in next generation sequencing data. Plant Biotech J 7(4): 312-317.
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 291-322.
50. International Brachypodium Initiative (2010) The genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.
51. Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9: 166-177.
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: 102-108.
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: 1362-1372.
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: 893-905.
55. Laat AMMD, Blaas J (1984) Flow-cytometric characterization and sorting of plant chromosomes. Theor Appl Genet 67: 463-467.
56. Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J, Edwards D (2011) WheatGenome. info: an integrated database and portal for wheat genome information. Plant Cell Physiol 53: 1-7.
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: 743-749.
58. Lai K, Lorenc MT, Edwards D (2012b) Genomic databases for crop improvement. Agronomy 2: 62-73.
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.
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).
61. Leitch AR, Leitch IJ (2008) Genomic plasticity and the diversity of polyploid plants. Science 320: 481-483.
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.
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: 1573-1586.
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).
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: 15780-15785.
66. Lysak MA, Koch MA, Pecinka A, Schubert I (2005) Chromosome triplication found across the tribe Brassiceae. Genome Res 15: 516-525.
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: 19.
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: 496-505.
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: 1249-1263.
70. McKay JK, Leach JE (2011) Linkage illuminates a complex genome. Nat Biotech 29: 717-718.
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: 737-740.
72. Metzker M (2010) Sequencing technologies-the next generation. Nat Rev Genet 11: 31-46.
73. Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
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: 240-248.
75. Muers M (2011) Technology: getting Moore from DNA sequencing. Nat Rev Genet 12: 586-587.
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).
77. Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456: 720-723.
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: 519-525.
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: 765-781.
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: 463-474.
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: 101-104.
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: 1467-1480.
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, USA.
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: 1431-1440.
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).
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.
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: 348-352.
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: 119-130.
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.
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: R88.
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: 178-183.
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: 1112-1115.
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: 4069-4074.
94. Snowdon R, Iniguez Luy (2012) Breeding oilseed rape and canola in the genomics era. Plant Breed 131: 351-360.
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: e1000734.
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: 91-96.
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: 102-112.
98. Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Nat Biotech 7: 257-264.
99. The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475: 189-195.
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: 709-715.
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: 1348-1359.
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: 334-346.
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: 967-979.
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: 522-530.
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: 695-706.
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: 2033-2041.
107. Wang L, Li PH, Brutnell TP (2010) Exploring plant transcriptomes using ultra high-throughput sequencing. Brief Funct Genomics 9: 118-128.
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: 101.
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: 1035-1040.
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: 576-587.
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: 733-742.
112. Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48: 391-407.
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: 59.
114. Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551.
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: 283-290.