Prefacе ....................................................... vii
Acknowledgements ............................................... ix
Contributors ................................................. xiii
1 Historical Overview of Transposable Element Research ......... 1
Peter A. Peterson
2 Distinguishing Variable Phenotypes from Variegation Caused
by Transposon Activities .................................... 11
Virginia Walbot
3 Using Transposons for Genetic Mosaic Analysis of Plant
Development ................................................. 21
Philip W. Becraft
4 Survey of Natural and Transgenic Gene Markers Used to
Monitor Transposon Activity ................................. 43
Labhminarasimhan Krishnaswamy and Thomas Peterson
5 Molecular Biology of Maize Ac/Ds Elements: An Overview ...... 59
Katina Lazarow, My-Linh Doll, and Reinhard Kunze
6 Gene Tagging with Engineered Ds Elements in Maize ........... 83
Yubin Li, Gregorio Segal, Qinghua Wang, and Hugo K. Dooner
7 Plant Regeneration Methods for Rapid Generation of a Large
Scale Ds Transposant Population in Rice .................... 101
Yuan Hu Xuan, Jin Huang, Gihwan Yi, Dong-Soo Park, Soo
Kwon Park, Moo Young Eun, Doh Won Yun, Gang-Seob Lee,
Toe Ho Kim, and Chang-deok Han
8 Isolation of Sequences Flanking А с Insertion Sites by
Ac Casting ................................................. 117
Dafang Wang and Thomas Peterson
9 Regulation of the Mutator System of Transposons in Maize ... 123
Damon Lisch
10 Using MuDR/Mu Transposons in Directed Tagging Strategies ... 143
Virginia Walbot and Julia Qüesta
11 Genetic and Molecular Analyses of UniformMu Transposon
Insertion Lines ............................................ 157
Donald R. McCarty, Masaharu Suzuki, Charles Hunter,
Joseph Collins, Wayne T. Avigne, and Karen E. Koch
12 Digestion-Ligation-Amplification (DLA): A Simple Genome
Walking Method to Amplify Unknown Sequences Flanking
Mutator (Mu) Transposons and Thereby Facilitate Gene
Cloning .................................................... 167
Sanzhen Liu, An-Ping Hsia, and Patrick S. Schnable
13 Molecular Genetics and Epigenetics of CACTA Elements ....... 177
Nina V. Fedoroff
14 Activation Tagging Using the Maize En-I Transposon System
for the Identification of Abiotic Stress Resistance Genes
in Arabidopsis ............................................. 193
Amal Harb and Andy Pereira
15 Reverse Genetics in Rice Using Tosl7 ....................... 205
Delphine Mieulet, Anne Diévart, Gaëtan Droc, Nadège Lanau,
and Emmanuel Guiderdoni
16 Identification and Applications of the Petunia Class II
Act1/dTph1 Transposable Element System .................... 223
Tom Gerats, Jan Zethof, and Michiel Vandenbussche
17 Transposon Display: A Versatile Method for Transposon
Tagging .................................................... 239
Michiel Vandenbussche, Jan Zethof, and Tom Gerats
18 Massive Indexed Parallel Identification of Transposon
Flanking Sequences ......................................... 251
Michiel Vandenbussche, Jan Zethof, and Tom Gerats
19 Use of Next Generation Sequencing (NGS) Technologies
for the Genome-Wide Detection of Transposition ............. 265
Moaine Elbaidouri, Cristian Chaparro, and Olivier Panaud
20 Overview of Repeat Annotation and De Novo Repeat
Identification ............................................. 275
Ning Jiang
21 Computational Methods for Identification of DNA
Transposons ................................................ 289
Ning Jiang
22 TEnest 2.0: Computational Annotation and Visualization
of Nested Transposable Elements ............................ 305
Brent A. Kronmiller and Roger P. Wise
Index ......................................................... 321
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