Molecular Biotechnology

, Volume 50, Issue 3, pp 250–266 | Cite as

Emerging Knowledge from Genome Sequencing of Crop Species

  • Delfina Barabaschi
  • Davide Guerra
  • Katia Lacrima
  • Paolo Laino
  • Vania Michelotti
  • Simona Urso
  • Giampiero Valè
  • Luigi Cattivelli


Extensive insights into the genome composition, organization, and evolution have been gained from the plant genome sequencing and annotation ongoing projects. The analysis of crop genomes provided surprising evidences with important implications in plant origin and evolution: genome duplication, ancestral re-arrangements and unexpected polyploidization events opened new doors to address fundamental questions related to species proliferation, adaptation, and functional modulations. Detailed paleogenomic analysis led to many speculation on how chromosomes have been shaped over time in terms of gene content and order. The completion of the genome sequences of several major crops, prompted to a detailed identification and annotation of transposable elements: new hypothesis related to their composition, chromosomal distribution, insertion models, amplification rate, and evolution patterns are coming up. Availability of full genome sequence of several crop species as well as from many accessions within species is providing new keys for biodiversity exploitation and interpretation. Re-sequencing is enabling high-throughput genotyping to identify a wealth of SNP and afterward to produce haplotype maps necessary to accurately associate molecular variation to phenotype. Conservation genomics is emerging as a powerful tool to explain adaptation, genetic drift, natural selection, hybridization and to estimate genetic variation, fitness and population’s viability.


Whole genome sequencing Whole genome duplication Transposable elements Biodiversity Re-sequencing 



Bacterial artificial chromosome


Calcium-dependent protein kinases


Chromosome inversion


Copy-number variation


Chromosome segment substitution line


DNA transposable element


Genome-wide association study


Haplotype map


Horizontal transfer


Identical sequence region


Inversion deletion


Linkage disequilibrium


Long interspersed nuclear element


Long terminal repeat


Long terminal repeat retrotransposons


Mutator-like element


Million years ago


Nested association mapping


Nucleotide-binding site–leucine-rich repeat


Nested chromosome fusion


Next generation sequencing


Next–next generation sequencing


Oryza map alignment project


Presence–absence variation


Quantitative trait locus




Reference sequence


Restriction fragment-length-polymorphism


Recombinant inbred line


Single nucleotide polymorphism


Transposable element


Terminal inverted repeat


Whole genome duplication



The authors would like to thank Dr. Giacomo Morreale for critical reading of the manuscript and to acknowledge the funding support from the Italian Ministry of Agriculture: “Physical Mapping of wheat chromosome 5A.”


  1. 1.
    Goff, S. A., Ricke, D., Lan, T. H., Presting, G., Wang, R., Dunn, M., et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92–100.Google Scholar
  2. 2.
    Yu, J., Hu, S., Wang, J., Wong, G. K., Li, S., Liu, B., et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science, 296, 79–92.Google Scholar
  3. 3.
    International Rice Genome Sequencing Project. (2005). The map-based sequence of the rice genome. Nature, 436, 793–800.Google Scholar
  4. 4.
    Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., et al. (2009). The B73 maize genome: Complexity, diversity and dynamics. Science, 326, 1112–1115.Google Scholar
  5. 5.
    Gregory, T. R., Nicol, J. A., Tamm, H., Kullman, B., Kullman, K., Leitch, I. J., et al. (2007). Eukaryotic genome size databases. Nucleic Acids Research, 35, D332–D338.Google Scholar
  6. 6.
    Delseny, M., Hanb, B., & Ie Hsingc, Y. (2010). High throughput DNA sequencing: The new sequencing revolution. Plant Science, 179, 407–422.Google Scholar
  7. 7.
    Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D. A., Cestaro, A., Pruss, D., et al. (2007). A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One, 2, e1326.Google Scholar
  8. 8.
    Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., et al. (2009). The genome of the cucumber, Cucumis sativus L. Nature Genetics, 41, 1275–1281.Google Scholar
  9. 9.
    Feuillet, C., Leach, J. E., Rogers, J., Schnable, P. S., & Eversole, K. (2010). Crop genome sequencing: Lessons and rationales. Trends in Plant Science, 16, 77–88.Google Scholar
  10. 10.
    Hobert, O. (2010). The impact of whole genome sequencing on model system genetics: Get ready for the ride. Genetics, 184, 317–319.Google Scholar
  11. 11.
    Choulet, F., Wicker, T., Rustenholz, C., Paux, E., Salse, J., Leroy, P., 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.Google Scholar
  12. 12.
    Doležel, J., Kubaláková, M., Paux, E., Bartoš, J., & Feuillet, C. (2007). Chromosome-based genomics in the cereals. Chromosome Research, 15, 51–66.Google Scholar
  13. 13.
    Paux, E., Legeai, F., Guilhot, N., Adam-Blondon, A.-F., Alaux, M., Salse, J., et al. (2008). Physical mapping in large genomes: Accelerating anchoring of BAC contigs to genetic maps through in silico analysis. Functional and Integrative Genomics, 8, 29–32.Google Scholar
  14. 14.
    Stewart, C. N. (Ed.). (2009). Weedy and invasive plant genomics. Hoboken: Wiley-Blackwell.Google Scholar
  15. 15.
    Reinhardt, J. A., Baltrus, D. A., Nishimura, M. T., Jeck, W. R., Jones, C. D., & Dangl, J. L. (2009). De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. Oryzae. Genome Research, 19, 294–305.Google Scholar
  16. 16.
    Hancock, J. F. (2004). Plant evolution and the origin of crop species. Wallingford: CABI Publishing.Google Scholar
  17. 17.
    Chao, S., Sharp, P. J., & Gale, M. D. (1988). A linkage map of wheat homoeologous group 7 chromosomes using RFLP markers. In T. E. Miller & R. M. D. Koebner (Eds.), Proceeding of the 7th international wheat genetic symposium (pp. 493–498). Cambridge: IPSR.Google Scholar
  18. 18.
    Devos, K. M., & Gale, M. D. (1997). Comparative genetics in the grasses. Plant Molecular Biology, 35, 3–15.Google Scholar
  19. 19.
    Salse, J., Bolot, S., Throude, M., Jouffe, V., Piegu, B., Masood, U., et al. (2008). Identification and characterization of conserved duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell, 20, 11–24.Google Scholar
  20. 20.
    Abrouk, M., Murat, F., Pont, C., Messing, J., Jackson, S., Faraut, T., et al. (2010). Palaeogenomics of plants: Synteny based modelling of extinct ancestors. Trends in Plant Science, 15, 479–487.Google Scholar
  21. 21.
    Paterson, A. H., Freeling, M., Tang, H., & Wang, X. (2010). Insights from the comparison of plant genome sequences. Annual Review in Plant Biology, 61, 349–372.Google Scholar
  22. 22.
    Murat, F., Xu, J. H., Tannier, E., Abrouk, M., Guilhot, N., Pont, C., et al. (2010). Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Research, 20, 1545–1557.Google Scholar
  23. 23.
    Salse, J., Abrouk, M., Bolot, S., Guilhot, N., Courcelle, E., Faraut, T., et al. (2009). Reconstruction of monocotyledoneous proto-chromosomes reveals faster evolution in plants than in animals. Proceedings of National Academy of Science of USA, 106, 14908–14913.Google Scholar
  24. 24.
    Salse, J., & Feuillet, C. (2011). Paleogenomics in cereal: modeling of ancestor for modern species improvement. Comptes Rendus Biologies, 334, 205–211.Google Scholar
  25. 25.
    Kirkpatrick, M. (2010). How and why chromosome inversions evolve. PLoS Biology, 8, e1000501. doi: 10.1371/journal.pbio.1000501.Google Scholar
  26. 26.
    Jaillon, O., Aury, J. M., Noel, B., Policriti, A., Clepet, C., Casagrande, A., et al. (2007). The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449, 463–467.Google Scholar
  27. 27.
    Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., et al. (2010). Genome sequence of the palaeopolyploid soybean. Nature, 463, 178–183.Google Scholar
  28. 28.
    Velasco, R., Zharkikh, A., Affourtit, J., Dhingra, A., Cestaro, A., Kalyanaraman, A., et al. (2010). The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics, 42, 833–839.Google Scholar
  29. 29.
    Tuskan, G. A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., et al. (2006). The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313, 1596–1604.Google Scholar
  30. 30.
    The Potato Genome Sequencing Consortium. (2011). Genome sequence and analysis of the tuber crop potato. Nature, 475, 189–195.Google Scholar
  31. 31.
    Sax, K. (1933). The origin of the Pomoideae. Proceedings of the American Society of Horticultural Science, 30, 147–150.Google Scholar
  32. 32.
    Stebbins, G. L. (1985). Polyploidy, hybridization and the invasion of new habitats. Annals of the Missouri Botanical Garden, 72, 824–832.Google Scholar
  33. 33.
    Evans, R. C., & Campbell, C. S. (2002). The origin of the apple subfamily (Maloideae; Rosaceae) is clarified by DNA sequence data from duplicated GBSSI genes. American Journal of Botany, 89, 1478–1484.Google Scholar
  34. 34.
    Illa, E., Sargent, D. J., Lopez Girona, E., Bushakra, J., Cestaro, A., Crowhurst, R., et al. (2011). Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evolutionary Biology, 11, 9. doi: 10.1186/1471-2148-11-9.Google Scholar
  35. 35.
    Celton, J. M., Tustin, D. S., Chagne, D., & Gardiner, S. E. (2009). Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences. Tree Genetics and Genomes, 5, 93–107.Google Scholar
  36. 36.
    Jackson, S., & Chen, Z. J. (2010). Genomic and expression plasticity of polyploidy. Current Opinion in Plant Biology, 13, 153–159.Google Scholar
  37. 37.
    Schnable, J. C., Springer, N. M., & Freeling, M. (2011). Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proceedings of National Academy of Science of USA, 108, 4069–4074.Google Scholar
  38. 38.
    Throude, M., Bolot, S., Bosio, M. M., Pont, C., Sarda, X., Quraishi, U. M., et al. (2009). Structure and expression analysis of rice paleo-duplications. Nucleic Acids Research, 37, 1248–1259.Google Scholar
  39. 39.
    Paterson, A. H., Bowers, J. E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., et al. (2009). The Sorghum bicolor genome and the diversification of grasses. Nature, 457, 551–556.Google Scholar
  40. 40.
    Mizukami, Y., & Ma, H. (1992). Ectopic expression of the floral homeotic gene AGAMOUS in transgenic Arabidopsis plants alters floral organ identity. Cell, 71, 119–131.Google Scholar
  41. 41.
    Martinez-Castilla, L. P., & Alvarez-Buylla, E. R. (2003). Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny. Proceedings of National Academy of Science of USA, 100, 13407–13412.Google Scholar
  42. 42.
    Moore, R. C., & Purugganan, M. D. (2005). The evolutionary dynamics of plant duplicate genes. Current Opinion in Plant Biology, 8, 122–128.Google Scholar
  43. 43.
    Geng, S., Zhao, Y., Tang, L., Zhang, R., Sun, M., Guo, H., et al. (2011). Molecular evolution of two duplicate CDPK genes CPK7 and CPK12 in grasses species: A case study in wheat (Triticum aestivum L.). Gene, 475, 94–103.Google Scholar
  44. 44.
    Li, A. L., Zhu, Y.-F., Tan, X.-M., Wang, X., Wie, B., Guo, H.-Z., et al. (2008). Evolutionary and functional study of the CDPK gene family in wheat (Triticum aestivum L.). Plant Molecular Biology, 66, 429–443.Google Scholar
  45. 45.
    Sun, H. Z., & Ge, S. (2010). Molecular evolution of the duplicated TFIIAγ genes in Oryzeae and its relatives. BMC Evolutionary Biology, 10, 128.Google Scholar
  46. 46.
    Iyer, A. S., & McCouch, S. R. (2004). The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Molecular Plant Microbe Interaction, 17, 1348–1354.Google Scholar
  47. 47.
    Van de Peer, Y., Maere, S., & Meyer, A. (2009). The evolutionary significance of ancient genome duplications. Nature Reviews Genetics, 10, 725–732.Google Scholar
  48. 48.
    Flagel, L. E., & Wende, J. F. (2009). Gene duplication and evolutionary novelty in plants. New Phytologist, 183, 557–564.Google Scholar
  49. 49.
    Roulin, A., Piegu, B., Wing, R. A., & Panaud, O. (2008). Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza. Plant Journal, 53, 950–959.Google Scholar
  50. 50.
    Goicoechea, J. L., Ammiraju, J. S. S., Marri, P. R., Chen, M., Jackson, S., Yu, Y., et al. (2010). The future of rice genomics: Sequencing the collective Oryza genome. Rice, 3, 89–97.Google Scholar
  51. 51.
    Korbel, J. O., Abyzov, A., Mu, X. J., Carriero, N., Cayting, P., Zhang, Z., et al. (2009). PEMer: A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biology, 10, R23.Google Scholar
  52. 52.
    Kidd, J. M., Cooper, G. M., Donahue, W. F., Hayden, H. S., Sampas, N., Graves, T., et al. (2008). Mapping and sequencing of structural variation from eight human genomes. Nature, 453, 56–64.Google Scholar
  53. 53.
    Ammiraju, J. S. S., Lu, F., Sanyal, A., Yu, Y., Song, X., Jiang, N., et al. (2008). Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell, 20, 3191–3209.Google Scholar
  54. 54.
    Ammiraju, J. S. S., Zuccolo, A., Yu, Y., Song, X., Piegu, B., Chevalier, F., et al. (2007). Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant Journal, 52, 342–351.Google Scholar
  55. 55.
    Ma, J., Devos, K. M., & Bennetzen, J. L. (2004). Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Research, 14, 860–869.Google Scholar
  56. 56.
    Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., et al. (2007). A unified classification system for eukaryotic transposable elements. Nature, 8, 973–982.Google Scholar
  57. 57.
    Grover, C., & Wendel, J. F. (2010). Recent insights into mechanisms of genome size change in plants. Journal of Botany, 164, 10–15.Google Scholar
  58. 58.
    Du, J., Tian, Z., Hans, C. S., Laten, H. M., Cannon, S. B., Jackson, S. A., et al. (2010). Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant Journal, 63, 584–598.Google Scholar
  59. 59.
    Tenaillon, M. I., Hollister, J. D., & Gaut, B. S. (2010). A triptych of the evolution of plant transposable elements. Trends in Plant Science, 15, 471–478.Google Scholar
  60. 60.
    Shulaev, V., Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., et al. (2011). The genome of woodland strawberry (Fragaria vesca). Nature Genetics, 43, 109–116.Google Scholar
  61. 61.
    Park, M., Jo, S., Kwon, J.-K., Park, J., Ahn, J. H., Kim, S., et al. (2011). Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements. BMC Genomics, 12, e85.Google Scholar
  62. 62.
    Flutre, T., Duprat, E., Feuillet, C., & Quesneville, H. (2011). Considering transposable element diversification in de novo annotation approaches. PLoS One, 6, 1–15.Google Scholar
  63. 63.
    Devos, K. M. (2010). Grass genome organization and evolution. Current Opinion in Plant Biology, 13, 139–145.Google Scholar
  64. 64.
    Vogel, J. P., Garvin, D. F., Mockler, T. C., Schmutz, J., Rokhsar, D., Bevan, M. W., et al. (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463, 763–768.Google Scholar
  65. 65.
    Hanada, K., Kuromori, T., Myouga, F., Toyoda, T., & Shinozaki, K. (2009). Increased expression and protein divergence in duplicate genes is associated with morphological diversification. PLoS Genetics, 5, 1–7.Google Scholar
  66. 66.
    Yang, L., & Bennetzen, J. L. (2009). Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proceedings of National Academy of Science of USA, 106, 19922–19927.Google Scholar
  67. 67.
    Morgante, M., Brunner, S., Pea, G., Fengler, K., Zuccolo, A., & Rafalski, A. (2005). Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nature Genetics, 37, 997–1002.Google Scholar
  68. 68.
    Kapitonov, V. V., & Jurka, J. (2007). Helitrons on a roll: Eukaryotic rolling-circle transposons. Trends in Genetics, 23, 521–529.Google Scholar
  69. 69.
    Morgante, M. (2006). Plant genome organisation and diversity: The year of the junk!. Current Opinion in Biotechnology, 17, 168–173.Google Scholar
  70. 70.
    Lisch, D. (2009). Epigenetic regulation of transposable elements in plants. Annual Review in Plant Biology, 60, 43–66.Google Scholar
  71. 71.
    Ding, Y., Wang, X., Su, L., Zhai, J., Cao, S., Zhang, D., et al. (2007). SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. Plant Cell, 19, 9–22.Google Scholar
  72. 72.
    Girard, A., & Hannon, G. J. (2008). Conserved themes in small-RNA-mediated transposon control. Trends Cell Biology, 18, 136–148.Google Scholar
  73. 73.
    Cantu, D., Vanzetti, L. S., Sumner, A., Dubcovsky, M., Matvienko, M., Distelfeld, A., et al. (2010). Small RNAs, DNA methylation and transposable elements in wheat. BMC Genomics, 11, 1–15.Google Scholar
  74. 74.
    Aprile, A., Mastrangelo, A. M., De Leonardis, A. M., Galiba, G., Roncaglia, E., Ferrari, F., et al. (2009). Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome. BMC Genomics, 10, art n. 279.Google Scholar
  75. 75.
    Parisod, C., Alix, K., Just, J., Petit, M., Sarilar, V., Mhiri, C., et al. (2010). Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytologist, 186, 37–45.Google Scholar
  76. 76.
    Bock, R. (2009). The give-and-take of DNA: Horizontal gene transfer in plants. Trends in Plant Science, 15, 11–22.Google Scholar
  77. 77.
    Loreto, E. L., Carareto, C. M., & Capy, P. (2008). Revisiting horizontal transfer of transposable elements in Drosophila. Heredity, 100, 545–554.Google Scholar
  78. 78.
    Roulin, A., Piegu, B., Fortune, P. M., Sabot, F., D’Hont, A., Manicacci, D., et al. (2009). Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae. BMC Evolutionary Biology, 9, art n. 58.Google Scholar
  79. 79.
    Diao, Y., Qi, Y., Ma, Y., Xia, A., Sharakhov, I., Chen, X., et al. (2011). Next-generation sequencing reveals recent horizontal transfer of a DNA transposon between divergent mosquitoes. PLoS One, 106, e16743.Google Scholar
  80. 80.
    Morgante, M., De Paoli, E., & Radovic, S. (2007). Transposable elements and the plant pan-genomes. Current Opinion in Plant Biology, 10, 149–155.Google Scholar
  81. 81.
    Mira, A., Martín-Cuadrado, A. B., D’Auria, G., & Rodríguez-Valera, F. (2010). The bacterial pan-genome: A new paradigm in microbiology. International Microbiology, 13, 45–57.Google Scholar
  82. 82.
    Brunner, S., Fengler, K., Morgante, M., Tingey, S., & Rafalski, A. (2005). Evolution of DNA sequence non homologies among maize inbreds. Plant Cell, 17, 343–360.Google Scholar
  83. 83.
    Wang, Q., & Dooner, H. K. (2006). Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proceedings of National Academy of Science of USA, 103, 17644–17649.Google Scholar
  84. 84.
    Yu, J., Wang, J., Lin, W., Li, S., Li, H., Zhou, J., et al. (2005). The genomes of Oryza sativa: A history of duplications. PLoS Biology, 3, 266–281.Google Scholar
  85. 85.
    Scherrer, B., Isidore, E., Klein, P., Kim, J.-S., Bellec, A., et al. (2005). Large intraspecific haplotype variability at the Rph7 locus results from rapid and recent divergence in the barley genome. Plant Cell, 17, 361–374.Google Scholar
  86. 86.
    Borrelli, G. M., De Vita, P., Mastrangelo, A. M., & Cattivelli, L. (2009). Molecular plant breeding: Modern approaches for an old topic. In O. V. Sadras & F. D. Calderoni (Eds.), Crop physiology: Application for genetic improvement and agronomy (pp. 327–354). London: Academic Press.Google Scholar
  87. 87.
    Varshney, R. K., Hoisington, D. A., & Tyagi, A. K. (2006). Advances in cereal genomics and applications in crop breeding. Trends in Biotechnology, 24, 490–499.Google Scholar
  88. 88.
    Rounsley, S. D., & Last, R. L. (2010). Shotguns and SNPs: How fast and cheap sequencing is revolutionizing plant biology. Plant Journal, 61, 922–927.Google Scholar
  89. 89.
    Hudson, M. E. (2008). Sequencing breakthroughs for genomic ecology and evolutionary biology. Molecular Ecology Resources, 8, 3–17.Google Scholar
  90. 90.
    Gore, M. A., Chia, J. M., Elshire, R. J., Sun, Q., Ersoz, E. S., Hurwitz, B. L., et al. (2009). A first-generation haplotype map of maize. Science, 326, 1115–1117.Google Scholar
  91. 91.
    Dempewwolf, H. (2010). Getting domestication straight: ramosa1 in maize. Molecular Ecology, 19, 1267–1269.Google Scholar
  92. 92.
    Myles, S., Peiffer, J., Brown, P. J., Ersoz, E. S., Zhang, Z., Costich, D. E., et al. (2009). Association mapping: Critical considerations shift from genotyping to experimental design. The Plant Cell, 21, 2194–2202.Google Scholar
  93. 93.
    Xie, W. B., Feng, Q., Yu, H. H., Huang, X. H., Zhao, Q., Xing, Y. Z., et al. (2010). Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proceedings of National Academy of Science of USA, 107, 10578–10583.Google Scholar
  94. 94.
    McNally, K., Kevin, L., Childs, K. L., Bohnert, R., Davidson, R. M., Zhao, K., et al. (2009). Genome wide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of National Academy of Science of USA, 106, 12273–12278.Google Scholar
  95. 95.
    Wu, X., Ren, C., Joshi, T., Vuong, T., Xu, D., & Nguyen, H. H. (2010). SNP discovery by high-throughput sequencing in soybean. BMC Genomics, 11, 469–479.Google Scholar
  96. 96.
    Huang, X. H., Feng, Q., Qian, Q., Zhao, Q., Wang, L., Wang, A. H., et al. (2009). High-throughput genotyping by whole-genome resequencing. Genome Research, 19, 1068–1076.Google Scholar
  97. 97.
    Huang, X., Wei, X., Sang, T., Zhao, Q., Feng, Q., Zhao, Y., et al. (2010). Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics, 42, 961–967.Google Scholar
  98. 98.
    Lam, H.-M., Xu, X., Liu, X., Chen, W., Yang, G., Wong, F.-L., et al. (2010). Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics, 42, 1053–1059.Google Scholar
  99. 99.
    Myles, S., Chia, J.-M., Hurwitz, B., Simon, C., Zhong, G. Y., Buckler, E., et al. (2010). Rapid genomic characterization of the genus Vitis. PLoS One, 5, e8219.Google Scholar
  100. 100.
    Ossowski, S., Schneeberger, K., Lucas-Lledo, J. I., Warthmann, N., Clark, R. M., Shaw, R., et al. (2010). The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science, 327, 92–94.Google Scholar
  101. 101.
    Uchida, N., Sakamoto, T., Kurata, T., & Tasaka, M. (2011). Identification of EMS-induced causal mutations in a non-reference Arabidopsis thaliana accession by whole genome sequencing. Plant Cell Physiology, 52, 716–722.Google Scholar
  102. 102.
    Rigola, D., van Oeveren, J., Janssen, A., Bonné, A., Schneiders, H., van der Poel, H. J. A., et al. (2009). High-throughput detection of induced mutations and natural variation using KeyPoint technology. PLoS One, 4, e4761.Google Scholar
  103. 103.
    Martinez-Zapater, J. M., Carmona, M. J., Dìaz-Riquelme, J., Fernàndez, L., & Lijavetzky, D. (2010). Grapevine genetics after the genome sequence: Challenges and limitations. Australian Journal of Grape and Wine Research, 16, 33–46.Google Scholar
  104. 104.
    Allendorf, F. W., Hohenlohe, P. A., & Luikart, G. (2010). Genomics and the future of conservation genetics. Nature Genetics, 11, 697–709.Google Scholar
  105. 105.
    Qin, J., Li, R., Raes, J., Arumugam, M., Solvsten Burgdorf, K., Manichanh, C., et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59–67.Google Scholar
  106. 106.
    Lai, J., Li, R., Xu, X., Jin, W., Xu, M., Zhao, H., et al. (2010). Genome-wide patterns of genetic variation among elite maize inbred lines. Nature Genetics, 42, 1027–1031.Google Scholar
  107. 107.
    Cannon, S. B., May, G. D., & Jackson, S. A. (2009). Three sequenced legume genomes and many crop species: Rich opportunities for translational genomics. Plant Physiology, 151, 970–977.Google Scholar
  108. 108.
    Swanson-Wagner, R. A., Eichten, S. R., Kumari, S., Tiffin, P., Stein, J. C., Ware, D. et al. (2010). Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Research. doi: 10.1101/gr.109165.110.
  109. 109.
    Vielle-Calzada, J.-P., de la Vega, O. M., Hernández-Guzmán, G., Ibarra-Laclette, E., Alvarez-Mejía, C., Vega-Arreguín, J. C., et al. (2009). The Palomero genome suggests metal effects on domestication. Science, 326, 1078.Google Scholar
  110. 110.
    Springer, N. M., Ying, K., Fu, Y., Ji, T., Yeh, C.-T., Jia, Y., et al. (2009). Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genetics, 5, e1000734.Google Scholar
  111. 111.
    Schneeberger, K., & Weigel, D. (2011). Fast-forward genetics enabled by new sequencing technologies. Trends in Plant Science, 16, 282–288.Google Scholar
  112. 112.
    Faccioli, P., Stanca, A. M., Morcia, C., & Terzi, V. (2009). From DNA sequence to plant phenotype: Bioinformatics meets crop science. Current Bioinformatics, 4, 173–176.Google Scholar
  113. 113.
    Edwards, D., & Batley, J. (2010). Plant genome sequencing: Applications for crop improvement. Plant Biotechnology Journal, 8, 2–9.Google Scholar
  114. 114.
    Sonah, H., Deshmukh, R. K., Singh, V. P., Gupta, D. K., Singh, N. K., & Sharma, T. R. (2011). Genomic resources in horticultural crops: Status, utility and challenges. Biotechnology Advances, 29, 199–209.Google Scholar
  115. 115.
    Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J. H., et al. (2008). The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature, 452, 991–996.Google Scholar
  116. 116.
    Chan, A., Crabtree, J., Zhao, Q., Lorenzi, H., Orvis, J., Puiu, D., et al. (2010). Draft genome sequence of the oilseed species Ricinus communis. Nature Biotechnology, 28, 951–956.Google Scholar
  117. 117.
    Argout, X., Salse, J., Aury, J.-M., Guiltinan, M. J., Droc, G., Gouzy, J., et al. (2011). The genome of Theobroma cacao. Nature Genetics, 43, 101–108.Google Scholar
  118. 118.
    Yang, B., Xu, X., Guo, X., Li, R., & Wang, J. (2010). Whole genome resequencing for capturing biodiversity, rediscovering domestication and beyond. ASA, CSSA, and SSSA international annual meetings, Long Beach, CA.Google Scholar
  119. 119.
    Xu, J., Zhao, Q., Du, P., Xu, C., Wang, B., Feng, Q., et al. (2010). Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.). BMC Genomics, 11, 656–669.Google Scholar
  120. 120.
    Lijavetzky, D., Cabezas, J. A., Ibáñez, A., Rodríguez, V., & Martínez-Zapater, J. (2007). High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology. BMC Genomics, 8, 424–434.Google Scholar
  121. 121.
    Proost, S., Pattyn, P., Gerats, T., & Van de Peer, Y. (2011). Journey through the past: 150 million years of plant genome evolution. The Plant Journal, 66, 58–65.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Delfina Barabaschi
    • 1
  • Davide Guerra
    • 2
  • Katia Lacrima
    • 2
  • Paolo Laino
    • 2
  • Vania Michelotti
    • 2
  • Simona Urso
    • 2
  • Giampiero Valè
    • 2
    • 3
  • Luigi Cattivelli
    • 2
  1. 1.CRA, Viticolture Research CentreSuseganaItaly
  2. 2.CRA, Genomics Research CentreFiorenzuola d’ArdaItaly
  3. 3.CRA, Rice Research UnitVercelliItaly

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