The volume provides detailed protocols that have been developed or modified exclusively for the study of oat. The topics discussed in this book are a selection of various molecular biology and biotechnology methods, such as the application of molecular markers for polymorphism analyses and cytological manipulations, the production of synthetic polyploids, and in vitro cultures and genetic modifications. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and comprehensive, Oat: Methods and Protocols is a useful resource in the development of new research approaches toward organizing the oat genome and the identification of new and useful traits for further improvements of this exceptional crop.

Preface...
Table of Contents...
Contributing Authors...

Part I Cytological Methods

1. Fluorescence In Situ Hybridization in Oat
Eva Wegel

2. Oat Doubled Haploids Following Maize Pollination
Philip A. Davies and Parminder K. Sidhu

3. Wide Hybridization between Oat and Pearl Millet
Takayoshi Ishii

4. Protocol for Producing Synthetic Polyploid Oats
Toshinobu Morikawa

5. Manipulation of Oat Protoplasts for Transient Expression Assays
Robyn Roberts, Jincan Zhang, Nicole Mihelish, Danielle Savino, Aurlie M. Rakotondrafara

6. Oat Anther Culture and Use of DH-Lines for Genetic Mapping
Elina Kiviharju, Sirpa Moisander, and Pirjo Tanhuanp

7. Agrobacterium-Mediated Transformation of Leaf Base Segments
Sebastian Gasparis

Part III Quality Assessment

8. Chromatographic Methods to Evaluate Nutritional Quality in Oat
Gracia Montilla-Bascn, Corey D. Broeckling, Owen A. Hoekenga, Elena Prats, Mark Sorrells, and Julia Isidro-Snchez

9. Determination of T-2 and HT-2 Toxins in Oats and Oat-Based Breakfast Cereals by Liquid-Chromatography Tandem Mass Spectrometry
Veronica M.T. Lattanzio and Michelangelo Pascale

10. Multiplex Dipstick Immunoassay for Semi-Quantitative Determination of Fusarium Mycotoxins in Oat
Veronica M.T. Lattanzio and Noan Nivarlet

11. Microarray-Based Immunoassay for Parallel Quantification of Multiple Mycotoxins in Oat
Susanna Oswald, Richard Dietrich, Erwin Mrtlbauer, Reinhard Niessner, and Dietmar Knopp

Part IV Genomic Studies

12. M13-Tailed Simple Sequence Repeat (SSR) Markers in Studies of Genetic Diversity and Population Structure of Common Oat Germplasm
Agnieszka Onyśk and Maja Boczkowska

13. Genotyping-By-Sequencing and its Application to Oat Genomic Research
Yong-Bi Fu and Mo-Hua Yang

14. Genome-Wide Association Analysis using R
Julio Isidro Snchez, Deniz Akdemir, and Gracia Montilla-Bascn

15. de novo Transcriptome Assembly in Polyploid Species
Juan J. Gutierrez-Gonzalez and David F. Garvin

Part V Proteomics Methods

16. Isolation of Oat (Avena sativa L.) Total Proteins and their Prolamin Fractions for 2-D Electrophoresis
Dorota Nalęcz, Marta Dziuba, and Iwona Szerszunowicz

17. 2-DE Separation and Identification of Oat (Avena sativa L.) Proteins and their Prolamin Fractions
Dorota Nalęcz, Iwona Szerszunowicz, Marta Dziuba, and Piotr Minkiewicz

18. Selected Bioinformatic Tools and MS (MALDI-TOF, PMF) Techniques used in the Strategy for the Identification of Oat Proteins after 2-DE
Iwona Szerszunowicz, Dorota Nalęcz, and Marta Dziuba