Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ix
PART I ARABIDOPSIS RESOURCES
1 Handling Arabidopsis and Other Brassicaceae: Growth,
Preservation of Seeds, Transformation, and Genetic Crosses. . . . . . . . . . . . . . . . . .
3
Christopher Calhoun, Deborah Crist, Emma Knee,
Julie Miller, Eva Nagy, and David E. Somers
2 Bioinformatic Tools in Arabidopsis Research. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
G. Alex Mason, Alex Cant o-Pastor, Siobhan M. Brady,
and Nicholas J. Provart
PART II GENETIC TECHNIQUES IN ARABIDOPSIS
3 Analyses of Natural Variation: Field Experiments
and Nucleotide Diversity for Your Favorite Gene . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Carlos Alonso-Blanco, Bele ´n Me ´ndez-Vigo, and F. Xavier Pic o
4 Non-sterile Grafting Methods for Arabidopsis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Nien-Chen Huang and Tien-Shin Yu
5 CRISPR/Cas9-Based Genome Editing Toolbox
for Arabidopsis thaliana . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Daisuke Miki, Gaurav Zinta, Wenxin Zhang, Fangnan Peng,
Zhengyan Feng, and Jian-Kang Zhu
6 Transient Transformation of A. thaliana Seedlings
by Vacuum Infiltration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Ce ´sar Bernat-Silvestre, Vanessa De Sousa Vieira, Judit Sa ´ nchez-Simarro,
Fernando Aniento, and Marı ´a Jesu ´ s Marcote
7 Transient Expression of Fluorescent Fusion Proteins
in Arabidopsis Protoplasts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Yonglun Zeng, Changyang Ji, Youshun Lin, and Liwen Jiang
8 Arabidopsis Photosynthetic and Heterotrophic Cell
Suspension Cultures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Enrico Cortese, Luca Carraretto, Barbara Baldan,
and Lorella Navazio
9 Genome-Wide Association Studies in Arabidopsis thaliana:
Statistical Analysis and Network-Based Augmentation of Signals . . . . . . . . . . . . . . 187
Tak Lee and Insuk Lee
vii
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ix
PART I ARABIDOPSIS RESOURCES
1 Handling Arabidopsis and Other Brassicaceae: Growth,
Preservation of Seeds, Transformation, and Genetic Crosses. . . . . . . . . . . . . . . . . .
3
Christopher Calhoun, Deborah Crist, Emma Knee,
Julie Miller, Eva Nagy, and David E. Somers
2 Bioinformatic Tools in Arabidopsis Research. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
G. Alex Mason, Alex Cant o-Pastor, Siobhan M. Brady,
and Nicholas J. Provart
PART II GENETIC TECHNIQUES IN ARABIDOPSIS
3 Analyses of Natural Variation: Field Experiments
and Nucleotide Diversity for Your Favorite Gene . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Carlos Alonso-Blanco, Bele ´n Me ´ndez-Vigo, and F. Xavier Pic o
4 Non-sterile Grafting Methods for Arabidopsis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Nien-Chen Huang and Tien-Shin Yu
5 CRISPR/Cas9-Based Genome Editing Toolbox
for Arabidopsis thaliana . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Daisuke Miki, Gaurav Zinta, Wenxin Zhang, Fangnan Peng,
Zhengyan Feng, and Jian-Kang Zhu
6 Transient Transformation of A. thaliana Seedlings
by Vacuum Infiltration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Ce ´sar Bernat-Silvestre, Vanessa De Sousa Vieira, Judit Sa ´ nchez-Simarro,
Fernando Aniento, and Marı ´a Jesu ´ s Marcote
7 Transient Expression of Fluorescent Fusion Proteins
in Arabidopsis Protoplasts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Yonglun Zeng, Changyang Ji, Youshun Lin, and Liwen Jiang
8 Arabidopsis Photosynthetic and Heterotrophic Cell
Suspension Cultures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Enrico Cortese, Luca Carraretto, Barbara Baldan,
and Lorella Navazio
9 Genome-Wide Association Studies in Arabidopsis thaliana:
Statistical Analysis and Network-Based Augmentation of Signals . . . . . . . . . . . . . . 187
Tak Lee and Insuk Lee
vii