Chromosome and Genomic Engineering in Plants: Methods and Protocols

1. Production of Engineered Minichromosome Vectors via the Introduction of Telomere Sequences
Nathaniel Graham, Nathan Swyers, Jon Cody, Morgan McCaw, Changzeng Zhao, and James A. Birchler

2. Method for Biolistic Site-Specific Integration in Rice and Tobacco Catalyzed by Bxb1 Integrase
Ruyu Li, Zhiguo Han, Lili Hou, Gurminder Kaur, Qian Yin, and David W. Ow

3. Protocol for In Vitro Stacked Molecules Compatible with In Vivo Recombinase Mediated Gene Stacking
Weiqiang Chen and David W. Ow

4. Generation and Analysis of Transposon Ac/Ds-Induced Chromosomal Rearrangements in Rice Plants
Yuan Hu Xuan, Thomas Peterson, and Chang-deok Han

5. One-Step Generation of Chromosomal Rearrangements in Rice
Minoru Murata, Asaka Kanatani, and Kazunari Kashihara

6. Genome Elimination by Tailswap CenH3: In Vivo Haploid Production in Arabidopsis thaliana
Ravi Maruthachalam and Ramesh Bondada

7. Gametocidal Systems for Dissecting Wheat Chromosomes
Hisashi Tsujimoto

8. CRISPR/Cas-Mediated Site-Specific Mutagenesis in Arabidopsis thaliana Using Cas9 Nucleases and Paired Nickases
Simon Schiml, Friedrich Fauser, and Holger Puchta

9. Targeted Mutagenesis in Rice Using and TALENs and the CRISPR/Cas9 System
Masaki Endo, Ayako Nishizawa-Yokoi, and Seiichi Toki

10. Seamless Genome Editing in Rice via Gene Targeting and Precise Marker Elimination
Ayako Nishizawa-Yokoi, Hiroaki Saika, and Seiichi Toki

11.      Development of Genome Engineering Tools from Plant-Specific PPR Proteins Using Animal Cultured Cells
Takehito Kobayashi, Yusuke Yagi, and Takahiro Nakamura

12. Chromosomal Allocation of DNA Sequences in Wheat Using Flow-Sorted Chromosomes
Petr Cápal, Jan Vrána, Marie Kubaláková, Takashi R. Endo, and Jaroslav Dolezel

13. Image Analysis of DNA Fiber and Nucleus in Plants
Nobuko Ohmido, Toshiyuki Wako, Seiji Kato, and Kiichi Fukui

14. Detection of Transgenes on DNA Fibers
Fukashi Shibata 

15. Three-Dimensional, Live-Cell Imaging of Chromatin Dynamics in Plant Nuclei Using Chromatin Tagging Systems
Takeshi Hirakawa and Sachihiro Matsunaga

16. Chromatin Immunoprecipitation for Detecting Epigenetic Marks on Plant Nucleosomes
Kiyotaka Nagaki

17. Mapping of T-DNA and Ac/Ds by TAIL-PCR to Analyze Chromosomal Rearrangements<Satoru Fujimoto, Sachihiro Matsunaga, and Minoru Murata