Advertisement

Natural and artificially induced genetic variability in crop and model plant species for plant systems biology

  • Christophe Rothan
  • Mathilde Causse
Part of the Experientia Supplementum book series (EXS, volume 97)

Abstract

The sequencing of plant genomes which was completed a few years ago for Arabidopsis thaliana and Oryza sativa is currently underway for numerous crop plants of commercial value such as maize, poplar, tomato grape or tobacco. In addition, hundreds of thousands of expressed sequence tags (ESTs) are publicly available that may well represent 40–60% of the genes present in plant genomes. Despite its importance for life sciences, genome information is only an initial step towards understanding gene function (functional genomics) and deciphering the complex relationships between individual genes in the framework of gene networks. In this chapter we introduce and discuss means of generating and identifying genetic diversity, i.e., means to genetically perturb a biological system and to subsequently analyse the systems response, e.g., the changes in plant morphology and chemical composition. Generating and identifying genetic diversity is in its own right a highly powerful resource of information and is established as an invaluable tool for systems biology.

Keywords

Quantitative Trait Locus Reverse Genetic Quantitative Trait Locus Detection Curr Opin Plant Biol Model Plant Species 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Rensink WA, Lee Y, Liu J, Iobst S, Ouyang S, Buell RC (2005) Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts. BMC Genomics 6: 124PubMedCrossRefGoogle Scholar
  2. 2.
    Diévart A, Clark SE (2003) Using mutant alleles to determine the structure and function of leucine-rich repeat receptor-like kinases. Curr Opin Plant Biol 6: 507–516PubMedCrossRefGoogle Scholar
  3. 3.
    Tanksley SD, Ganal MW, Martin GB (1995) Chromosome landing — a paradigm for map-based gene cloning in plants with large genomes. Trends Genet 11: 63–68PubMedCrossRefGoogle Scholar
  4. 4.
    Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol 129: 440–450PubMedCrossRefGoogle Scholar
  5. 5.
    Xu YB, McCouch SR, Zhang QF (2005) How can we use genomics to improve cereals with rice as a reference genome? Plant Mol Biol 59: 7–26PubMedCrossRefGoogle Scholar
  6. 6.
    Hackett CA (2002) Statistical methods for QTL mapping in cereals. Plant Mol Biol 48: 585–599PubMedCrossRefGoogle Scholar
  7. 7.
    Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185–199PubMedGoogle Scholar
  8. 8.
    Lincoln SE, Daly MJ, Lander ES (1992) Constructing genetic maps with MAPMAKER/ EXP version 3.0. A tutorial and reference manual http://linkage.rockeffeller.edu/soft/ mapmakerGoogle Scholar
  9. 9.
    Jansen RC, Stam P (1994) High-resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447–1455PubMedGoogle Scholar
  10. 10.
    Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457–1468PubMedGoogle Scholar
  11. 11.
    Churchill GA, Doerge RW (1996) Empirical threshold values for quantitative trait mapping. Genetics 138: 963–971Google Scholar
  12. 12.
    Darvasi A, Soller M (1997) Simple method to calculate resolving power and confidence interval of QTL map location. Behav Genet 27: 125–132PubMedCrossRefGoogle Scholar
  13. 13.
    Lee M, Sharopova N, Beavis WD, Grant D, Katt M, Blair D, Hallauer A (2002) Expanding the genetic map of maize with the intermated B73 x Mo17 (IBM) population. Plant Mol Biol 48: 453–461PubMedCrossRefGoogle Scholar
  14. 14.
    Grattapaglia D, Bertolucci FL, Sederoff RR (1995) Genetic mapping of QTLs controlling vegetative propagation in Eucalyptus grandis and E. urophylla using a pseudo-testcross mapping strategy and RAPD markers. Theor Appl Genet 90: 933–947CrossRefGoogle Scholar
  15. 15.
    Bradshaw HD, Stettler RF (1995) Molecular genetics of growth and development in Populus. IV. Mapping QTLs with large effects on growth, form and phenology traits in a forest tree. Genetics 139: 963–973PubMedGoogle Scholar
  16. 16.
    Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92: 191–203CrossRefGoogle Scholar
  17. 17.
    Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield associated QTLs. Genetics 141: 1147–1162PubMedGoogle Scholar
  18. 18.
    Ronin Y, Korol A, Shtemberg M, Nevo E, Soller M (2003) High-resolution mapping of quantitative trait loci by selective recombinant genotyping. Genetics 164: 1657–1666PubMedGoogle Scholar
  19. 19.
    Lynch M, Walsh B (eds) (1998) Genetics and analysis of quantitative traits. Sinauer AssociatesGoogle Scholar
  20. 20.
    De Vienne D, Causse M (2002) Mapping and characterizing quantitative trait loci. In: D de Vienne (ed): Molecular markers in Plant genetics and Biotechnology. Sci Publisher Inc, 89–125Google Scholar
  21. 21.
    Xu SZ (2003) Theoretical basis of the Beavis effect. Genetics 165: 2259–2268PubMedGoogle Scholar
  22. 22.
    Kearsey MJ, Farquhar AGL (1998) QTL analysis in plants; where are we now? Heredity 80: 137–142PubMedCrossRefGoogle Scholar
  23. 23.
    Kroymann J, Mitchell-Olds T (2005) Epistasis and balanced polymorphism influencing complex trait variation. Nature 435: 95–98PubMedCrossRefGoogle Scholar
  24. 24.
    Grandillo S, Ku HM, Tanksley SD (1999) Identifying the loci responsible for natural variation in fruit size and shape in tomato. Theor Appl Genet 99: 978–987CrossRefGoogle Scholar
  25. 25.
    Fulton TM, Bucheli P, Voirol E, López J, Pétiard V, Tanksley SD (2002) Quantitative trait loci (QTL) affecting sugars, organic acids and other biochemical properties possibly contributing to flavor, identified in four advanced backcross populations of tomato. Euphytica 127: 163–177CrossRefGoogle Scholar
  26. 26.
    Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L, Murigneux A, Charcosset A (2004) Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics 168: 2169–2185PubMedCrossRefGoogle Scholar
  27. 27.
    Bernacchi D, Beck-Bunn T, Emmatty D, Eshed Y, Inai S, Lopez J, Petiard V, Sayama H, Uhlig J, Zamir D et al. (1998) Advanced back-cross QTL analysis of tomato. II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium. Theor Appl Genet 97: 1191–1196CrossRefGoogle Scholar
  28. 28.
    Fatokun CA, Menanciohautea DI, Danesh D, Young ND (1992) Evidence for orthologous seed weight genes in cowpea and mung bean based on rflp mapping. Genetics 132: 841–846PubMedGoogle Scholar
  29. 29.
    Timmerman-Vaughan GM, Mccallum JA, Frew TJ, Weeden NF, Russell AC (1996) Linkage mapping of quantitative trait loci controlling seed weight in pea (Pisum sativum L.). Theor Appl Genet 93: 431–439CrossRefGoogle Scholar
  30. 30.
    Maughan PJ, Maroof MAS, Buss GR (1996) Molecular-marker analysis of seed-weight: genomic locations, gene action, and evidence for orthologous evolution among three legume species. Theor Appl Genet 93: 574–579Google Scholar
  31. 31.
    Paterson AH, Lin YR, Li Z, Schertz KF, Doebley JF, Pinson SR, Liu SC, Stansel JW, Irvine JE (1995) Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269: 1714–1718CrossRefPubMedGoogle Scholar
  32. 32.
    Devos M, Gale D (1997) Comparative genetics in the grasses. Plant Mol Biol 35: 3–15PubMedCrossRefGoogle Scholar
  33. 33.
    Frary A, Doganlar S, Daunay MC, Tanksley SD (2003) QTL analysis of morphological traits in eggplant and implications for conservation of gene function during evolution of solanaceous species. Theor Appl Genet 107: 359–370PubMedCrossRefGoogle Scholar
  34. 34.
    Tanksley SD (1993) Mapping Polygenes. Annu Rev Genet 27: 205–233PubMedCrossRefGoogle Scholar
  35. 35.
    Eshed Y, Zamir D (1996) Less-than-additive epistatic interactions of quantitative trait loci in tomato. Genetics 143: 1807–1817PubMedGoogle Scholar
  36. 36.
    Doebley J, Stec A, Hubbard L (1997) The evolution of apical dominance in maize. Nature 386: 485–488PubMedCrossRefGoogle Scholar
  37. 37.
    Chaib J, Lecomte L, Buret M, Causse M (2006) Stability over genetic backgrounds, generations and years of quantitative trait locus (QTLs) for organoleptic quality in tomato. Theor Appl Genet 112: 934–944PubMedCrossRefGoogle Scholar
  38. 38.
    Prioul JL, Quarrie SA, Causse M, de Vienne D (1997) Dissecting complex physiological functions through the use of molecular quantitative genetics. J Exp Bot 48: 1151–1163CrossRefGoogle Scholar
  39. 39.
    Lefebvre V, Palloix A (1996). Both epistatic and additive effects of QTLs are involved in polygenic induced resistance to disease: a case study, the interaction pepper-Phytophthora capsici Leonian. Theor Appl Genet 93: 503–511Google Scholar
  40. 40.
    Sergeeva LI, Keurentjes JJB, Bentsink L, Vonk J, van der Plas LHW, Koornneef M, Vreugdenhil D (2006) Vacuolar invertase regulates elongation of Arabidopsis thaliana roots as revealed by QTL and mutant analysis. Proc Natl Acad Sci USA 103: 2994–2999PubMedCrossRefGoogle Scholar
  41. 41.
    Korol AB, Ronin YI, Itskovich AM, Peng J, Nevo E (2001) Enhanced efficiency of quantitative trait loci mapping analysis based on multivariate complexes of quantitative traits. Genetics 157: 1789–1803PubMedGoogle Scholar
  42. 42.
    Paterson AH, de Verna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124: 735–742PubMedGoogle Scholar
  43. 43.
    Monforte AJ, Tanksley SD (2000) Fine mapping of a quantitative trait locus (QTL) from Lycopersicon hirsutum chromosome 1 affecting fruit characteristics and agronomic traits: breaking linkage among QTLs affecting different traits and dissection of heterosis for yield. Theor Appl Genet 100: 471–479CrossRefGoogle Scholar
  44. 44.
    Lecomte L, Saliba-Colombani V, Gautier A, Gomez-Jimenez MC, Duffé P, Buret M, Causse M (2004) Fine mapping of QTLs of chromosome 2 affecting the fruit architecture and composition of tomato. Mol Breeding 13: 1–14CrossRefGoogle Scholar
  45. 45.
    Zeng ZB (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci USA 90: 10972–10976PubMedCrossRefGoogle Scholar
  46. 46.
    Jansen RC, van Ooijen JW, Stam P, Lister C, Dean C (1995) Genotype-by environment interaction in genetic mapping of multiple quantitative trait loci. Theor Appl Genet 91: 33–37CrossRefGoogle Scholar
  47. 47.
    Romagosa I, Ullrich SE, Han F, Hayes PM (1996) Use of the additive main effects and multiplicative interaction model in QTL mapping for adaptation in barley. Theor Appl Genet 93: 30–37CrossRefGoogle Scholar
  48. 48.
    Moreau L, Charcosset A, Gallais A (2004) Use of trial clustering to study QTL x environment effects for grain yield and related traits in maize. Theor Appl Genet 110: 92–105PubMedCrossRefGoogle Scholar
  49. 49.
    Loudet O, Chaillou S, Merigout P, Talbotec J, Daniel-Vedele F (2003) Quantitative trait loci analysis of nitrogen use efficency in Arabidopsis. Plant Physiol 131: 345–358PubMedCrossRefGoogle Scholar
  50. 50.
    Juenger TE, Mckay JK, Hausmann N, Keurentjes JJB, Sen S, Stowe KA, Dawson TE, Simms EL, Richards JH (2005) Identification and characterization of QTL underlying whole-plant physiology in Arabidopsis thaliana: delta C-13, stomatal conductance and transpiration efficiency. Plant Cell Environ 28: 697–708CrossRefGoogle Scholar
  51. 51.
    Reymond M, Muller B, Leonardi A, Charcosset A, Tardieu F (2003) Combining quantitative trait loci analysis and an ecophysiological model to analyze the genetic variability of the response of maize leaf growth to temperature and water deficit. Plant Physiol 131: 664–675PubMedCrossRefGoogle Scholar
  52. 52.
    Quilot B, Kervella J, Genard M, Lescourret F (2005) Analysing the genetic control of peach fruit quality through an ecophysiological model combined with a QTL approach. J Exp Bot 56: 3083–3092PubMedCrossRefGoogle Scholar
  53. 53.
    Yin XY, Struik PC, Kropff MJ (2004) Role of crop physiology in predicting gene-to-phenotype relationships. Trends Plant Sci 9: 426–432PubMedCrossRefGoogle Scholar
  54. 54.
    Paran I, Zamir D (2003) Quantitative traits in plants: beyond the QTL. Trends Genet 19: 303–306PubMedCrossRefGoogle Scholar
  55. 55.
    Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci 10: 298–304CrossRefGoogle Scholar
  56. 56.
    Tuinstra MR, Ejeta G, Goldbrough PB (1997) Heterogeneous inbred families (HIF) analysis: a method for developing near-isogenic lines that differ at quantitative trait loci. Theor Appl Genet 95: 1005–1011CrossRefGoogle Scholar
  57. 57.
    Zamir D (2001) Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2: 983–988PubMedCrossRefGoogle Scholar
  58. 58.
    Durrett RT, Chen KY, Tanksley SD (2002) A simple formula useful for positional cloning. Genetics 160: 353–355PubMedGoogle Scholar
  59. 59.
    Fridman E, Pleban T, Zamir D (2000) A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proc Natl Acad Sci USA 97: 4718–4723PubMedCrossRefGoogle Scholar
  60. 60.
    Fridman E, Carrari F, Liu YS, Fernie AR, Zamir D (2004) Zooming in on a quantitative trait for tomato yield using interspecific introgressions. Science 305: 1786–1789PubMedCrossRefGoogle Scholar
  61. 61.
    Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289: 85–88PubMedCrossRefGoogle Scholar
  62. 62.
    Pflieger S, Lefebvre V, Causse M (2001) The candidate gene approach. A Review. Molecular Breeding 7: 275–291CrossRefGoogle Scholar
  63. 63.
    Byrne PF, McMullen MD, Snooks ME, Musket TA, Theuri JM, Widstrom NW, Wiseman BR, Coe EH (1996) Quantitative trait loci and metabolic pathways: genetic control of the concentration of maysin, a corn earworm resistance factor, in maize silks. Proc Natl Acad Sci USA 93: 8820–8825PubMedCrossRefGoogle Scholar
  64. 64.
    Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28: 286–289PubMedCrossRefGoogle Scholar
  65. 65.
    Olsen KM, Halldorsdottir SS, Stinchcombe JR, Weinig C, Schmitt J, Purugganan MD (2004) Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 167: 1361–1369PubMedCrossRefGoogle Scholar
  66. 66.
    Osterberg MK, Shavorskaya O, Lascoux M, Lagercrantz U (2002) Naturally occurring indel variation in the Brassica nigra COL1 gene is associated with variation in flowering time. Genetics 161: 299–306PubMedGoogle Scholar
  67. 67.
    Gupta V, Mukhopadhyay A, Arumugam N, Sodhi YS, Pental D, Pradhan AK (2004) Molecular tagging of erucic acid trait in oilseed mustard (Brassica juncea) by QTL mapping and single nucleotide polymorphisms in FAE1 gene. Theor Appl Genet 108: 743–749PubMedCrossRefGoogle Scholar
  68. 68.
    Guillet-Claude C, Birolleau-Touchard C, Manicacci D, Rogowsky PM, Rigau J, Murigneux A, Martinant JP, Barriere Y (2004) Nucleotide diversity of the ZmPox3 maize peroxidase gene: Relationships between a MITE insertion in exon 2 and variation in forage maize digestibility. BMC Genetics 5: Art. No. 19Google Scholar
  69. 69.
    El-Assal SED, Alonso-Blanco C, Peeters AJM, Raz V, Koornneef M (2001) A QTL for flowering time in Arabidopsis reveals a novel allele of CRY2. Nat Genet 29: 435–440CrossRefGoogle Scholar
  70. 70.
    Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A (2004) Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-Iike gene expression independently of Hd1l. Genes Dev 18: 926–936PubMedCrossRefGoogle Scholar
  71. 71.
    Ren ZH, Gao JP, Li LG, Cai XL, Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Lin HX (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37: 1141–1146PubMedCrossRefGoogle Scholar
  72. 72.
    Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2. Proc Natl Acad Sci USA 98: 7922–7927PubMedCrossRefGoogle Scholar
  73. 73.
    Mouchel CF, Briggs GC, Hardtke CS (2004) Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell proliferation and elongation in the root. Genes Dev 18: 700–714PubMedCrossRefGoogle Scholar
  74. 74.
    Liu JP, Van Eck J, Cong B, Tanksley SD (2002) A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc Natl Acad Sci USA 99: 13302–13306PubMedCrossRefGoogle Scholar
  75. 75.
    Cong B, Liu JP, Tanksley SD (2002) Natural alleles at a tomato fruit size quantitative trait locus differ by heterochronic regulatory mutations. Proc Natl Acad Sci USA 99: 13606–13611PubMedCrossRefGoogle Scholar
  76. 76.
    Werner JD, Borevitz JO, Warthmann N, Trainer GT, Ecker JR, Chory J, Weigel D (2005) Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation. Proc Natl Acad Sci USA 102: 2460–2465PubMedCrossRefGoogle Scholar
  77. 77.
    Clark RM, Linton E, Messing J, Doebley JF (2004) Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc Natl Acad Sci USA 101: 700–707PubMedCrossRefGoogle Scholar
  78. 78.
    Kroymann J, Donnerhacke S, Schnabelrauch D, Mitchell-Olds T (2003) Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus. Proc Natl Acad Sci USA 100: 14587–14592PubMedCrossRefGoogle Scholar
  79. 79.
    Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y et al. (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS Plant Cell 12: 2473–2483PubMedCrossRefGoogle Scholar
  80. 80.
    Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43: 1096–1105PubMedCrossRefGoogle Scholar
  81. 81.
    Doebley J, Stec A, Hubbard L (1997) The evolution of apical dominance in maize. Nature 386: 485–488PubMedCrossRefGoogle Scholar
  82. 82.
    Van der Hoeven R, Ronning C, Giovannoni J, Martin G, 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: 1441–1456PubMedCrossRefGoogle Scholar
  83. 83.
    Schmidt R (2000) Synteny: recent advances and future prospects. Current Opin Plant Biol 3: 97–102CrossRefGoogle Scholar
  84. 84.
    Fulton TM, Van der Hoeven R, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 1457–1467PubMedCrossRefGoogle Scholar
  85. 85.
    Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, Weigel D, Berry CC, Winzeler E, Chory J (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13: 513–523PubMedCrossRefGoogle Scholar
  86. 86.
    Wayne ML, McIntyre LM (2002) Combining mapping and arraying: An approach to candidate gene identification. Proc Natl Acad Sci USA 99: 14903–14906PubMedCrossRefGoogle Scholar
  87. 87.
    Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G et al. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297–302PubMedCrossRefGoogle Scholar
  88. 88.
    Gibson G, Weir B (2005) The quantitative genetics of transcription. Trends Genet 21: 616–623PubMedCrossRefGoogle Scholar
  89. 89.
    Guillaumie S, Charmet G, Linossier L, Torney V, Robert N, Ravel C (2004) Colocation between a gene encoding the bZip factor SPA and an eQTL for a high-molecular-weight glutenin subunit in wheat (Triticum aestivum). Genome 47: 705–713PubMedCrossRefGoogle Scholar
  90. 90.
    Damerval C, Maurice A, Josse JM, de Vienne D (1994) Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression. Genetics 137: 289–301PubMedGoogle Scholar
  91. 91.
    de Vienne D, Leonardi A, Damerval C, Zivy M (1999) Genetics of proteome variation for QTL characterization: application to drought-stress responses in maize. J Exp Bot 50: 303–309CrossRefGoogle Scholar
  92. 92.
    Consoli L, Lefevre A, Zivy M, de Vienne D, Damerval C (2002) QTL analysis of proteome and transcriptome variations for dissecting the genetic architecture of complex traits in maize. Plant Mol Biol 48: 575–581PubMedCrossRefGoogle Scholar
  93. 93.
    Schauer N, Semel Y, Roessner U, Gur A, Balbo I, Carrari F, Pleban T, Perez-Melis A, Brudigam C, Kopka J et al. (2006) Genetics of metabolite in fruits of interspecific introgressions of tomato. Nat Biotechnol 24: 447–454PubMedCrossRefGoogle Scholar
  94. 94.
    Ostergaard L, Yanofsky MF (2004) Establishing gene function by mutagenesis in Arabidopsis thaliana. Plant J 39: 682–696PubMedCrossRefGoogle Scholar
  95. 95.
    Krysan PJ, Young JC, Sussman MR (1999) T-DNA as an insertional mutagen in Arabidopsis. Plant Cell 11: 2283–2290PubMedCrossRefGoogle Scholar
  96. 96.
    Schneider A, Kirch T, Gigoshvili T, Mock H-P, Sonnewald U, Simon R, Flügge U-I, Werr W (2005) A transposon-based activation-tagging population in Arabidopsis thaliana (TAMARA) and its application in the identification of dominant developmental and metabolic mutations. FEBS Lett 579: 4622–4628PubMedGoogle Scholar
  97. 97.
    Waterhouse PM, Heliwell CA (2003) Exploring plant genomes by RNAi-induced gene silencing. Nat Rev Genet 4: 29–38PubMedCrossRefGoogle Scholar
  98. 98.
    Karimi M, Inzé D, Depicker A (2002) GATEWAY vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci 7: 193–195PubMedCrossRefGoogle Scholar
  99. 99.
    Meinke DW, Meinke LK, Showalter TC, Schissel AM, Mueller LA, Tzafrir I (2003) A sequence-based map of Arabidopsis genes with mutant phenotypes. Plant Physiology 131: 409–418PubMedCrossRefGoogle Scholar
  100. 100.
    An G, Jeong D-H, Jung K-H, Lee S (2005) Reverse genetics approaches for functional genomics of rice. Plant Mol Biol 59: 111–123PubMedCrossRefGoogle Scholar
  101. 101.
    Hirochika H, Guiderdoni E, An G, Hsing Y-I, Eun MY, Han C-D, Upadhyaya N, Ramachandran R, Zhang Q, Pereira A et al. (2004) Rice mutant resources for gene discovery. Plant Mol Biol 54: 325–334PubMedCrossRefGoogle Scholar
  102. 102.
    Meissner R, Jacobson Y, Melamed S, Levyatuv S, Shalev G, Ashri A, Elkind Y, Levy AA (1997) A new model system for tomato genetics. Plant J 12: 1465–1472CrossRefGoogle Scholar
  103. 103.
    Meissner R, Chague V, Zhu Q, Emmanuel E, Elkind Y, Levy AA (2000) A high throughput system for transposon tagging and promoter trapping in tomato. Plant J 38: 861–872Google Scholar
  104. 104.
    Gidoni D, Fuss E, Burbidge A, Speckmann GJ, James S, Nijkamp D, Mett A, Feiler J, Smoker M, de Vroomen MJ et al. (2003) Multi-functional T-DNA/Ds tomato lines designed for gene cloning and molecular and physical dissection of the tomato genome. Plant Mol Biol 51: 83–98PubMedCrossRefGoogle Scholar
  105. 105.
    Mathews H, Clendennen SK, Caldwell CG, Connors K, Matheis N, Schuster DK, Menasco DJ, Wagoner W, Lightner J, Wagner DR (2003) Activation tagging in tomato identifies a transcriptional regulator of anthocyanin biosynthesis, modification, and transport. Plant Cell 15: 1689–1703PubMedCrossRefGoogle Scholar
  106. 106.
    Emmanuel E, Levy AA (2002) Tomato mutants as tools for functional genomics. Curr Opin Plant Biol 5: 112–117PubMedCrossRefGoogle Scholar
  107. 107.
    Li X, Song Y, Century K, Straight S, Ronald P, Dong X, Lassner M, Zhang Y (2001) A fast neutron deletion mutagenesis-based reverse genetics system for plants. Plant J 27: 235–242PubMedCrossRefGoogle Scholar
  108. 108.
    McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeted screening for induced mutations. Nat Biotechnol 18: 455–457PubMedCrossRefGoogle Scholar
  109. 109.
    Colbert T, Till BJ, Tompa R, Reynolds S, Steine MN, Yeung AT, McCallum CM, Comai L, Henikoff S (2001) High-throughput screening for induced point mutations. Plant Physiol 126: 480–484PubMedCrossRefGoogle Scholar
  110. 110.
    Koornneef M, Dellaert LWM, van den Veen JH (1982) EMS-and radiation-induced mutation frequencies at individual loci in Arabidospis thaliana (L.) Heynh. Mutat Res 93: 109–123PubMedGoogle Scholar
  111. 111.
    Menda N, Semel Y, Peled D, Eshed Y, Zamir D (2004) In silico screening of a saturated mutation library of tomato. Plant J 38: 861–872PubMedCrossRefGoogle Scholar
  112. 112.
    Li X, Zhang Y (2002) Reverse genetics by fast neutron mutagenesis in higher plants. Funct Integr Genomics 2: 254–258PubMedCrossRefGoogle Scholar
  113. 113.
    Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of CROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292: 2077–2080PubMedCrossRefGoogle Scholar
  114. 114.
    Yeung AT, Hattangadi D, Blakesley L, Nicolas E (2005) Enzymatic mutation detection technologies. Biotechniques 38: 749–758PubMedCrossRefGoogle Scholar
  115. 115.
    Winkler S, Schwabedissen A, Backasch D, Bökel C, Seidel C, Bönisch S, Fürthauer M, Kuhrs A, Cobreros L, Bran M, Gonzalez-Gaitan M (2005) Target-selected mutant screen by TILLING in Drosophila. Genome Res 15: 718–723PubMedCrossRefGoogle Scholar
  116. 116.
    Greene EA, Codomo CA, Taylor NE, Henikoff JG, Till BJ, Reynolds SH, Enns LC, Burtner C, Johnson JE, Odden AR et al. (2003) Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics 164: 731–740PubMedGoogle Scholar
  117. 117.
    Perry JA, Wang TL, Welham TJ, Gardner S, Pike JM, Yoshida S, Parniske M (2003) A TILLING reverse genetics tool and a web-accessible collection of mutants of the legume Lotus japonicus. Plant Physiol 131: 866–871PubMedCrossRefGoogle Scholar
  118. 118.
    Caldwell DG, McCallum N, Shaw P, Muehlbauer GJ, Marshall DF, Waugh R (2004) A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). Plant J 40: 143–150PubMedCrossRefGoogle Scholar
  119. 119.
    Till BJ, Reynolds SH, Weil C, Springer N, Burtner C, Young K, Bowers E, Codomo CA, Enns LC, Odden AR et al. (2004) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biology 4: 12PubMedCrossRefGoogle Scholar
  120. 120.
    Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti D (2005) A reverse genetic, non transgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 23: 75–81PubMedCrossRefGoogle Scholar
  121. 121.
    Henikoff S, Comai L (2003) Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol 54: 375–401PubMedCrossRefGoogle Scholar
  122. 122.
    Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Young K, Taylor NE et al. (2003) Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res 13: 524–530PubMedCrossRefGoogle Scholar
  123. 123.
    Gilchrist EJ, Haughn GW (2005) TILLING without a plough: a new method with applications for reverse genetics. Curr Opin Plant Biol 8: 211–215PubMedCrossRefGoogle Scholar
  124. 124.
    Comai L, Henikoff S (2006) TILLING: practical single-nucleotide mutation discovery. Plant J 45: 684–694PubMedCrossRefGoogle Scholar
  125. 125.
    Wienholds E, van Eeden F, Kosters M, Mudde J, Plasterk RHA, Cuppen E (2003) Efficient target-selected mutagenesis in zebrafish. Genome Res 13: 2700–2707PubMedCrossRefGoogle Scholar
  126. 126.
    Wu JL, Wu C, Lei C, Baraoidan M, Bordeos A, Madamba MRS, Ramos-Pamplona R, Mauleon R, Portugal A, Ulat J et al. (2005) Chemical-and irradiation-induced mutants of Indica Rice IR64 for forward and reverse genetics. Plant Mol Biol 59: 85–97PubMedCrossRefGoogle Scholar
  127. 127.
    Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: Unlocking genetic potential from the wild. Science 277: 1063–1066PubMedCrossRefGoogle Scholar
  128. 128.
    Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR et al. (2004) Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. Plant J 37: 778–786PubMedCrossRefGoogle Scholar
  129. 129.
    Qiu P, Shandilya H, D’Alessio JM, O’Connor K, Durocher J, Gerard GF (2004) Mutation detection using Surveyor nuclease. Biotechniques 36: 702–707PubMedGoogle Scholar
  130. 130.
    Urbanczyk-Wochniak E, Luedemann A, Kopka J, Selbig J, Roessner-Tunali U, Wilmitzer L, Fernie AR (2003) Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO rep 4: 1–5CrossRefGoogle Scholar
  131. 131.
    Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37: 914–939PubMedCrossRefGoogle Scholar
  132. 132.
    Sweetlove LJ, Fernie AR (2005) Regulation of metabolic networks: understanding metabolic complexity in the system biology era. New Phytol 168: 9–24PubMedCrossRefGoogle Scholar
  133. 133.
    Fridman E, Pichersky E (2005) Metabolomics, genomics, proteomics and the identification of enzymes and their substrates and products. Curr Opin Plant Biol 8: 242–248PubMedCrossRefGoogle Scholar
  134. 134.
    Blank LM, Kuepfer L, Sauer U (2005) Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutation in yeast. Genome Biol. 6: R49PubMedCrossRefGoogle Scholar
  135. 135.
    Tewari M, Hu PJ, Ahn JS, Ayivi-Guedelhoussou N, Vidalain P-O, Li S, Milstein S, Armstrong CM, Boxem M, Butler MD et al. (2004) Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-β signalling network. Mol Cell 13: 469–482PubMedCrossRefGoogle Scholar
  136. 136.
    Enns LC, Kanaoka MM, Torii KU, Comai L, Okada K, Cleland RE (2005) Two callose synthases, GSL1 and GSL5, play an essential and redundant role in plant and pollen development and in fertility. Plant Mol Biol 58: 333–349PubMedCrossRefGoogle Scholar
  137. 137.
    Weckwerth W, Loureiro ME, Wenzel K, Fiehn O (2004) Differential metabolic pathways unravel the effect of silent plant phenotypes. Proc Natl Acad Sci USA 101: 7809–7811PubMedCrossRefGoogle Scholar
  138. 138.
    Scholtz M, Gatzek S, Sterling A, Fiehn O, Selbig J (2004) Metabolite fingerprinting: detecting biological features by independent component analysis. Bioinformatics 20: 2447–2454CrossRefGoogle Scholar
  139. 139.
    Fernie AR, Trethevey RN, Krotzky AJ, Wilmitzer L (2004) Metabolite profiling: from diagnostic to system biology. Nat Rev 5: 1–7CrossRefGoogle Scholar
  140. 140.
    Sweetlove LJ, Last RL, Fernie AR (2003) Predictive metabolic engineering: a goal for systems biology. Plant Physiol 132: 420–425PubMedCrossRefGoogle Scholar
  141. 141.
    Rontein D, Dieuaide-Noubhani M, Dufourc EJ, Raymond P, Rolin D (2002) The metabolic architecture of plant cells: Stability of central metabolism and flexibility of anabolic pathways during the growth cycle of tomato cells. J Biol Chem 277: 43948–43960PubMedCrossRefGoogle Scholar

Copyright information

© Birkhäuser Verlag/Switzerland 2007

Authors and Affiliations

  • Christophe Rothan
    • 1
  • Mathilde Causse
    • 2
  1. 1.INRA-UMR 619 Biologie des FruitsIBVI-INRA BordeauxVillenave d’Ornon cedexFrance
  2. 2.Unité de Génétique et Amélioration des Fruits et LégumesINRA-UR 1052Montfavet cedexFrance

Personalised recommendations