Part I: Plant Germline Development: From Investigation to Application
1. An Introduction to Male Germline Development
Hannes Vogler, Ueli Grossniklaus, and Afif Hedhly
2. Apomixis: Engineering the Ability to Harness Hybrid Vigor in Crop Plants
Joann A. Conner and Peggy Ozias-Akins
Part II: Clearing, Imaging Techniques, and Immunolocalization to Study Cell Lineage, Cell Type Specificity, Cytoskeleton, Cell Cycle, Signaling, and Hormones
3. 3D Imaging of Whole-Mount Ovules at Cellular Resolution to Study Female Germline Development in Rice
Ethel Mendocilla Sato, Wenjing She, and Célia Baroux
4. Live-Cell Imaging of F-Actin Dynamics During Fertilization in Arabidopsis thaliana
Daichi Susaki, Daisuke Maruyama, Ramesh Yelagandula, Frederic Berger, and Tomokazu Kawashima
5. Development and Observation of Mature Megagametophyte Cell-Specific Fluorescent Markers
Mark A. Chamberlin and Shai J. Lawit
6. Analysis of Fluorescent Reporter Activity in the Male Germline During Pollen Development by Confocal Microscopy
David Twell and Lynette Brownfield
7. In Vivo Ploidy Determination of Arabidopsis thaliana Male and Female Gametophytes
Burcu Nur Keçeli, Nico De Storme, and Danny Geelen
8. Staining and Clearing of Arabidopsis Reproductive Tissue for Imaging of Fluorescent Proteins
Daniel Slane, Patrick Bürgel, and Martin Bayer
9. Live Cell Imaging of Auxin and Cytokinin Signaling in Maize Female Gametophytes
Antony M. Chettoor and Matthew M.S. Evans
10. Imaging Ca2+ Dynamics in Wild-Type and NADPH Oxidase-Deficient Mutant Pollen Tubes with Yellow Cameleon and Confocal Laser Scanning Microscopy
Christina Maria Franck, Jens Westermann, and Aurélien Boisson-Dernier
11. Immunolocalization of AGPs and Pectins in Quercus suber Gametophytic Structures
Mário Luís da Costa, Ana Lúcia Lopes, Maria Isabel Amorim, and Sílvia Coimbra
Part III: Chromosome Spreading, Whole Mount In Situ, and Transmission Electron Microscopy (TEM)
12.
Optimization of Cell Spreading and Image Quality for the Study of Chromosomes in Plant Tissues
Laksana Kantama, Erik Wijnker, and Hans de Jong
13. Whole Mount RNA-FISH on Ovules and Developing Seeds
Andrea Bleckmann and Thomas Dresselhaus
14. Analysis of Peroxisome Biogenesis in Pollen by Confocal Microscopy and Transmission Electron Microscopy
Peng-Fei Jia, Hong-Ju Li, and Wei-Cai Yang
15. Transmission Electron Microscopy (TEM) to Study Histology of Pollen and Pollen Tubes
Peng-Fei Jia, Hong-Ju Li, and Wei-Cai Yang
Part IV: Isolation of Specific Cells of the Male and Female Germlines
16. Isolation of Arabidopsis Pollen, Sperm Cells, and Vegetative Nuclei by Fluorescence-Activated Cell Sorting (FACS)
Mário R. Santos, Cláudia Bispo, and Jörg D. Becker
17. Isolation of Rice Sperm Cells for Transcriptional Profiling
Scott D. Russell, Daniel S. Jones, Sarah Anderson, Xinkun Wang, Venkatesan Sundaresan, and Xiaoping Gou
18. Manual Isolation of Living Cells from the Arabidopsis thaliana Female Gametophyte by Micromanipulation
Maria Englhart, Lucija Šoljić, and Stefanie Sprunck
Part V: Omics Technologies and Bioinformatic Analyses
19. Isolation and Detection of Small RNAs from Pollen
German Martinez
20. Analysis of Proteins Enriched in Rice Gamete
Takashi Okamoto
21. Phosphoprotein Enrichment from Tobacco Mature Pollen Crude Protein Extract
Jan Fíla and David Honys
22. Identification of Cis-Regulatory Modules that Function in the Male Germline of Flowering Plants
Benjamin Peters, Jack Aidley, Murray Cadzow, David Twell, and Lynette Brownfield
23. RNA-Seq Data Analysis: From Raw Data Quality Control to Differential Expression Analysis
Weihong Qi, Ralph Schlapbach, and Hubert Rehrauer
24. RNA-Seq Data Analysis Protocol: Combining In-House and Publicly Available Data
Marc W. Schmid
Part VI: Technologies with Outreach for Plant Manipulation, Studies of Pathways, and Applications in Crop Species
25. Impedance Flow Cytometry as a Tool to Analyze Microspore and Pollen Quality
Iris Heidmann and Marco Di Berardino
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26. Agrobacterium-Mediated Sorghum Transformation
Emily Wu and Zuo-Yu Zhao
27. Use of the Cas9 Orthologues from Streptococcus thermophilus and Staphylococcus aureus for Non-Homologous End-Joining Mediated Site-Specific Mutagenesis in Arabidopsis thaliana
Jeannette Steinert, Carla Schmidt, and Holger Puchta
28. Transgenic Reproductive Cell Ablation
Shai J. Lawit and Mark A. Chamberlin
29. In Vivo Reporters for Protein Half-Life
Pavel Reichman and Nico Dissmeyer
30. Conditional Modulation of Biological Processes by Low-Temperature Degrons
Nico Dissmeyer
