Contents

Part I Plant Breeding in the Genomics Era

1 QTL Analysis in Plant Breeding 3

Maria J. Asins, Guillermo P. Bernet, Irene Villalta, and Emilio A. Carbonell

2 Comparative Genomics in Crop Plants 23

Mehboob-ur-Rahman and Andrew H. Paterson

3 Functional Genomics For Crop Improvement 63

Seedhabadee Ganeshan, Pallavi Sharma, and Ravindra N. Chibbar

4 Bioinformatics Tools for Crop Research and Breeding 97

Jayashree B and Dave Hoisington

Part II Molecular Markers and Their Application

5 Gene-Based Marker Systems in Plants: High Throughput Approaches for Marker Discovery and Genotyping 119

Rajeev K Varshney

6 Automation of DNA Marker Analysis for Molecular

Breeding in Crops 143

Christophe Dayteg and Stine Tuvesson

7 Pyramiding Genes for Enhancing Tolerance to Abiotic and Biotic Stresses 163

Raveendran Muthurajan and Ponnuswami Balasubramanian

8 Application of Molecular Markers for Breeding

Disease Resistant Varieties in Crop Plants 185

Ana M. Torres viii Contents

9 Molecular Markers Based Approaches for Drought Tolerance 207

Deepmala Sehgal and Rattan Yadav

10 Molecular Markers for Characterizing and Conserving

Crop Plant Germplasm 231

G. Barcaccia

Part III Genomics

11 Rice Genomics 257

Narayana M. Upadhyaya and Elizabeth S. Dennis

12 Genomics for Wheat Improvement 281

Michael G. Francki

13 TILLING for Mutations in Model Plants and Crops 307

Zerihun Tadele, Chikelu MBA, and Bradley J. Till

14 Microarray Analysis for Studying the Abiotic Stress

Responses in Plants 333

Motoaki Seki, Masanori Okamoto, Akihiro Matsui, Jong-Myong Kim, Yukio Kurihara, Junko Ishida, Taeko Morosawa, Makiko Kawashima, Taiko Kim To, and Kazuo Shinozaki

15 Roles of MicroRNAs in Plant Abiotic Stress 357

Ricky Lewis, Venugopal Mendu, David Mcnear, and Guiliang Tang

16 Molecular Tools for Enhancing Salinity Tolerance in Plants 373

Jesus Cuartero, Maria C. Bolarin, Vicente Moreno, and Benito Pineda

17 DNA Microarray as Part of a Genomic-Assisted

Breeding Approach 407

Eva Vincze and Steve Bowra

18 Unravelling Gene Function Through Mutagenesis 437

Andrea Hricová, Pedro Robles, and Víctor Quesada

19 Techniques in Plant Proteomics 469

Ludovít Skultéty, Maxym Danchenko, Anna Pret'ová, and Martin Hajduch

Metabolomics: Novel Tool for Studying

Complex Biological Systems

Federica Maltese and Robert Verpoorte

21 Transcriptomic Analysis of Multiple Enviornmental

Stresses in Plants 511

Niranjani Jambunathan, Michael Puckette, and Ramamurthy Mahalingam

Part IV Transgenic Technologies

22 Marker-Free Targeted Transformation 527

Hiroyasu Ebinuma and Kazuya Nanto

23 Promoter Trapping in Plants Using T-DNA Mutagenesis 545

R. Srinivasan and Dipnarayan Saha

24 Plant Genome Engineering Using Zinc Finger Nucleases 579

Sandeep Kumar and William F. Thompson

25 Cisgenesis 591

Evert Jacobsen and Henk J. Schouten

26 Gene Stacking 613

E. Douglas and C. Halpin

27 Gene Silencing 631

Sunee Kertbundit, Miloslav Juricek, and Timothy C. Hall

28 Plant RNAi and Crop Improvement 653

Masayuki Isshiki and Hiroaki Kodama

29 Metabolomics in Fruit Development 675

Kati Hanhineva and Asaph Aharoni

30 Genetic Engineering in Floriculture 695

Yoshikazu Tanaka and Ryutaro Aida

31 Transgenesis and Genomics in Forage Crops 719

Toshihiko Yamada, Ken-ichi Tamura, Xun Wang, and Yukiko Aoyagi

Author Index

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