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Table of Contents
Intro; Preface to the Series; Preface; Acknowledgements; Contents; 1 Economic and Academic Importance of Barley; Abstract; 1.1 Background; 1.2 World Barley Production; 1.3 Barley End Uses; 1.3.1 New Trends in Barley End Uses; 1.4 Academic Importance of Barley; 1.4.1 Examples of the Broad Impact of Barley Research; 1.4.1.1 Domestication; 1.4.1.2 Disease Resistance; 1.4.1.3 Mutation Research; 1.4.1.4 Grain Development and Germination; 1.5 Conclusions; References; 2 Taxonomy of the Genus Hordeum and Barley (Hordeum vulgare); Abstract; 2.1 Taxonomic Principles; 2.2 Hordeum and Triticeae
2.3 The Genus Hordeum and Subgeneric Units Within2.4 The Gene Pool Concept in Barley; 2.5 The Taxonomy of Barley in the Light of Its Evolution; 2.6 Conclusions; References; 3 Cytogenetics and Genetic Stocks for Physical Mapping and Sequencing; Abstract; 3.1 Identification of Barley Chromosomes; 3.2 Chromatin Composition of Barley; 3.3 Telomeres and Their Application for the Generation of Barley Mini-Chromosomes; 3.4 Analysis of the Barley Centromere and Its Role in the Process of Haploidization; 3.5 Barley Cytogenetic Stocks; 3.5.1 Trisomics
3.5.2 Wheat-Barley Addition, Substitution and Translocation Lines3.5.3 Translocations Lines; 3.6 Cytological Mapping of Barley Chromosomes; 3.6.1 Deletion Stocks and Their Use in Cytological Mapping; 3.7 Application of FISH to Correlate the Genetic with the Cytological Map of Barley; References; 4 Chromosomal Genomics of Barley; Abstract; 4.1 Development of Barley Chromosomal Genomics; 4.2 Applications of Flow Cytogenetics; 4.2.1 Physical Mapping; 4.2.2 Next-Generation Sequencing; 4.2.3 Preparation of High-Molecular-Weight DNA and Its Applications
4.2.4 Chromosomal Genomics in the Post-sequencing EraAcknowledgements; References; 5 Barley Genome Sequencing and Assembly-A First Version Reference Sequence; Abstract; 5.1 Introduction; 5.2 Whole-Genome Sequencing; 5.2.1 Sequencing Strategy and Assembly; 5.2.2 Genetic and Physical Ordering-Chromosome-Like Assemblies; 5.2.3 Barley RefSeq v1.0-Practical Considerations; 5.3 More Barley Genomes: The Barley Pan-Genome; Acknowledgements; References; 6 Gene Prediction in the Barley Genome; Abstract; 6.1 Introduction; 6.2 Evidence for Automated Gene Prediction; 6.3 Automated Gene Prediction Pipeline
6.4 ORF Prediction and Selection6.5 Confidence Classification of Gene Predictions; 6.6 Evaluation of Gene Calls; 6.6.1 Comparison to Gene Models in the WGS Assembly of Barley cv. Morex; 6.6.2 Benchmarking Universal Single-Copy Orthologs (BUSCO); 6.7 (Automated) Functional Annotation of Gene Models in Barley; 6.8 Characteristics and Number of Predicted Gene Models; 6.9 Data Availability and Download; 6.10 Annotation Shortcomings and Ways to Improve the Annotation; References; 7 The Expressed Portion of the Barley Genome; Abstract; 7.1 Introduction; 7.2 Dynamics of Gene Expression in Barley
2.3 The Genus Hordeum and Subgeneric Units Within2.4 The Gene Pool Concept in Barley; 2.5 The Taxonomy of Barley in the Light of Its Evolution; 2.6 Conclusions; References; 3 Cytogenetics and Genetic Stocks for Physical Mapping and Sequencing; Abstract; 3.1 Identification of Barley Chromosomes; 3.2 Chromatin Composition of Barley; 3.3 Telomeres and Their Application for the Generation of Barley Mini-Chromosomes; 3.4 Analysis of the Barley Centromere and Its Role in the Process of Haploidization; 3.5 Barley Cytogenetic Stocks; 3.5.1 Trisomics
3.5.2 Wheat-Barley Addition, Substitution and Translocation Lines3.5.3 Translocations Lines; 3.6 Cytological Mapping of Barley Chromosomes; 3.6.1 Deletion Stocks and Their Use in Cytological Mapping; 3.7 Application of FISH to Correlate the Genetic with the Cytological Map of Barley; References; 4 Chromosomal Genomics of Barley; Abstract; 4.1 Development of Barley Chromosomal Genomics; 4.2 Applications of Flow Cytogenetics; 4.2.1 Physical Mapping; 4.2.2 Next-Generation Sequencing; 4.2.3 Preparation of High-Molecular-Weight DNA and Its Applications
4.2.4 Chromosomal Genomics in the Post-sequencing EraAcknowledgements; References; 5 Barley Genome Sequencing and Assembly-A First Version Reference Sequence; Abstract; 5.1 Introduction; 5.2 Whole-Genome Sequencing; 5.2.1 Sequencing Strategy and Assembly; 5.2.2 Genetic and Physical Ordering-Chromosome-Like Assemblies; 5.2.3 Barley RefSeq v1.0-Practical Considerations; 5.3 More Barley Genomes: The Barley Pan-Genome; Acknowledgements; References; 6 Gene Prediction in the Barley Genome; Abstract; 6.1 Introduction; 6.2 Evidence for Automated Gene Prediction; 6.3 Automated Gene Prediction Pipeline
6.4 ORF Prediction and Selection6.5 Confidence Classification of Gene Predictions; 6.6 Evaluation of Gene Calls; 6.6.1 Comparison to Gene Models in the WGS Assembly of Barley cv. Morex; 6.6.2 Benchmarking Universal Single-Copy Orthologs (BUSCO); 6.7 (Automated) Functional Annotation of Gene Models in Barley; 6.8 Characteristics and Number of Predicted Gene Models; 6.9 Data Availability and Download; 6.10 Annotation Shortcomings and Ways to Improve the Annotation; References; 7 The Expressed Portion of the Barley Genome; Abstract; 7.1 Introduction; 7.2 Dynamics of Gene Expression in Barley