Lotus japonicus Handbook

Contents List of editors Preface Colour plates 1 Lotus japonicus, a general introduction J. Stougaard and A.J. Márquez 1.1 Lotus japonicus as a model system E. Pajuelo and J. Stougaard 1.2 Lotus-related species and their agronomic importance P. Díaz, O. Borsani, and J. Monza 1.3 Drought and saline stress P. Díaz, J. Monza, and A.J. Márquez Symbiotic processes M. Udvardi and M. Parniske 2.1 Methods for studying nodule development and function M. Hayashi, M.L. Tansengco, N. Suganuma, K. Szczyglowski, L. Krusell, T. Ott, and M. Udvardi 2.2 A procedure for in vitro nodulation studies A. Barbulova and M. Chiurazzi 2.3 Arbuscular mycorrhiza S. Kosuta, T. Winzer, and M. Parniske 3 Cell and molecular biology protocols H.P. Spaink and M. Parniske 3.1 Concurrent visualization of gusA and lacZ reporter gene expression C. Díaz, H.R.M. Schlaman, and H.P. Spaink 3.2 Embedding root and nodule tissue in plastic (BMM) M. GrÆ nlund, A. Agalou, M.C. Rubio, G.E.M. Lamers, A. Roussis, and H.P. Spaink 3.3 RNA isolation using phase extraction and LiCl precipitation C. Kistner and M. Matamoros 3.4 RNA isolation using CsCl gradients T. Ott, L. Krussell, and M. Udvardi 3.5 96-well DNA isolation method J. Perry and M. Parniske 4 Functional genomics M. Udvardi and G. Saalbach 4.1 Genome structural analysis S. Tabata 4.2 Transcriptome analysis using cDNA arrays T. Ott, L. Krusell, S. Freund, and M. Udvardi 4.3 Lotus japonicus expression database S. Kloska, P. Krüger, and J. Selbig 4.4 Procedures for mass spectrometric proteome analysis G. Saalbach 4.5 Isolation of peribacteroid membranes for proteome analysis S. Wienkoop 4.6 Metabolome analysis using GC-MS G. Debrosses, D. Steinhauser, J. Kopka, and M. Udvardi Mutants, gene-tagging, and genetic analysis J. Stougaard and K.J.Webb 5.1 Mutagenesis K.J. Webb, M. Robbins, T.L. Wang, M. Parniske, and A.J. Márquez 5.2 A mutant catalogue of Lotus japonicus E. Pajuelo 5.3 TILLING J. Perry, T. Welham, S. Cheminant, M. Parniske, and T. Wang 5.4 Ds gene tagging L. Tirichine, J.A. Herrera-Cervera, and J. Stougaard 5.5 Mapping and map-based cloning N. Sandal, K. Krause, M. Frantescu, S. Radutoiu, L. Krusell, L.H. Madsen, N. Kanamori, E. Madsen, L. Tirichine, and J. Stougaard 5.6 An in silico strategy using comparative sequence analysis L. Schauser, S. Subrahmanyam, L.H. Madsen, N. Sandal, and J. Stougaard 5.7 Information transfer: mapping and cloning in other legumes L.H. Madsen and J. Stougaard 6 Transformation and reverse genetic analysis M. Chiurazzi 6.1 Agrobacterium-mediated in vitro transformation P. Lombari, E. Ercolano, H. El Alaoui, and M. Chiurazzi 6.2 Induction of hairy roots for symbiotic gene expression studies C.L. Diaz, M. Gronlund, H.R.M. Schlaman, and H.P. Spaink 6.3 Transformation-regeneration procedure L. Tirichine, J.A. Herrera, and J. Stougaard 6.4 Agrobacterium rhizogenes pRi TL-DNA integration system S. Radutoiu, L.H. Madsen, E.B. Madsen, and J. Stougaard 6.5 Vectors for reverse genetics and expression analysis S.U. Andersen, C. Cvitanich, M. Gronlund, H. Busk, D.B. Jensen, and E.O. Jensen 7 Primary and secondary metabolism A.J. Marquez and K.J. Webb 7.1 Nitrate assimilation: Influence of nitrogen supply A. Orea, P. Pajuelo, J.M. Romero, and A.J. Márquez 7.2 Nitrate and ammonium assimilatory enzymes