Interdisciplinary Bio Central

Korean Society for Bioinformatics (한국생명정보학회)
권호 표지
DOI QR코드

DOI QR Code

Systematic Development of Tomato BioResources in Japan

  • Ariizumi, Tohru (Graduate School of Life and Environmental Sciences, University of Tsukuba) ;
  • Aoki, Koh (Kazusa DNA Research Institute) ;
  • Ezura, Hiroshi (Graduate School of Life and Environmental Sciences, University of Tsukuba)
  • Received : 2010.12.22
  • Accepted : 2011.01.05
  • Published : 2011.03.31
Download PDF
⟨ Previous Next ⟩

Abstract

Recently, with the progress of genome sequencing, materials and information for research on tomato (Solanum lycopersicum) have been systematically organized. Tomato genomics tools including mutant collections, genome sequence information, full-length cDNA and metabolomic datasets have become available to the research community. In Japan, the National BioResource Project Tomato (NBRP Tomato) was launched in 2007, with aims to collect, propagate, maintain and distribute tomato bioresources to promote functional genomics studies in tomato. To this end, the dwarf variety Micro-Tom was chosen as a core genetic background, due to its many advantages as a model organism. In this project, a total of 12,000 mutagenized lines, consisting of 6000 EMS-mutagenized and 6000 gamma-ray irradiated M2 seeds, were produced, and the M3 offspring seeds derived from 2236 EMS-mutagenized M2 lines and 2700 gamma-ray irradiated M2 lines have been produced. Micro-Tom mutagenized lines in the M3 generation and monogenic Micro-Tom mutants are provided from NBRP tomato. Moreover, tomato cultivated varieties and its wild relatives, both of these are widely used for experimental study, are available. In addition to these bioresources, NBRP Tomato also provides 13,227 clones of full-length cDNA which represent individual transcripts non-redundantly. In this paper, we report the current status of NBRP Tomato and its future prospects.

Keywords

References

  1. Tanksley, S.D. (2004). The genetic, developmental, and molecular bases of fruit size and shape variation in tomato. Plant Cell 16 Suppl, S181-189. https://doi.org/10.1105/tpc.018119
  2. Yamazaki, Y., Akashi, R., Banno, Y., Endo, T., Ezura, H., Fukami-Kobayashi, K., Inaba, K., Isa, T., Kamei, K., Kasai, F., et al. (2010). NBRP databases: databases of biological resources in Japan. Nucleic Acids Res 38, D26-32. https://doi.org/10.1093/nar/gkp996
  3. Emmanuel, E., and Levy, A.A. (2002). Tomato mutants as tools for functional genomics. Curr Opin Plant Biol 5, 112-117. https://doi.org/10.1016/S1369-5266(02)00237-6
  4. Pnueli, L., Carmel-Goren, L., Hareven, D., Gutfinger, T., Alvarez, J., Ganal, M., Zamir, D., and Lifschitz, E. (1998). The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development 125, 1979-1989.
  5. Iijima, Y., Nakamura, Y., Ogata, Y., Tanaka, K., Sakurai, N., Suda, K., Suzuki, T., Suzuki, H., Okazaki, K., Kitayama, M., et al. (2008). Metabolite annotations based on the integration of mass spectral information. Plant J 54, 949-962. https://doi.org/10.1111/j.1365-313X.2008.03434.x
  6. Van der Hoeven, R., Ronning, C., Giovannoni, J., Martin, G., and Tanksley, S. (2002). Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell 14, 1441-1456. https://doi.org/10.1105/tpc.010478
  7. Scott, J.W., and Harbaugh, B.K. (1989). Micro-Tom A miniature dwarf tomato. Agricultural Experiment Station, Institute of Food and Agricultural Sciences, University of Florida Circular S370, 1-6.
  8. Meissner, R., Jacobson, Y., Melmed, S., Levyatuv, S., Shalev, G., Ashri, A., Elkind, Y., and Levy, A.A. (1997). A new model system for tomato genetics. Plant J 12, 1465-1472. https://doi.org/10.1046/j.1365-313x.1997.12061465.x
  9. Dan, Y., Yan, H., Munyikwa, T., Dong, J., Zhang, Y., and Armstrong, C.L. (2006). MicroTom--a high-throughput model transformation system for functional genomics. Plant Cell Rep 25, 432-441. https://doi.org/10.1007/s00299-005-0084-3
  10. Sun, H.J., Uchii, S., Watanabe, S., and Ezura, H. (2006). A highly efficient transformation protocol for Micro-Tom, a model cultivar for tomato functional genomics. Plant Cell Physiol 47, 426-431. https://doi.org/10.1093/pcp/pci251
  11. Mathews, H., Clendennen, S.K., Caldwell, C.G., Liu, X.L., Connors, K., Matheis, N., Schuster, D.K., Menasco, D.J., Wagoner, W., Lightner, J., et al. (2003). Activation tagging in tomato identifies a transcriptional regulator of anthocyanin biosynthesis, modification, and transport. Plant Cell 15, 1689-1703. https://doi.org/10.1105/tpc.012963
  12. Bishop, G.J., Harrison, K., and Jones, J.D. (1996). The tomato Dwarf gene isolated by heterologous transposon tagging encodes the first member of a new cytochrome P450 family. Plant Cell 8, 959-969. https://doi.org/10.1105/tpc.8.6.959
  13. Bishop, G.J., Nomura, T., Yokota, T., Harrison, K., Noguchi, T., Fujioka, S., Takatsuto, S., Jones, J.D., and Kamiya, Y. (1999). The tomato DWARF enzyme catalyses C-6 oxidation in brassinosteroid biosynthesis. Proc Natl Acad Sci U S A 96, 1761-1766. https://doi.org/10.1073/pnas.96.4.1761
  14. Marti, E., Gisbert, C., Bishop, G.J., Dixon, M.S., and Garcia-Martinez, J.L. (2006). Genetic and physiological characterization of tomato cv. Micro-Tom. J Exp Bot 57, 2037-2047. https://doi.org/10.1093/jxb/erj154
  15. Matsukura, C., Aoki, K., Fukuda, N., Mizoguchi, T., Asamizu, E., Saito, T., Shibata, D., and Ezura, H. (2008). Comprehensive resources for tomato functional genomics based on the miniature model tomato micro-tom. Curr Genomics 9, 436-443. https://doi.org/10.2174/138920208786241225
  16. Watanabe, S., Mizoguchi, T., Aoki, K., Kubo, Y., Mori, H., Imanishi, S., Yamazaki, Y., Shibata, D., and Ezura, H. (2007). Ethylmethanesulfonate (EMS) mutagenesis of Solanum lycopersicum cv. Micro-Tom for large-scale mutant screens. Plant Biotechnology 24, 33-38. https://doi.org/10.5511/plantbiotechnology.24.33
  17. Till, B.J., Zerr, T., Comai, L., and Henikoff, S. (2006). A protocol for TILLING and Ecotilling in plants and animals. Nat Protoc 1, 2465-2477 https://doi.org/10.1038/nprot.2006.329
  18. Gady, A.L., Hermans, F.W., Van de Wal, M.H., van Loo, E.N., Visser, R.G., and Bachem, C.W. (2009). Implementation of two high through-put techniques in a novel application: detecting point mutations in large EMS mutated plant populations. Plant Methods 5, 13. https://doi.org/10.1186/1746-4811-5-13
  19. Piron, F., Nicolai, M., Minoia, S., Piednoir, E., Moretti, A., Salgues, A., Zamir, D., Caranta, C., and Bendahmane, A. (2010). An induced mutation in tomato eIF4E leads to immunity to two potyviruses. PLoS One 5, e11313. https://doi.org/10.1371/journal.pone.0011313
  20. Rigola, D., van Oeveren, J., Janssen, A., Bonne, A., Schneiders, H., van der Poel, H.J., van Orsouw, N.J., Hogers, R.C., de Both, M.T., and van Eijk, M.J. (2009). High-throughput detection of induced mutations and natural variation using KeyPoint technology. PLoS One 4, e4761. https://doi.org/10.1371/journal.pone.0004761
  21. Sreelakshmi, Y., Gupta, S., Bodanapu, R., Chauhan, V.S., Hanjabam, M., Thomas, S., Mohan, V., Sharma, S., Srinivasan, R., and Sharma, R. (2010). NEATTILL: A simplified procedure for nucleic acid extraction from arrayed tissue for TILLING and other high-throughput reverse genetic applications. Plant Methods 6, 3. https://doi.org/10.1186/1746-4811-6-3
  22. Aoki, K., Yano, K., Suzuki, A., Kawamura, S., Sakurai, N., Suda, K., Kurabayashi, A., Suzuki, T., Tsugane, T., Watanabe, M., et al. (2010). Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. BMC Genomics 11, 210. https://doi.org/10.1186/1471-2164-11-210
  23. Ozaki, S., Ogata, Y., Suda, K., Kurabayashi, A., Suzuki, T., Yamamoto, N., Iijima, Y., Tsugane, T., Fujii, T., Konishi, C., et al. (2010). Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. DNA Res 17, 105-116. https://doi.org/10.1093/dnares/dsq002
  24. Mueller, L.A., Solow, T.H., Taylor, N., Skwarecki, B., Buels, R., Binns, J., Lin, C., Wright, M.H., Ahrens, R., Wang, Y., et al. (2005). The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. Plant Physiol 138, 13101317.
  25. Mueller, L.A., Tanksley, S.D., Giovannoni, J.J., van Eck, J., Stack, S., Choi, D., Kim, B.D., Chen, M., Cheng, Z., Li, C., et al. (2005). The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL). Comp Funct Genomics 6, 153-158. https://doi.org/10.1002/cfg.468
  26. Minoia, S., Petrozza, A., D'Onofrio, O., Piron, F., Mosca, G., Sozio, G., Cellini, F., Bendahmane, A., and Carriero, F. (2010). A new mutant genetic resource for tomato crop improvement by TILLING technology. BMC Res Notes 3, 69. https://doi.org/10.1186/1756-0500-3-69
  27. Menda, N., Semel, Y., Peled, D., Eshed, Y., and Zamir, D. (2004). In silico screening of a saturated mutation library of tomato. Plant J 38, 861-872. https://doi.org/10.1111/j.1365-313X.2004.02088.x

Cited by

  1. Red/Far Red Light Controls Arbuscular Mycorrhizal Colonization via Jasmonic Acid and Strigolactone Signaling 2015, https://doi.org/10.1093/pcp/pcv135
  2. Functional genomics of tomato in a post-genome-sequencing phase vol.63, pp.1, 2013, https://doi.org/10.1270/jsbbs.63.14
  3. From randomly to inevitable: Accelerating tomato breeding by comprehensive tools and information vol.63, pp.1, 2013, https://doi.org/10.1270/jsbbs.63.1
  4. Technological progress in Japanese horticultural production and its academic aspects pp.1129, 2016, https://doi.org/10.17660/ActaHortic.2016.1129.2
  5. SABRE2: A Database Connecting Plant EST/Full-Length cDNA Clones with Arabidopsis Information vol.55, pp.1, 2014, https://doi.org/10.1093/pcp/pct177
  6. Structural analyses of the tomato genome vol.30, pp.3, 2011, https://doi.org/10.5511/plantbiotechnology.13.0707a
  7. Mutation Breeding in Tomato: Advances, Applicability and Challenges vol.8, pp.5, 2019, https://doi.org/10.3390/plants8050128