Sequencing crop genomes: Approaches and applications

New Phytologist

Volumn 191, Issue 4, 2011, Pages 915-925

  Jackson, Scott A ^a   Iwata, Aiko ^a   Lee, Suk Ha ^b   Schmutz, Jeremy ^c   Shoemaker, Randy ^d  

^a UNIVERSITY OF GEORGIA   (United States)

^b Seoul National University   (South Korea)

^c HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Breeding; Crops; Genetics; Genomics; Resequencing

Indexed keywords

AGRICULTURAL LAND; CLIMATE PREDICTION; CROP IMPROVEMENT; CROP PLANT; CROP PRODUCTION; GENETIC ANALYSIS; GENOME; GENOMICS; INFORMATICS; PHENOTYPE; WEATHER MODIFICATION;

BREEDING; CHROMOSOME MAP; CROP; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETIC MARKER; GENETIC VARIABILITY; GENETICS; GENOMICS; GENOTYPE; METHODOLOGY; PLANT GENOME; POLYPLOIDY; QUANTITATIVE TRAIT LOCUS; REVIEW;

BREEDING; CHROMOSOME MAPPING; CROPS, AGRICULTURAL; GENE EXPRESSION REGULATION, PLANT; GENETIC MARKERS; GENETIC VARIATION; GENOME, PLANT; GENOMICS; GENOTYPE; POLYPLOIDY; QUANTITATIVE TRAIT LOCI; SEQUENCE ANALYSIS, DNA;

EID: 80051578403     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2011.03804.x     Document Type: Review

References (96)

1. Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, Tannier E, Plomion C, Cooke R, Feuillet C et al. 2010. Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends in Plant Science 15: 479-487.
2. Akhunov E, Nicolet C, Dvorak J. 2009. Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina Goldengate assay. Theoretical and Applied Genetics 119: 507-517.
3. 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.
4. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. 2002. ARACHNE: a whole-genome shotgun assembler. Genome Research 12: 177-189.
5. Bennetzen JL, Ma J, Devos KM. 2005. Mechanisms of recent genome size variation in flowering plants. Annals of Botany 95: 127-132.
6. Blanc G, Wolfe KH. 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667-1678.
7. Bouchez A, Hospital F, Causse M, Gallais A, Charcosset A. 2002. Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines. Genetics 162: 1945-1959.
8. Bouwman AF. 1997. Long-term scenarios of livestock-crop-land use interactions in developing countries. Land and Water Bulletin No. 6. Rome, Italy: Food and Agriculture Organization of the United Nations.
9. Bowers JE, Chapman BA, Rong J, Paterson AH. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433-438.
10. Brown ME, Funk CC. 2008. Climate. Food security under climate change. Science 319: 580-581.
11. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC et al. 2009. The genetic architecture of maize flowering time. Science 325: 714-718.
12. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. 2008. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Research 18: 810-820.
13. Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T et al. 2006. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proceedings of the National Academy of Sciences, USA 103: 14959-14964.
14. Chenu K, Chapman SC, Tardieu F, McLean G, Welcker C, Hammer GL. 2009. Simulating the yield impacts of organ-level quantitative trait loci associated with drought response in maize: a "gene-to-phenotype" modeling approach. Genetics 183: 1507-1523.
15. Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P, Schlub S, Le Paslier MC, Magdelenat G, Gonthier C et al. 2010. Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22: 1686-1701.
16. Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H. 2009. Continuous base identification for single-molecule nanopore DNA sequencing. Nature Nanotechnology 4: 265-270.
17. Crow JF. 1998. 90years ago: the beginning of hybrid maize. Genetics 148: 923-928.
18. Crow JF. 2001. Plant breeding giants. Burbank, the artist; Vavilov, the scientist. Genetics 158: 1391-1395.
19. Doebley J, Stec A, Hubbard L. 1997. The evolution of apical dominance in maize. Nature 386: 485-488.
20. Doyle JJ, Doyle JL, Brown AH, Palmer RG. 2002. Genomes, multiple origins, and lineage recombination in the Glycine tomentella (leguminosae) polyploid complex: histone h3-d gene sequences. Evolution 56: 1388-1402.
21. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B et al. 2009. Real-time DNA sequencing from single polymerase molecules. Science 323: 133-138.
22. Evenson RE, Gollin D. 2003. Assessing the impact of the green revolution, 1960 to 2000. Science 300: 758-762.
23. Fleury D, Jefferies S, Kuchel H, Langridge P. 2010. Genetic and genomic tools to improve drought tolerance in wheat. Journal of Experimental Botany 61: 3211-3222.
24. Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC et al. 2009. The challenges of sequencing by synthesis. Nature Biotechnology 27: 1013-1023.
25. Gaut BS, Doebley JF. 1997. DNA sequence evidence for the segmental allotetraploid origin of maize. Proceedings of the National Academy of Sciences, USA 94: 6809-6814.
26. Gilbert JE, Lewis RV, Wilkinson MJ, Caligari PDS. 1999. Developing an appropriate strategy to assess genetic variability in plant germplasm collections. Theoretical and Applied Genetics 98: 1125-1131.
27. Gill N, Findley S, Walling JG, Hans C, Ma J, Doyle J, Stacey G, Jackson SA. 2009. Molecular and chromosomal evidence for allopolyploidy in soybean. Plant Physiology 151: 1167-1174.
28. Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J et al. 2009. A first-generation haplotype map of maize. Science 326: 1115-1117.
29. Gregory TR, Nicol JA, Tamm H, Kullman B, Kullman K, Leitch IJ, Murray BG, Kapraun DF, Greilhuber J, Bennett MD. 2007. Eukaryotic genome size databases. Nucleic Acids Research 35: D332-D338.
30. Gupta PK, Roy JK, Prasad M. 2001. Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Current Science India 80: 524-535.
31. Gupta PK, Rustgi S, Mir RR. 2008. Array-based high-throughput DNA markers for crop improvement. Heredity 101: 5-18.
32. Hammer K. 2003. A paradigm shift in the discipline of plant genetic resources. Genetic Resources and Crop Evolution 50: 3-10.
33. Hansen BG, Halkier BA, Kleibenstein DA. 2008. Identifying the molecular basis of QTLs: eQTLs add a new dimension. Trends in Plant Science 13: 1360-1385.
34. Hoisington D, Khairallah M, Reeves T, Ribault J-M, Skovmand B, Taba S, Warburton M. 1999. Plant genetic resources: what can they contribute toward increased crop productivity? Proceedings of the National Academy of Sciences, USA 96: 5937-5943.
35. Holloway B, Li B. 2010. Expression QTLs: applications for crop improvement. Molecular Breeding 26: 381-391.
36. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P et al. 2009. The genome of the cucumber, Cucumis sativus L. Nature Genetics 41: 1275-1281.
37. Huang S, Sirikhachornkit A, Su X, Faris J, Gill B, Haselkorn R, Gornicki P. 2002. Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proceedings of the National Academy of Sciences, USA 99: 8133-8138.
38. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z et al. 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics 42: 961-967.
39. Hubner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, Maciver F, Mueller M, Hummel O, Monti J, Zidek V. 2005. Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nature Genetics 37: 243-253.
40. Hyten DL, Cannon SB, Song Q, Weeks NT, Fickus EW, Shoemaker R, Specht JE, May GD, Cregan PB. 2010. High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11: 38.
41. Hyten DL, Song Q, Zhu Y, Choi I-Y, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Cregan PB. 2006. Impacts of genetic bottlenecks on soybean genome diversity. Proceedings of the National Academy of Sciences, USA 103: 16666-16671.
42. Initiative TAG. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
43. Innes RW, Ameline-Torregrosa C, Ashfield T, Cannon E, Cannon SB, Chacko B, Chen NW, Couloux A, Dalwani A, Denny R et al. 2008. Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiology 148: 1740-1759.
44. IRGSP. 2005. The map-based sequence of the rice genome. Nature 436: 793-800.
45. Jackson DA, Symons RH, Berg P. 1972. Biochemical method for inserting new genetic information into DNA of simian virus 40: circular sv40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. Proceedings of the National Academy of Sciences, USA 69: 2904-2909.
46. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C et al. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467.
47. Jansen RC, Nap J-P. 2001. Genetical genomics: the added value from segregation. Trends in Genetics 17: 388-391.
48. Jordan MC, Somers DJ, Banks TW. 2007. Identifying regions of wheat genome controlling seed development by mapping expression quantitative trait loci. Plant Biotechnology Journal 8: 442-453.
49. Keurentjes JJB, Fu J, Terpstra IR, Garcia JM, van den Ackerveken G, Basten Snoek L, Peeters AJM, Vreugdenhil D, Koornneef M, Jansen RC. 2007. Regulatory network construction in arabidospsi by using genome-wide gene expression quantitative trait loci. Proceedings of the National Academy of Sciences, USA 104: 1708-1713.
50. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
51. Lewis D. 1945. The science of plant breeding. Nature 155: 355-356.
52. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y et al. 2009. The sequence and de novo assembly of the giant panda genome. Nature 463: 311-317.
53. Mackay TFC. 2001. The genetic architecture of quantitative traits. Annual Review of Genetics 35: 303-339.
54. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
55. McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C et al. 2009. Genetic properties of the maize nested association mapping population. Science 325: 737-740.
56. Meinke DW, Cherry JM, Dean C, Rounsley SD, Koornneef M. 1998. Arabidopsis thaliana: a model plant for genome analysis. Science 282: 662, 679-682.
57. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L et al. 2007. The chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318: 245-250.
58. Meuwissen THE, Hayes BJ, Goddard ME. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
59. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL et al. 2008. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya linnaeus). Nature 452: 991-996.
60. Moose SP, Mumm RH. 2008. Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiology 147: 969-977.
61. Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S et al. 1999. A complete BAC-based physical map of the Arabidopsis thaliana genome. Nature Genetics 22: 271-275.
62. van Oeveren J, de Ruiter M, Jesse T, van der Poel H, Tang J, Yalcin F, Janssen A, Volpin H, Stormo KE, Bogden R et al. 2011. Sequence-based physical mapping of complex genomes by whole genome profiling. Genome Research 21: 618-625.
63. O'Rourke J, Nelson R, Grant D, Schmutz J, Grimwood J, Cannon SB, Vance C, Graham M, Shoemaker RC. 2009. Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response. BMC Genomics 10: 376-393.
64. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A et al. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
65. Paterson AH, Bowers JE, Chapman BA. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proceedings of the National Academy of Sciences, USA 101: 9903-9908.
66. Paterson AH, Freeling M, Tang H, Wang X. 2010. Insights from the comparison of plant genome sequences. Annual Review of Plant Biology 61: 349-372.
67. Piegu B, Guyot R, Picault N, Roulin A, Saniyal A, Kim H, Collura K, Brar DS, Jackson S, Wing RA et al. 2006. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Research 16: 1262-1269.
68. Potokina E, Druka A, Luo Z, Wise R, Waugh R, Kearsey M. 2008. Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation. Plant Journal 53: 90-101.
69. Raghuvanshi S, Kapoor M, Tyagi S, Khurana P, Khurana J, Akhilesh T. 2010. Rice genomics moves ahead. Molecular Breeding 26: 257-273.
70. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y et al. 2008. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319: 64-69.
71. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z et al. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768.
72. Schlueter JA, Dixon P, Granger C, Grant D, Clark L, Doyle JJ, Shoemaker RC. 2004. Mining EST databases to resolve evolutionary events in major crop species. Genome 47: 868-876.
73. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J et al. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183.
74. Schnable P, Ware D, Fulton R, 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.
75. Severin AJ, Woody JL, Bolon YT, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE et al. 2010. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biology 10: 160.
76. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Research 19: 1117-1123.
77. Soderlund C, Longden I, Mott R. 1997. FPC: a system for building contigs from restriction fingerprinted clones. Computer Applications in the Biosciences 13: 523-535.
78. Soltis DE, Soltis PS, Tate J. 2004. Advances in the study of polyploidy since plant speciation. New Phytologist 161: 173-191.
79. Swigonova Z, Lai J, Ma J, Ramakrishna W, Llaca V, Bennetzen JL, Messing J. 2004. Close split of sorghum and maize genome progenitors. Genome Research 14: 1916-1923.
80. Tanksley SD, McCouch SR. 1997. Seed banks and molecular maps: unlocking genetic potential from the wild. Science 227: 1063-1066.
81. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ESt. 2001. Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics 28: 286-289.
82. Turner WR, Oppenheimer M, Wilcove DS. 2009. A force to fight global warming. Nature 462: 278-279.
83. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A et al. 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.
84. United Nations. 2004. World population to 2300. New York, NY, USA: Dept of Economic and Social Affairs, 4-9.
85. Valkonen JPT, Nygren M, Ylönen A, Mannonen L. 1993. Nuclear DNA content of Pinus sylvestris (L.) as determined by laser flow cytometry. Genetica 92: 203-207.
86. Varshney RK, Nayak SN, May GD, Jackson SA. 2009. Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends in Biotechnology 27: 522-530.
87. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D et al. 2010. The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics 42: 833-839.
88. Wang H, Nussbaum-Wagler T, Li B, Zhao Q, Vigouroux Y, Faller M, Bomblies K, Lukens L, Doebley JF. 2005. The origin of the naked grains of maize. Nature 436: 714-719.
89. Weber JL, Myers EW. 1997. Human whole-genome shotgun sequencing. Genome Research 7: 401-409.
90. Wicker T, Taudien S, Houben A, Keller B, Graner A, Platzer M, Stein N. 2009. A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. Plant Journal 59: 712-722.
91. Yan J, Kandianis CB, Harjes CE, Bai L, Kim EH, Yang X, Skinner DJ, Fu Z, Mitchell S, Li Q et al. 2010a. Rare genetic variation at Zea mays crtRB1 increases beta-carotene in maize grain. Nature Genetics 42: 322-327.
92. Yan JB, Yang XH, Shah T, Sanchez-Villeda H, Li JS, Warburton M, Zhou Y, Crouch JH, Xu YB. 2010b. High-throughput snp genotyping with the goldengate assay in maize. Molecular Breeding 25: 441-451.
93. You FM, Huo N, Deal KR, Gu YQ, Luo MC, 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.
94. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829.
95. Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S et al. 2009. A single molecule scaffold for the maize genome. PLoS Genetics 5: e1000711.
96. Zhu W, Ouyang S, Iovene M, O'Brien K, Vuong H, Jiang J, Buell CR. 2008. Analysis of 90 mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition. BMC Genomics 9: 286.