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Note: Engl. Berichtbl. u.d.T.: Final report of subproject GS1 - "Automated acquisition and genetic analysis of quantitative drought tolerance components in spring barley" , Förderkennzeichen BMBF 0315530E. - Verbund-Nr. 01074436 , Unterschiede zwischen dem gedruckten Dokument und der elektronischen Ressource können nicht ausgeschlossen werden , Systemvoraussetzungen: Acrobat reader.

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Note: Förderkennzeichen BMBF 0312830. - Literaturverz. - Engl. Titel: Establishment of the federal ex situ genebank for agricultural and horticultural crop plants: merging the genebanks of the IPK and the BAZ Braunschweig , Unterschiede zwischen dem gedruckten Dokument und der elektronischen Ressource können nicht ausgeschlossen werden , Systemvoraussetzungen: Acrobat reader.

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Note: Intro -- Foreword -- Foreword -- Preface -- Contents -- Contributors -- Part I Managing Genetic Resources -- Chapter 1 Building a Global Plant Genetic Resources System -- 1.1 Introduction: Global Situation -- 1.1.1 World Population, Hunger and Malnutrition -- 1.1.2 Food Production Situation -- 1.1.3 Climate Change -- 1.2 How can Agriculture Meet Those Challenges? -- 1.2.1 Changes Needed in Agricultural Systems -- 1.2.2 Use of Genetic Diversity and Agrobiodiversity -- 1.2.3 Genetic Resources in Details -- 1.3 A Global System for the Conservation and Sustainable Use of Plant Genetic Resources -- 1.3.1 Today's Situation -- 1.3.2 An Evolving Global System: Some Historical References -- 1.3.3 Elements of a Global System -- 1.3.3.1 The Policy Elements -- 1.3.3.2 The Technical Elements -- Collaborative activities -- 1.3.3.3 The Financial Elements and Mechanisms -- 1.4 Conclusion -- References -- Chapter 2 Genomic Approaches and Intellectual Property Protection for Variety Release: A Perspective from the Private Sector -- 2.1 Critical Needs to Increase Genetic Gain -- 2.2 Intellectual Property Protection -- 2.2.1 Methods of IPP Used in Plant Breeding -- 2.3 Technical Aspects of Obtaining IPP -- 2.3.1 Concerns About the Use of Molecular Markers to Describe Varieties de novo -- 2.3.2 Concerns About the Use of Phenotypic Characteristics to Describe Varieties de novo -- 2.4 Improving the DUS process: The rationale for Change to the Use of Molecular Characteristics -- 2.4.1 Criteria Required for the Development of Standardized Procedures for DUS -- 2.4.2 Evaluation of SNPs and Development of Standardized Procedures for DUS, EDV, and Variety Identification in Maize -- 2.5 Conclusions -- References -- Chapter 3 The Use of Molecular Marker Data to Assistin the Determination of Essentially Derived Varieties -- 3.1 Introduction. , 3.2 Main Objectives for Introducing and Implementing the EDV Concept -- 3.2.1 Who Determines EDV Status? -- 3.2.2 Why Have Breeders Taken the Initiative to Help Determine What Constitutes an EDV? -- 3.2.3 How is EDV Status Determined? -- 3.3 Predominant Derivation -- 3.4 Measure of Conformity: A Clear Starting Point -- 3.5 The Use of Molecular Markers to Help Determine EDV Status -- 3.5.1 What Degree of Similarity is Required to Determine that a Variety is ``Essentially Derived''? -- 3.5.2 Using Molecular Markers to Help Determine Essential Derivation in Maize: A Case Study -- 3.6 Ruling by the Court of Appeals, The Hague in Danziger Flower Farm vs. Astee Flowers on Technical Issues -- 3.7 Concluding Comments -- References -- Chapter 4 Application of Molecular Markers in Spatial Analysis to Optimize In Situ Conservation of Plant Genetic Resources -- 4.1 Introduction -- 4.2 Application of Molecular Markers to Optimize In Situ Conservation -- 4.3 Geospatial Analysis Techniques for Mapping Molecular Genetic Diversity -- 4.4 Case Study: Climate Change Impact on Cherimoya: Microsatellite Diversity and its Distribution Currentlyand in the Future -- 4.4.1 Introduction -- 4.4.2 Methods -- 4.4.2.1 Sampling and SSR Analysis -- 4.4.2.2 Spatial Analysis -- 4.4.3 Results and Discussion -- References -- Chapter 5 Historical and Prospective Applications of `Quantitative Genomics' in UtilisingGermplasm Resources -- 5.1 Introduction -- 5.2 The Pedigree Era -- 5.2.1 The Infinitesimal Model -- 5.2.2 The Concept of Breeding Values -- 5.2.3 Selection Indices -- 5.2.4 Best Linear Unbiased Prediction (BLUP) -- 5.3 The Molecular Era -- 5.3.1 QTL Mapping -- 5.3.2 The Candidate Gene Approach -- 5.3.3 Gene Introgression and QTL Pyramiding -- 5.4 The Genomic Era -- 5.4.1 Genome-Wide Selection -- 5.4.2 Stepwise Regression, BLUP and the Bayesian Alphabet. , 5.4.3 How Many Markers Do We Need? -- 5.4.4 The Use of Low Density SNP Chips -- 5.4.5 Training Population Size and Design -- 5.4.6 Marker Assisted Recurrent Selection (MARS) -- 5.4.7 Maintaining Genetic Diversity -- 5.5 GWS or MAS/MARS? -- References -- Part II Platforms and Approaches to Investigate Plant Genetic Resources -- Chapter 6 High-throughput SNP Profiling of Genetic Resources in Crop Plants Using Genotyping Arrays -- 6.1 Introduction -- 6.2 Identification of SNPs -- 6.2.1 Transcriptome Sequencing -- 6.2.2 Reduced Complexity Sequencing -- 6.2.3 Whole Genome Sequencing -- 6.3 Selection of SNPs for a Genotyping Array -- 6.4 SNP Calling Based on Array Data -- 6.5 Analysis of SNP Genotyping Data from a Large Array -- 6.6 Large SNP arrays in crop plants and examples for their use -- 6.6.1 Availability of Large Genotyping Arrays for Crop Plants -- 6.6.2 Examples for the Use of Large Genotyping Arrays for the Characterization of Plant Germplasm and Varieties -- 6.7 Summary and Future Trends -- References -- Chapter 7 Paleogenomics as a Guide for Traits Improvement -- 7.1 Introduction -- 7.1.1 Genome Sequences Available and Sequencing Strategies -- 7.1.1.1 Genome Sequencing Strategies -- 7.1.1.2 Released Plant Genome Sequences -- 7.1.2 Comparative Genomics Methods, Data and Online Tools -- 7.1.2.1 Comparative Genomics Parameters and Standards -- 7.1.2.2 Plant Synteny Viewer Tools -- 7.1.3 Plant Genome Ancestors and Reconstructed Karyotypes -- 7.1.3.1 Plant Genome Syntenies -- 7.1.3.2 Plant Genome Duplications -- 7.1.3.3 Ancestral Plant Karyotypes -- 7.1.3.4 Paleohistorical Shuffling Events -- 7.1.3.5 Structural and Functional Consequences of Evolution -- 7.1.4 CAr aNd Derived COS for Genetic and Physical Mapping -- 7.1.4.1 Computed Gene Order in Complex Non-Sequenced Genomes -- 7.1.4.2 Universal Conserved Orthologous Set (COS) markers. , 7.1.4.3 Strategy of Physical and Genetic Mapping from Ancestral Karyotypes -- 7.1.5 Complex Traits Dissection -- 7.1.5.1 Examples of Conserved and Non-Conserved Traits/Genes in Grasses -- 7.1.5.2 Comparative Genomics-Based Trait Dissection in Grasses -- 7.1.5.3 From Paleogenomics Data to Traits Improvement -- 7.2 Future ChalLenges -- References -- Chapter 8 Non-invasive Phenotyping Methodologies Enable the Accurate Characterization of Growth and Performance of Shoots and Roots -- 8.1 A Growing Number of Imaging Applications Enrich the Plant Phenotyping Portfolio -- 8.2 Precision Phenotyping of Canopies Structure and Photosynthetic Performance -- 8.3 Non-invasive Fluorescence Imaging of Arabidopsis Enables the Quantification of Phenotypic Diversity Driven by Genetic and Environmental Factors -- 8.4 Nuclear Magnetic Resonance Imaging (MRI): A Tool for Characterizing and Optimizing the Dynamic Processes of Rhizogenesis and Root Growth of Cuttings -- 8.5 Conclusions -- References -- Chapter 9 Association Mapping of Genetic Resources: Achievements and Future Perspectives -- 9.1 Introduction -- 9.1.1 Population Structure and Association Mapping Methods -- 9.1.2 Nested Association Mapping (NAM) -- 9.1.3 Software for Association Mapping -- 9.1.4 Computational Speed -- 9.2 Achievements -- 9.2.1 Association Mapping in Plants -- 9.2.2 GWAS in Plants -- 9.2.3 Arabidopsiss -- 9.2.4 Maize -- 9.2.5 Rice -- 9.2.6 Community Resources in Wheat, Barley, Soybean, and Sorghum -- 9.3 Challenges and Opportunities -- 9.3.1 Missing Heritability -- 9.3.2 New Gene Identification -- 9.3.3 Genotyping-by-Sequencing (GBS) -- 9.3.4 Rare Alleles -- 9.3.5 Genic and Nongenic Contribution -- References -- Chapter 10 Exploiting Barley Genetic Resources for Genome Wide Association Scans (GWAS) -- 10.1 Introduction -- 10.2 Multi Parent Populations -- 10.3 Linkage Disequilibrium. , 10.4 Population Structure -- 10.5 Genetic Markers -- 10.6 Ascertainment Bias -- 10.7 GWAS -- 10.8 Future Prospects -- References -- Chapter 11 Production and Molecular Cytogenetic Identification of Wheat-Alien Hybrids and Introgression Lines -- 11.1 Introduction -- 11.1.1 Interspecific and Intergeneric Hybridization of Plant Species -- 11.1.2 Molecular Cytogenetic Techniques -- 11.1.2.1 Chromosome Banding Techniques -- 11.1.2.2 In situ Hybridization -- 11.2 Wide Hybridization of Wheat -- 11.2.1 Wheat Barley Hybridization -- 11.2.1.1 Production of Wheat Barley Hybrids and Addition Lines -- 11.2.1.2 Wheat/Barley Translocations -- 11.2.2 Wheat Rye Hybrids -- 11.2.2.1 Wheat Rye Crossability -- 11.2.2.2 Wheat-Rye Addition and Substitution Lines -- 11.2.2.3 Wheat/Rye Translocations -- 11.2.3 Wheat Aegilops Hybrids -- 11.2.3.1 Aegilops (goatgrass) Species -- 11.2.3.2 Production of Wheat Aegilops Hybrids, Addition and Translocation Lines -- 11.2.4 Wheat Thinopyrum (syn. Agropyron) Hybrids -- 11.2.4.1 Agropyron Species -- 11.2.4.2 Exploitation of Thinopyrum Species for Wheat Improvement -- 11.3 Conclusions -- References -- Chapter 12 Radiation Hybrids: A valuable Tool for Genetic, Genomic and Functional Analysis of Plant Genomes -- 12.1 Effects of Radiation on Plant Genomes -- 12.1.1 Considerations on the Radiation Effect for Mutant Population Development -- 12.2 Application of Radiation Mutagenesis in Crop Improvement -- 12.2.1 Mutation Breeding Contribution to Crop Improvement -- 12.2.2 Advantages and Disadvantages of Mutation Breeding -- 12.3 Radiation Hybrid Mapping of Genomes -- 12.3.1 Why Radiation Hybrid Mapping? -- 12.3.1.1 Uniform Mapping Resolution Across the Chromosome -- 12.3.1.2 Higher Resolution Without Increasing the Population Size -- 12.3.1.3 Polymorphism is Not a Requirement for RH Mapping. , 12.3.2 Radiation Hybrid Mapping in Animal Systems.

Note: Intro -- Foreword -- Foreword -- Preface -- Contents -- Contributors -- Part I Harnessing Plant Genetic Diversity for Enhancing Crop Production and Its Sustainability -- Chapter 1 Genetics and Genomics of Flowering Time Regulation in Sugar Beet -- 1.1 The Sugar Beet Crop and Its Cultivated and Wild Relatives -- 1.2 Sugar Beet Breeding and Genetics -- 1.3 Phenology of Beta Species -- 1.4 Genomic Resources for Beet -- 1.5 Genetics of Bolting Time in Beet -- 1.6 Flowering Time Genes and Their Regulation in Beet -- 1.6.1 Beet Homologs of the FLC Gene and Putative Regulators -- 1.6.2 Photoperiodic Pathway and CO Homologs -- 1.6.3 Two Copies of FT Homologs with Different Function in Beet -- 1.6.4 GA Metabolism and Early Bolting -- 1.7 A Model for Bolting Time Regulation in Beet -- 1.8 Exploiting Natural Variation for Bolting Time -- 1.9 Strategies to Breed Winter Beets by Manipulating Major Bolting Time Regulators -- References -- Chapter 2 Mining the Genus Solanum for Increasing Disease Resistance -- 2.1 Introduction -- 2.1.1 General Introduction -- 2.1.2 Solanaceae Resources -- 2.1.3 Resistance Genes -- 2.2 Functional Resistance Screens -- 2.2.1 Screening for Disease Resistant Accessions in Gene Bank Material -- 2.2.2 QTL Mapping/LD Mapping -- 2.3 Techniques for Allele Mining -- 2.3.1 Molecular Tools for Allele Tagging -- 2.3.1.1 NBS Profiling -- 2.3.1.2 (Eco)-tilling -- 2.3.1.3 Amplification of Specific Allelic Variants -- 2.3.2 Next Generation Sequencing in Allele Mining -- 2.3.3 Functional Analysis of Newly Identified Alleles -- 2.4 Examples of Allele Mining in Solanum -- 2.4.1 Genetic Mapping -- 2.4.2 Cloning Functional Alleles -- 2.4.3 Uncovering Allelic Variation for Specific Genes -- 2.4.4 Alleles in Natural Populations of Solanum -- References. , Chapter 3 Dissection of Potato Complex Traits by Linkage and Association Genetics as Basis for Developing Molecular Diagnostics in Breeding Programs -- 3.1 Introduction -- 3.2 Methods for the Genetic Dissection of Complex Traits in Potato -- 3.2.1 Linkage Mapping -- 3.2.2 Association Mapping -- 3.3 Resistance to Pests and Diseases -- 3.3.1 Late Blight: Phytophthora Infestans -- 3.3.2 Root Cyst Nematodes: Globodera Pallida -- 3.3.3 Fungi -- 3.3.4 Viruses: PLRV -- 3.3.5 Bacteria: Erwinia (Pectobacterium) -- 3.3.6 Insect Resistance -- 3.4 Tuber Traits -- 3.4.1 Tuber Starch Content and Starch Yield -- 3.4.2 Reducing Sugars, Cold Induced Sweetening and Chip Quality -- 3.4.3 Enzymatic Discoloration, Tuber Bruising and After Cooking Darkening -- 3.4.4 Potato Tuber Yield, Size and Tuber Initiation (Tuberization) -- 3.4.5 Tuber Shape and Eye Depth -- 3.4.6 Tuber Dormancy, Sprouting -- 3.4.7 Tuber Texture and Flavour -- 3.4.8 Tuber Flesh Colour (Carotenoids, Anthocyanins) -- 3.4.9 Glycoalkaloids -- 3.5 Conclusion and Outlook -- References -- Chapter 4 Introgression Libraries with Wild Relatives of Crops -- 4.1 Introduction -- 4.2 IL-Based Analyses of Complex Traits -- 4.3 The IL Approach in the Tomato Clade -- 4.3.1 The S. pennellii LA0716 Exotic Library -- 4.3.2 IL-Based System Analyses of Integrated Developmental Networks -- 4.3.3 Other Tomato Library Resources -- 4.4 Integrative Approaches to Genomic Introgression Mapping -- 4.5 Conclusions -- References -- Chapter 5 Microphenomics for Interactions of Barley with Fungal Pathogens -- 5.1 Introduction -- 5.1.1 Phenotype Driven Screens for Plant--Pathogen Interactions in Barley -- 5.1.2 Gene-Oriented Phenomics Strategy -- 5.1.2.1 Transcription Profiling -- 5.1.2.2 Gene Function -- 5.1.2.3 Fungal Genes -- 5.1.2.4 Random Selection of Genes -- 5.1.2.5 Genes Co-localizing with Resistance QTL. , 5.1.3 Genotype-Based Phenomics Strategy -- 5.1.3.1 Allelic Diversity in Plant Genetic Resources -- 5.1.3.2 Mutagenesis -- 5.2 Microphenomics Screen Workflow -- 5.2.1 RNAi Library Preparation -- 5.2.2 Microscopy -- 5.2.2.1 Haustoria Staining -- 5.2.2.2 Staining of Fungal Structure on the Leaf Surface -- 5.2.3 Image Analysis and Processing -- 5.2.3.1 Recognition of B. graminis Haustoria in Barley -- 5.2.3.2 HyphArea Platform -- 5.2.3.3 B. graminis Hyphal Growth Measurement -- 5.2.3.4 Recognition of Rhynchosporium secalis in Barley -- 5.2.4 Detailed Analysis and Gene Validation -- 5.2.5 TIGS Screening Results -- 5.2.6 Transcript Regulation as Selection Criterion -- 5.2.7 Selection Based on Function of the Genes -- 5.2.8 Co-localization with Resistance QTL -- 5.2.9 Fungal Genes -- 5.2.10 Random Selection of Candidates -- 5.3 Conclusions and Perspectives -- References -- Chapter 6 Genomics of Low-Temperature Tolerance for an Increased Sustainability of Wheat and Barley Production -- 6.1 Introduction -- 6.2 ``Omic'' Approaches to Study Cold Acclimation -- 6.2.1 Transcriptomics -- 6.2.2 Proteomics -- 6.2.3 Metabolomics -- 6.3 Molecular Networks: Key Steps in Cold Acclimation (Genomic Role of the CBF Regulon) -- 6.3.1 Function of the CBF Regulatory Hub -- 6.3.2 Early Events in the Cascade -- 6.3.3 Integration of the Circadian Control -- 6.3.4 CBF-Independent Hubs -- 6.4 Exploiting Genetic Resources and Genomic Selection for FT -- 6.4.1 Genetic Resources -- 6.4.2 Genomics-Assisted Breeding -- 6.4.2.1 LD-MAS for Freezing Tolerance -- 6.4.2.2 Genomic Selection (GS) -- 6.5 Conclusions and Perspectives -- References -- Chapter 7 Bridging Conventional Breeding and Genomics for A More Sustainable Wheat Production -- 7.1 The Importance of Genetic Variation and Genetic Resources -- 7.2 Sources of Variation -- 7.2.1 Sexual Hybridization. , 7.2.2 Modern Mutation Approaches for Creating Genetic Variation: TILLING (Targeting Induced Local Lesions IN Genomes) -- 7.2.3 Using Transgenic Approaches for Wheat Improvement -- 7.3 Measuring and Using Genetic Diversity -- 7.4 Genomics as an Aid for Selection -- 7.4.1 The Impact of Genomics on Marker Assisted Breeding -- 7.4.2 Genome-Wide Marker Data -- 7.5 Training Population and Selection Candidates -- 7.6 Genomic Selection Models -- 7.7 Future Research Needs, New Concepts -- 7.8 It is More than Genomics and Breeding: A Glimpse at the Future -- References -- Chapter 8 Genetic Dissection of Aluminium Tolerance in the Triticeae -- 8.1 Introduction -- 8.2 Improved Methods for Germplasm Evaluation for Al3+ Tolerance -- 8.3 Dissection of Al3+ Tolerance Loci -- 8.4 Molecular Marker Systems for Mapping of Al3+ Tolerance Loci -- 8.4.1 (1) Dissection of Al3+ Tolerance Genes in Wheat -- 8.5 Multiple Origin of Al3+ Tolerance in Wheat -- 8.6 Dissection of Al3+ Tolerance Genes in Barley -- 8.7 Dissection of Al3+ Tolerance Genes in Rice -- 8.8 Molecular Breeding for Al Tolerance Using Marker-Assisted Selection (MAS) -- 8.9 Conclusions -- References -- Chapter 9 Maintaining Food Value of Wild Rice (Zizania palustris L.) Using Comparative Genomics -- 9.1 Introduction -- 9.2 Wild Rice Genetics -- 9.3 Wild Rice Genetic Diversity -- 9.4 Wild Rice Breeding -- 9.5 Case Study: Breeding Wild Rice Using Marker-Assisted Breeding for Nonshattering -- References -- Part II Genomics-Assisted Crop Improvement for Food Security -- Chapter 10 Genomics-Assisted Allele Mining and its Integration Into Rice Breeding -- 10.1 Introduction -- 10.2 Discovery of Natural Variation for Use in Rice Breeding -- 10.2.1 Developing Advanced Plant Materials from Diverse Rice Accessions -- 10.2.2 Genetic Architecture of Heading Date Revealed by Analysis of Novel Plant Materials. , 10.3 Genetic Dissection of Agriculturally Important Traits -- 10.3.1 Characterization of Durable Resistance Genes for Rice Blast -- 10.3.2 Genetic Control of Rice Root Morphology -- 10.3.3 Isolation and Pyramiding of Yield-Related Genes -- 10.4 Application of Genome-Wide SNP Analysis -- 10.5 Conclusions and Future Prospects -- References -- Chapter 11 New Insights Arising from Genomics for Enhancing Rice Resistance Against the Blast Fungus -- 11.1 Introduction -- 11.2 Insights in Rice Blast Resistance Gained from the Genome Sequence -- 11.2.1 Mapping R-genes and QTLs -- 11.2.2 Forward-Genetics Approaches Applied to Arsenal Genes in the Genomic Era -- 11.2.3 Insights in Rice Blast Resistance Gained from Functional Genomics -- 11.3 Structure of Arsenal -- 11.3.1 A Few Surprises for R and PR Genes -- 11.3.2 Some Chromosomes are Richer than Others in Key Regulators -- 11.4 Structural and Functional Diversity of the Arsenal -- 11.4.1 Presence/Absence as a Source of Polymorphism -- 11.4.2 Alternative Splicing of the Rice Arsenal -- 11.4.3 Expression Diversity of the Arsenal -- 11.5 Breeding Perspectives -- 11.5.1 New Tools for Pre-Breeding -- 11.5.2 RNA-Based Breeding -- 11.6 Research Perspectives -- 11.7 Concluding Remarks: Insights from the Enemy -- References -- Chapter 12 Enhancing Abiotic Stress Tolerance in Plants by Modulating Properties of Stress Responsive Transcription Factors -- 12.1 Drought Definition in the Agricultural Context -- 12.1.1 Counter-Acting Drought and Associated Stresses Through Traditional Crop Breeding, Gene Discovery and Genetic Engineering -- 12.2 Stress-Responsive Mechanisms During Drought and Other Abiotic Stress Conditions -- 12.3 Transcriptional Regulation of Plant Responses to Drought and Other Stress Conditions. , 12.3.1 Signal Transduction Pathways During Drought are Mediated Through Abscisic Acid-Dependent and Abscisic Acid-Independent Pathways.

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