Oat: Methods and Protocols

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

Part II In Vitro Cultures and Genetic Transformation

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

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

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-Bascón, Corey D. Broeckling, Owen A. Hoekenga, Elena Prats, Mark Sorrells, and Julia Isidro-Sánchez

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 Märtlbauer, 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 Onysk 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 Sánchez, Deniz Akdemir, and Gracia Montilla-Bascón

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 Nalecz, Marta Dziuba, and Iwona Szerszunowicz

17. 2-DE Separation and Identification of Oat (Avena sativa L.) Proteins and their Prolamin Fractions
Dorota Nalecz, 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 Nalecz, and Marta Dziuba