Current challenges and future potential of tomato breeding using omics approaches

Breeding Science

Volumn 63, Issue 1, 2013, Pages 31-41

  Kusano, Miyako ^a,b   Fukushima, Atsushi ^a  

^a Elements Chemistry Laboratory   (Japan)

^b YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

Biochemical trait; Coexpression analysis; Metabolomics; Multinetwork; Solanum lycopersicum; Tomato; Transcriptomics

Indexed keywords

LYCOPERSICON ESCULENTUM;

EID: 84876896152     PISSN: 13447610     EISSN: 13473735     Source Type: Journal    
DOI: 10.1270/jsbbs.63.31     Document Type: Review

References (127)

1. Abel, S., M.D. Nguyen and A. Theologis (1995) The PS-IAA4/5-like family of early auxin-inducible mRNAs in Arabidopsis thaliana. J. Mol. Biol. 251: 533-549.
2. Adato, A., T. Mandel, S. Mintz-Oron, I. Venger, D. Levy, M. Yativ, E. Dominguez, Z.H. Wang, R.C.H. De Vos, R. Jetter et al. (2009) Fruit-surface flavonoid accumulation in tomato is controlled by a SIMYB12-regulated transcriptional network. PLoS Genet. 5.
3. Alkan, N., R. Fluhr and D. Prusky (2012) Ammonium secretion during Colletotrichum coccodes infection modulates salicylic and jasmonic acid pathways of ripe and unripe tomato fruit. Mol. Plant Microbe Interact. 25: 85-96.
4. Allen, E., A. Moing, T.M. Ebbels, M. Maucourt, A.D. Tomos, D. Rolin and M.A. Hooks (2010) Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis. BMC Syst. Biol. 4: 62.
5. Altaf-Ul-Amin, M., Y. Shinbo, K. Mihara, K. Kurokawa and S. Kanaya (2006) Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 7: 207.
6. Aoki, K., Y. Ogata and D. Shibata (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol. 48: 381-390.
7. Aoki, K., K. Yano, A. Suzuki, S. Kawamura, N. Sakurai, K. Suda, A. Kurabayashi, T. Suzuki, T. Tsugane, M. Watanabe 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.
8. Balaji, V., M. Mayrose, O. Sherf, J. Jacob-Hirsch, R. Eichenlaub, N. Iraki, S. Manulis-Sasson, G. Rechavi, I. Barash and G. Sessa (2008) Tomato transcriptional changes in response to Clavibacter michiganensis subsp. michiganensis reveal a role for ethylene in disease development. Plant Physiol. 146: 1797-1809.
9. Barrett, T., D.B. Troup, S.E. Wilhite, P. Ledoux, D. Rudnev, C. Evangelista, I.F. Kim, A. Soboleva, M. Tomashevsky, K.A. Marshall et al. (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res. 37: D885-890.
10. Bernard, S.M. and D.Z. Habash (2009) The importance of cytosolic glutamine synthetase in nitrogen assimilation and recycling. New Phytol. 182: 608-620.
11. Biais, B., J.W. Allwood, C. Deborde, Y. Xu, M. Maucourt, B. Beauvoit, W.B. Dunn, D. Jacob, R. Goodacre, D. Rolin et al. (2009) 1H NMR, GC-EI-TOFMS, and data set correlation for fruit metabolomics: application to spatial metabolite analysis in melon. Anal. Chem. 81: 2884-2894.
12. Bovy, A., E. Schijlen and R.D. Hall (2007) Metabolic engineering of flavonoids in tomato (Solanum lycopersicum): the potential for metabolomics. Metabolomics 3: 399-412.
13. Buer, C.S., N. Imin and M.A. Djordjevic (2010) Flavonoids: new roles for old molecules. J. Integr. Plant Biol. 52: 98-111.
14. Calvenzani, V., M. Martinelli, V. Lazzeri, D. Giuntini, C. Dall'Asta, G. Galaverna, C. Tonelli, A. Ranieri and K. Petroni (2010) Response of wild-type and high pigment-1 tomato fruit to UV-B depletion: flavonoid profiling and gene expression. Planta 231: 755-765.
15. Cantu, D., B. Blanco-Ulate, L. Yang, J.M. Labavitch, A.B. Bennett and A.L. Powell (2009) Ripening-regulated susceptibility of tomato fruit to Botrytis cinerea requires NOR but not RIN or ethylene. Plant Physiol. 150: 1434-1449.
16. Carmi, N., Y. Salts, B. Dedicova, S. Shabtai and R. Barg (2003) Induction of parthenocarpy in tomato via specific expression of the rolB gene in the ovary. Planta 217: 726-735.
17. Carreno-Quintero, N., A. Acharjee, C. Maliepaard, C.W. Bachem, R. Mumm, H. Bouwmeester, R.G. Visser and J.J. Keurentjes (2012) Untargeted metabolic quantitative trait loci analyses reveal a relationship between primary metabolism and potato tuber quality. Plant Physiol. 158: 1306-1318.
18. Chikina, M.D. and O.G. Troyanskaya (2011) Accurate quantification of functional analogy among close homologs. PLoS Comput. Biol. 7: e1001074.
19. Choi, J.K., U. Yu, O.J. Yoo and S. Kim (2005) Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 21: 4348-4355.
20. Davidson, R.M., M. Gowda, G. Moghe, H. Lin, B. Vaillancourt, S.H. Shiu, N. Jiang and C. Robin Buell (2012) Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. Plant J. 71: 492-502.
21. de la Fuente, A., N. Bing, I. Hoeschele and P. Mendes (2004) Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics 20: 3565-3574.
22. de la Fuente, A. (2010) From 'differential expression' to 'differential networking'-identification of dysfunctional regulatory networks in diseases. Trends Genet. 26: 326-333.
23. Deshmukh, A.P., A.J. Simpson and P.G. Hatcher (2003) Evidence for cross-linking in tomato cutin using HR-MAS NMR spectroscopy. Phytochemistry 64: 1163-1170.
24. Diaz, P., M. Betti, D.H. Sanchez, M.K. Udvardi, J. Monza and A.J. Marquez (2010) Deficiency in plastidic glutamine synthetase alters proline metabolism and transcriptomic response in Lotus japonicus under drought stress. New Phytol. 188: 1001-1013.
25. Druka, A., E. Potokina, Z.W. Luo, N. Jiang, X.W. Chen, M. Kearsey and R. Waugh (2010) Expression quantitative trait loci analysis in plants. Plant Biotechnol. J. 8: 10-27.
26. Ehlting, J., V. Sauveplane, A. Olry, J.F. Ginglinger, N.J. Provart and D. Werck-Reichhart (2008) An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana. BMC Plant Biol. 8: 47.
27. Fei, Z., J.G. Joung, X. Tang, Y. Zheng, M. Huang, J.M. Lee, R. McQuinn, D.M. Tieman, R. Alba, H.J. Klee et al. (2011) Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Res. 39: D1156-1163.
28. Ficklin, S.P. and F.A. Feltus (2011) Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice. Plant Physiol. 156: 1244-1256.
29. Field, B. and A.E. Osbourn (2008) Metabolic diversification-independent assembly of operon-like gene clusters in different plants. Science 320: 543-547.
30. Field, B., A.S. Fiston-Lavier, A. Kemen, K. Geisler, H. Quesneville and A.E. Osbourn (2011) Formation of plant metabolic gene clusters within dynamic chromosomal regions. Proc. Natl. Acad. Sci. USA 108: 16116-16121.
31. Fos, M., K. Proano, F. Nuez and J.L. Garcia-Martinez (2001) Role of gibberellins in parthenocarpic fruit development induced by the genetic system pat-3/pat-4 in tomato. Physiol. Plant. 111: 545-550.
32. Fukushima, A., M. Wada, S. Kanaya and M. Arita (2008) SVD-based anatomy of gene expressions for correlation analysis in Arabidopsis thaliana. DNA Res. 15: 367-374.
33. Fukushima, A., M. Kusano, H. Redestig, M. Arita and K. Saito (2009a) Integrated omics approaches in plant systems biology. Curr. Opin. Chem. Biol. 13: 532-538.
34. Fukushima, A., S. Kanaya and M. Arita (2009b) Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach. Plant Biotechnol. 26: 485-493.
35. Fukushima, A., M. Kusano, H. Redestig, M. Arita and K. Saito (2011) Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach. BMC Syst. Biol. 5: 1.
36. Fukushima, A., T. Nishizawa, M. Hayakumo, S. Hikosaka, K. Saito, E. Goto and M. Kusano (2012) Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches. Plant Physiol. 158: 1487-1502.
37. Gifford, M.L., A. Dean, R.A. Gutierrez, G.M. Coruzzi and K.D. Birnbaum (2008) Cell-specific nitrogen responses mediate developmental plasticity. Proc. Natl. Acad. Sci. USA 105: 803-808.
38. Gillis, J. and P. Pavlidis (2009) A methodology for the analysis of differential coexpression across the human lifespan. BMC Bioinformatics 10: 306.
39. Giuntini, D., V. Lazzeri, V. Calvenzani, C. Dall'Asta, G. Galaverna, C. Tonelli, K. Petroni and A. Ranieri (2008) Flavonoid profiling and biosynthetic gene expression in flesh and peel of two tomato genotypes grown under UV-B-depleted conditions during ripening. J. Agric. Food Chem. 56: 5905-5915.
40. Gorguet, B., P.M. Eggink, J. Ocana, A. Tiwari, D. Schipper, R. Finkers, R.G. Visser and A.W. van Heusden (2008) Mapping and characterization of novel parthenocarpy QTLs in tomato. Theor. Appl. Genet. 116: 755-767.
41. Guimera, R. and L.A. Nunes Amaral (2005) Functional cartography of complex metabolic networks. Nature 433: 895-900.
42. Gutierrez, R.A., L.V. Lejay, A. Dean, F. Chiaromonte, D.E. Shasha and G.M. Coruzzi (2007) Qualitative network models and genomewide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol. 8: R7.
43. Gutierrez, R.A., T.L. Stokes, K. Thum, X. Xu, M. Obertello, M.S. Katari, M. Tanurdzic, A. Dean, D.C. Nero, C.R. McClung et al. (2008) Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc. Natl. Acad. Sci. USA 105: 4939-4944.
44. Hamada, K., K. Hongo, K. Suwabe, A. Shimizu, T. Nagayama, R. Abe, S. Kikuchi, N. Yamamoto, T. Fujii, K. Yokoyama et al. (2011) OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. Plant Cell Physiol. 52: 220-229.
45. Ideker, T. and N.J. Krogan (2012) Differential network biology. Mol. Syst. Biol. 8: 565.
46. Katari, M.S., S.D. Nowicki, F.F. Aceituno, D. Nero, J. Kelfer, L.P. Thompson, J.M. Cabello, R.S. Davidson, A.P. Goldberg, D.E. Shasha et al. (2010) VirtualPlant: a software platform to support systems biology research. Plant Physiol. 152: 500-515.
47. Khodakovskaya, M.V., K. de Silva, D.A. Nedosekin, E. Dervishi, A.S. Biris, E.V. Shashkov, E.I. Galanzha and V.P. Zharov (2011) Complex genetic, photothermal, and photoacoustic analysis of nanoparticle-plant interactions. Proc. Natl. Acad. Sci. USA 108: 1028-1033.
48. Kimbara, J., M. Yoshida, H. Ito, K. Hosoi, M. Kusano, M. Kobayashi, T. Ariizumi, E. Asamizu and H. Ezura (2012) A novel class of sticky peel and light green mutations causes cuticle deficiency in leaves and fruits of tomato (Solanum lycopersicum). Planta 236: 1559- 1570.
49. Kootstra, A. (1994) Protection from UV-B-induced DNA damage by flavonoids. Plant Mol. Biol. 26: 771-774.
50. Kourmpetis, Y.A., A.D. van Dijk, R.C. van Ham and C.J. ter Braak (2011) Genome-wide computational function prediction of Arabidopsis proteins by integration of multiple data sources. Plant Physiol. 155: 271-281.
51. Kumar, R., M.K. Sharma, S. Kapoor, A.K. Tyagi and A.K. Sharma (2012) Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato. Mol. Genet. Genomics 287: 189-203.
52. Kusano, M., A. Fukushima, M. Arita, P. Jonsson, T. Moritz, M. Kobayashi, N. Hayashi, T. Tohge and K. Saito (2007) Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. BMC Syst. Biol. 1: 53.
53. Kusano, M., H. Redestig, T. Hirai, A. Oikawa, F. Matsuda, A. Fukushima, M. Arita, S. Watanabe, M. Yano, K. Hiwasa-Tanase et al. (2011a) Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment. PLoS One 6: e16989.
54. Kusano, M., T. Tohge, A. Fukushima, M. Kobayashi, N. Hayashi, H. Otsuki, Y. Kondou, H. Goto, M. Kawashima, F. Matsuda et al. (2011b) Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to UV-B light. Plant J. 67: 354-369.
55. Kusano, M., M. Tabuchi, A. Fukushima, K. Funayama, C. Diaz, M. Kobayashi, N. Hayashi, Y.N. Tsuchiya, H. Takahashi, A. Kamata et al. (2011c) Metabolomics data reveal a crucial role of cytosolic glutamine synthetase 1;1 in coordinating metabolic balance in rice. Plant J. 66: 456-466.
56. Lancu, O.D., S. Kawane, D. Bottomly, R. Searles, R. Hitzemann and S. McWeeney (2012) Utilizing RNA-Seq Data for de-novo coexpression network inference. Bioinformatics 28: 1592-1597.
57. Le Gall, G., I.J. Colquhoun, A.L. Davis, G.J. Collins and M.E. Verhoeyen (2003) Metabolite profiling of tomato (Lycopersicon esculentum) using 1H NMR spectroscopy as a tool to detect potential unintended effects following a genetic modification. J. Agric. Food Chem. 51: 2447-2456.
58. Lee, I., B. Ambaru, P. Thakkar, E.M. Marcotte and S.Y. Rhee (2010) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat. Biotechnol. 28: 149-156.
59. Lee, I., Y.S. Seo, D. Coltrane, S. Hwang, T. Oh, E.M. Marcotte and P.C. Ronald (2011) Genetic dissection of the biotic stress response using a genome-scale gene network for rice. Proc. Natl. Acad. Sci. USA 108: 18548-18553.
60. Less, H. and G. Galili (2009) Coordinations between gene modules control the operation of plant amino acid metabolic networks. BMC Syst. Biol. 3: 14.
61. Less, H., R. Angelovici, V. Tzin and G. Galili (2011) Coordinated gene networks regulating Arabidopsis plant metabolism in response to various stresses and nutritional cues. Plant Cell 23: 1264-1271.
62. Lisec, J., R.C. Meyer, M. Steinfath, H. Redestig, M. Becher, H. Witucka-Wall, O. Fiehn, O. Torjek, J. Selbig, T. Altmann et al. (2008) Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations. Plant J. 53: 960-972.
63. Lysenko, A., M. Defoin-Platel, K. Hassani-Pak, J. Taubert, C. Hodgman, C.J. Rawlings and M. Saqi (2011) Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. BMC Bioinformatics 12: 203.
64. Ma, S., Q. Gong and H.J. Bohnert (2007) An Arabidopsis gene network based on the graphical Gaussian model. Genome Res. 17: 1614- 1625.
65. Mao, L., J.L. Van Hemert, S. Dash and J.A. Dickerson (2009) Arabidopsis gene co-expression network and its functional modules. BMC Bioinformatics 10: 346.
66. Markowetz, F. and R. Spang (2007) Inferring cellular networks-a review. Bmc Bioinformatics 8 (Suppl 6): S5.
67. Martin, A., J. Lee, T. Kichey, D. Gerentes, M. Zivy, C. Tatout, F. Dubois, T. Balliau, B. Valot, M. Davanture et al. (2006) Two cytosolic glutamine synthetase isoforms of maize are specifically involved in the control of grain production. Plant Cell 18: 3252-3274.
68. Martinelli, F., S.L. Uratsu, R.L. Reagan, Y. Chen, D. Tricoli, O. Fiehn, D.M. Rocke, C.S. Gasser and A.M. Dandekar (2009) Gene regulation in parthenocarpic tomato fruit. J. Exp. Bot. 60: 3873-3890.
69. Matsuda, F., Y. Okazaki, A. Oikawa, M. Kusano, R. Nakabayashi, J. Kikuchi, J. Yonemaru, K. Ebana, M. Yano and K. Saito (2012) Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis. Plant J. 70: 624-636.
70. Mazourek, M., A. Pujar, Y. Borovsky, I. Paran, L. Mueller and M.M. Jahn (2009) A dynamic interface for capsaicinoid systems biology. Plant Physiol. 150: 1806-1821.
71. Mentzen, W.I. and E.S. Wurtele (2008) Regulon organization of Arabidopsis. BMC Plant Biol. 8: 99.
72. Mintz-Oron, S., T. Mandel, I. Rogachev, L. Feldberg, O. Lotan, M. Yativ, Z. Wang, R. Jetter, I. Venger, A. Adato et al. (2008) Gene expression and metabolism in tomato fruit surface tissues. Plant Physiol. 147: 823-851.
73. Mizutani, M. and D. Ohta (2010) Diversification of P450 genes during land plant evolution. Annu. Rev. Plant Biol. 61: 291-315.
74. Moco, S., J. Forshed, R.C.H. De Vos, R.J. Bino and J. Vervoort (2008) Intra- and inter-metabolite correlation spectroscopy of tomato metabolomics data obtained by liquid chromatography-mass spectrometry and nuclear magnetic resonance. Metabolomics 4: 202- 215.
75. Mol, J., E. Grotewold and R. Koes (1998) How genes paint flowers and seeds. Trends Plant Sci. 3: 212-217.
76. Morgenthal, K., W. Weckwerth and R. Steuer (2006) Metabolomic networks in plants: Transitions from pattern recognition to biological interpretation. Biosystems 83: 108-117.
77. Morreel, K., G. Goeminne, V. Storme, L. Sterck, J. Ralph, W. Coppieters, P. Breyne, M. Steenackers, M. Georges, E. Messens et al. (2006) Genetical metabolomics of flavonoid biosynthesis in Populus: a case study. Plant J. 47: 224-237.
78. Movahedi, S., Y. Van de Peer and K. Vandepoele (2011) Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiol. 156: 1316-1330.
79. Mueller, L.A., T.H. Solow, N. Taylor, B. Skwarecki, R. Buels, J. Binns, C. Lin, M.H. Wright, R. Ahrens, Y. Wang et al. (2005) The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. Plant Physiol. 138: 1310-1317.
80. Mutwil, M., S. Klie, T. Tohge, F.M. Giorgi, O. Wilkins, M.M. Campbell, A.R. Fernie, B. Usadel, Z. Nikoloski and S. Persson (2011) PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell 23: 895-910.
81. Nashilevitz, S., C. Melamed-Bessudo, Y. Izkovich, I. Rogachev, S. Osorio, M. Itkin, A. Adato, I. Pankratov, J. Hirschberg, A.R. Fernie et al. (2010) An orange ripening mutant links plastid NAD(P)H dehydrogenase complex activity to central and specialized metabolism during tomato fruit maturation. Plant Cell 22: 1977- 1997.
82. Nebenfuhr, A., T.J. White and T.L. Lomax (2000) The diageotropica mutation alters auxin induction of a subset of the Aux/IAA gene family in tomato. Plant Mol. Biol. 44: 73-84.
83. Owens, R.A., K.B. Tech, J.Y. Shao, T. Sano and C.J. Baker (2012) Global analysis of tomato gene expression during Potato spindle tuber viroid infection reveals a complex array of changes affecting hormone signaling. Mol. Plant Microbe Interact. 25: 582-598.
84. Ozaki, S., Y. Ogata, K. Suda, A. Kurabayashi, T. Suzuki, N. Yamamoto, Y. Iijima, T. Tsugane, T. Fujii, C. Konishi 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.
85. Parkinson, H., M. Kapushesky, N. Kolesnikov, G. Rustici, M. Shojatalab, N. Abeygunawardena, H. Berube, M. Dylag, I. Emam, A. Farne et al. (2009) ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res. 37: D868-872.
86. Pascual, L., J.M. Blanca, J. Canizares and F. Nuez (2009) Transcriptomic analysis of tomato carpel development reveals alterations in ethylene and gibberellin synthesis during pat3/pat4 parthenocarpic fruit set. BMC Plant Biol. 9: 67.
87. Peer, W.A. and A.S. Murphy (2007) Flavonoids and auxin transport: modulators or regulators? Trends Plant Sci. 12: 556-563.
88. Philouze, J. (1983) Natural parthenocarpy in tomato. 1. review of bibliography. Agronomie 3: 611-620.
89. Philouze, J. (1985) Natural parthenocarpy in tomato. 2. study of a varietal collection. Agronomie 5: 47-54.
90. Piasecka, B., M. Robinson-Rechavi and S. Bergmann (2012) Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human. Bioinformatics 28: 1865-1872.
91. Povero, G., S. Gonzali, L. Bassolino, A. Mazzucato and P. Perata (2011) Transcriptional analysis in high-anthocyanin tomatoes reveals synergistic effect of Aft and atv genes. J. Plant Physiol. 168: 270- 279.
92. Ren, X.Y., M.W. Fiers, W.J. Stiekema and J.P. Nap (2005) Local coexpression domains of two to four genes in the genome of Arabidopsis. Plant Physiol. 138: 923-934.
93. Ren, X.Y., W.J. Stiekema and J.P. Nap (2007) Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains. Plant Mol. Biol. 65: 205-217.
94. Reshef, D.N., Y.A. Reshef, H.K. Finucane, S.R. Grossman, G. McVean, P.J. Turnbaugh, E.S. Lander, M. Mitzenmacher and P.C. Sabeti (2011) Detecting novel associations in large data sets. Science 334: 1518-1524.
95. Riedelsheimer, C., J. Lisec, A. Czedik-Eysenberg, R. Sulpice, A. Flis, C. Grieder, T. Altmann, M. Stitt, L. Willmitzer and A.E. Melchinger (2012) Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize. Proc. Natl. Acad. Sci. USA 109: 8872-8877.
96. Saito, K., M.Y. Hirai and K. Yonekura-Sakakibara (2008) Decoding genes with coexpression networks and metabolomics-'majority report by precogs'. Trends Plant Sci. 13: 36-43.
97. Sakata, K., H. Ohyanagi, H. Nobori, T. Nakamura, A. Hashiguchi, Y. Nanjo, Y. Mikami, H. Yunokawa and S. Komatsu (2009) Soybean proteome database: a data resource for plant differential omics. J. Proteome Res. 8: 3539-3548.
98. Saladie, M., A.J. Matas, T. Isaacson, M.A. Jenks, S.M. Goodwin, K.J. Niklas, R. Xiaolin, J.M. Labavitch, K.A. Shackel, A.R. Fernie et al. (2007) A reevaluation of the key factors that influence tomato fruit softening and integrity. Plant Physiol. 144: 1012-1028.
99. Sato, S., S. Tabata, H. Hirakawa, E. Asamizu, K. Shirasawa, S. Isobe, T. Kaneko, Y. Nakamura, D. Shibata, K. Aoki et al. (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641.
100. Schauer, N., Y. Semel, U. Roessner, A. Gur, I. Balbo, F. Carrari, T. Pleban, A. Perez-Melis, C. Bruedigam, J. Kopka et al. (2006) Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat. Biotechnol. 24: 447-454.
101. Schauer, N., Y. Semel, I. Balbo, M. Steinfath, D. Repsilber, J. Selbig, T. Pleban, D. Zamir and A.R. Fernie (2008) Mode of inheritance of primary metabolic traits in tomato. Plant Cell 20: 509-523.
102. Schijlen, E.G., C.H. de Vos, S. Martens, H.H. Jonker, F.M. Rosin, J.W. Molthoff, Y.M. Tikunov, G.C. Angenent, A.J. van Tunen and A.G. Bovy (2007) RNA interference silencing of chalcone synthase, the first step in the flavonoid biosynthesis pathway, leads to parthenocarpic tomato fruits. Plant Physiol. 144: 1520-1530.
103. Semel, Y., J. Nissenbaum, N. Menda, M. Zinder, U. Krieger, N. Issman, T. Pleban, Z. Lippman, A. Gur and D. Zamir (2006) Overdominant quantitative trait loci for yield and fitness in tomato. Proc. Natl. Acad. Sci. USA 103: 12981-12986.
104. Stark, R.E., B. Yan, S.M. Stanley-Fernandez, Z.J. Chen and J.R. Garbow (2008) NMR characterization of hydration and thermal stress in tomato fruit cuticles. Phytochemistry 69: 2689-2695.
105. Steuer, R., J. Kurths, C.O. Daub, J. Weise and J. Selbig (2002) The mutual information: detecting and evaluating dependencies between variables. Bioinformatics 18 (Suppl 2): S231-240.
106. Sun, W., X. Xu, H. Zhu, A. Liu, L. Liu, J. Li and X. Hua (2010) Comparative transcriptomic profiling of a salt-tolerant wild tomato species and a salt-sensitive tomato cultivar. Plant Cell Physiol. 51: 997- 1006.
107. Suzuki, A., K. Suwabe and K. Yano (2009) Web databases for omics data in tomato. J. Japan. Soc. Hort. Sci. 78: 23-31.
108. Tabuchi, M., K. Sugiyama, K. Ishiyama, E. Inoue, T. Sato, H. Takahashi and T. Yamaya (2005) Severe reduction in growth rate and grain filling of rice mutants lacking OsGS1;1, a cytosolic glutamine synthetase1;1. Plant J. 42: 641-651.
109. Takos, A.M. and F. Rook (2012) Why biosynthetic genes for chemical defense compounds cluster. Trends Plant Sci. 17: 383-388.
110. Tikunov, Y., A. Lommen, C.H. de Vos, H.A. Verhoeven, R.J. Bino, R.D. Hall and A.G. Bovy (2005) A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles. Plant Physiol. 139: 1125-1137.
111. Toubiana, D., Y. Semel, T. Tohge, R. Beleggia, L. Cattivelli, L. Rosental, Z. Nikoloski, D. Zamir, A.R. Fernie and A. Fait (2012) Metabolic profiling of a mapping population exposes new insights in the regulation of seed metabolism and seed, fruit, and plant relations. PloS Genet. 8.
112. Ulm, R. and F. Nagy (2005) Signalling and gene regulation in response to ultraviolet light. Curr. Opin. Plant Biol. 8: 477-482.
113. Ursem, R., Y. Tikunov, A. Bovy, R. van Berloo and F. van Eeuwijk (2008) A correlation network approach to metabolic data analysis for tomato fruits. Euphytica 161: 181-193.
114. Usadel, B., T. Obayashi, M. Mutwil, F.M. Giorgi, G.W. Bassel, M. Tanimoto, A. Chow, D. Steinhauser, S. Persson and N.J. Provart (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ. 32: 1633- 1651.
115. Van Bel, M., S. Proost, E. Wischnitzki, S. Movahedi, C. Scheerlinck, Y. Van de Peer and K. Vandepoele (2012) Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol. 158: 590-600.
116. van der Meer, I.M., M.E. Stam, A.J. van Tunen, J.N. Mol and A.R. Stuitje (1992) Antisense inhibition of flavonoid biosynthesis in petunia anthers results in male sterility. Plant Cell 4: 253-262.
117. Van Dongen, S. (2000) Graph Clustering by Flow Simulation. PhD thesis. University of Utrecht.
118. Vidal, E.A., V. Araus, C. Lu, G. Parry, P.J. Green, G.M. Coruzzi and R.A. Gutierrez (2010) Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 107: 4477-4482.
119. Wada, M., H. Takahashi, M. Altaf-Ul-Amin, K. Nakamura, M.Y. Hirai, D. Ohta and S. Kanaya (2012) Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes. Gene 503: 56-64.
120. Wang, H., B. Jones, Z.G. Li, P. Frasse, C. Delalande, F. Regad, S. Chaabouni, A. Latche, J.C. Pech and M. Bouzayen (2005) The tomato Aux/IAA transcription factor IAA9 is involved in fruit development and leaf morphogenesis. Plant Cell 17: 2676-2692.
121. Wang, H., N. Schauer, B. Usadel, P. Frasse, M. Zouine, M. Hernould, A. Latche, J.C. Pech, A.R. Fernie and M. Bouzayen (2009) Regulatory features underlying pollination-dependent and -independent tomato fruit set revealed by transcript and primary metabolite profiling. Plant Cell 21: 1428-1452.
122. Weckwerth, W., M.E. Loureiro, K. Wenzel and O. Fiehn (2004) Differential metabolic networks unravel the effects of silent plant phenotypes. Proc. Natl. Acad. Sci. USA 101: 7809-7814.
123. Wentzell, A.M., H.C. Rowe, B.G. Hansen, C. Ticconi, B.A. Halkier and D.J. Kliebenstein (2007) Linking metabolic QTLs with network and cis-eQTLs controlling biosynthetic pathways. PLoS Genet. 3: 1687-1701.
124. Yu, H., N.M. Luscombe, H.X. Lu, X. Zhu, Y. Xia, J.D. Han, N. Bertin, S. Chung, M. Vidal and M. Gerstein (2004) Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 14: 1107-1118.
125. Zarrineh, P., A.C. Fierro, A. Sanchez-Rodriguez, B. De Moor, K. Engelen and K. Marchal (2011) COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms. Nucleic Acids Res. 39: e41.
126. Zhan, S., J. Horrocks and L.N. Lukens (2006) Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher-order chromosome domains. Plant J. 45: 347-357.
127. Zhang, Z., J. Yu, D. Li, F. Liu, X. Zhou, T. Wang, Y. Ling and Z. Su (2010) PMRD: plant microRNA database. Nucleic Acids Res. 38: D806-813.