Brachypodium Genomics: Methods and Protocols

1. Methods for Cytogenetic Chromosome Barcoding and Chromosome Painting in Brachypodium distachyon and its Relative Species
Dominika Idziak and Alexander Betekhtin

2. Transcriptional and Post-Transcriptional Regulation of Drought Stress Treatments in Brachypodium Leaves
Edoardo Bertolini, Mario Enrico Pè and Erica Mica

3. Brachypodium distachyon Long Non-Coding RNAs: Genome-Wide Identification and Expression Analysis
Concetta De Quattro, Erica Mica, Mario Enrico Pè and Edoardo Bertolini

4. A Highly Efficient and Reproducible Fusarium spp. Inoculation Method for Brachypodium distachyon
Anuj Rana, Aneesh Karunakaran, Timothy L. Fitzgerald, Rosalie Sabburg, Elizabeth A.B. Aitken, Robert J. Henry, Jonathan J. Powell, and Kemal Kazan

5. Tissue Culture (Somatic Embryogenesis) Induced Tnt1 Retrotransposon Based Mutagensis in Brachypodium Distrachyon
Upinder S. Gill, Juan C. Serrani-Yarce, Hee-Kyung Lee, and Kirankumar S. Mysore

6. Methods for Xyloglucan Structure Analysis in Brachypodium
Lifeng Liu

7. Genomic Approaches to Analyze Alternative Splicing: A Key Regulator of Transcriptome and Proteome Diversity in Brachypodium distachyon
Sonia Irigoyen, Renesh H. Bedre, Karen-Beth G. Schothof, and Kranthi K. Mandadi

8. Information Resources for Functional genomics Studies in Brachypodium distachyon
Keiichi Mochida and Kazuo Shinozaki

9. Methods for Functional Transgenics: Development of Highly Efficient Transformation Protocol in Brachypodium and its Suitability for Advancing Brachypodium Transgenics
Ron Vunsh

10. Molecular Markers in Whole Genome Evolution of Brachypodium
Xin-chun Mo, De-quan Zhang, Can Kou, and Ling-juan Yin

11. Estimate Condom Usage Bias using Condon Usage Analyzer (CUA)
Zhenguo Zhang and Gaurav Sablok


12. Identification of Pseudogenes in Brachypodium distachyon Chromosomes
Salvatore Camiolo and Andrea Porceddu

13. TILLING in Brachypodium distachyon
Louise de Bang, Anna Maria Torp, and Søren K. Rasmussen

14. Method for the Large Scale Identification of PhasiRNAs in Brachypodium distachyon
Kun Yang, Xiaopeng Wen, and Gaurav Sablok

15. Evaluation of Genome Wide Markers and Orthologous Markers in Brachypodium distachyon
Gaurav Sablok, Suresh B. Mudunuri, Korneliya Gudys, G.P. Saradhi Varma, and Miroslaw Kwasniewski

16. Protocol for Co-Expression Network Construction and Stress-Responsive Expression Analysis in Brachypodium
Sanchari Sircar, Nita Parekh, and Guarav Sablok

17. Whole Genome DNA Methylation Analysis using Next-General Sequencing (BS-Seq)
I-Hsuan Lin

18. Application of Tissue Culture and Transformation Techniques in Model Species, Brachypodium Distachyon
Bahar Sogutmaz Ozdemir and Hikmet Budak