Brachypodium Genomics Methods and Protocols

This volume presents protocols for Brachypodium genomics in numerous areas ranging from marker development, trait evolution, functional genomics, metabolomics, transcriptomics, genomics, and tilling. This book also explores techniques to study the widening genetic base of Brachypodium that will help researchers better understand the model plant using NGS technologies. 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, Brachypodium Genomics: Methods and Protocols is a valuable resource for bench-oriented molecular biologists and computational biologists working towards further evolving this field.

Methods for Cytogenetic Chromosome Barcoding and Chromosome Painting in Brachypodium distachyon and its Relative Species.- Transcriptional and Post-Transcriptional Regulation of Drought Stress Treatments in Brachypodium Leaves.- Brachypodium distachyon Long Non-Coding RNAs: Genome-Wide Identification and Expression Analysis.- A Highly Efficient and Reproducible Fusarium spp. Inoculation Method for Brachypodium distachyon.- Tissue Culture (Somatic Embryogenesis) Induced Tnt1 Retrotransposon Based Mutagensis in Brachypodium Distrachyon.- Methods for Xyloglucan Structure Analysis in Brachypodium.- Genomic Approaches to Analyze Alternative Splicing: A Key Regulator of Transcriptome and Proteome Diversity in Brachypodium distachyon.- Information Resources for Functional genomics Studies in Brachypodium distachyon.- Methods for Functional Transgenics: Development of Highly Efficient Transformation Protocol in Brachypodium and its Suitability for Advancing Brachypodium Transgenics.- Molecular Markers in Whole Genome Evolution of Brachypodium.- Estimate Condom Usage Bias using Condon Usage Analyzer (CUA).- Identification of Pseudogenes in Brachypodium distachyon Chromosomes.- TILLING in Brachypodium distachyon.- Method for the Large Scale Identification of PhasiRNAs in Brachypodium distachyon.- Evaluation of Genome Wide Markers and Orthologous Markers in Brachypodium distachyon.- Protocol for Co-Expression Network Construction and Stress-Responsive Expression Analysis in Brachypodium.- Whole Genome DNA Methylation Analysis using Next-General Sequencing (BS-Seq).- Application of Tissue Culture and Transformation Techniques in Model Species, Brachypodium Distachyon.