The Prologue -- Foreword -- Preface to the Series -- Preface to the Volume -- Contents -- List of Contributors -- List of Abbreviations -- 1. Fundamentals of Plant Genome Mapping -- 1. THE GENOME CONCEPTS -- 1.1 Types of Genomes -- 1.2 Nuclear DNA Content in Plant Genomes -- 1.3 Genome or Chromosome Mapping -- Genetic Map -- Physical Map -- 2. GENETIC MAPPING AND MARKERS IN THE ERA OF CLASSICAL GENETICS -- 3. GENETIC MAPPING AND MARKERS IN THE ERA OF MOLECULAR GENETICS -- 3.1 Isoenzyme Markers -- 3.2 Historical Background of DNA Markers -- 3.3 The DNA Markers -- 3.4 Molecular Genetic Mapping: New Concepts, Tools and Strategies -- 3.5 Mapping Populations and Genetic Stocks -- 3.6 Computer Programs for Molecular Mapping -- 4. APPLICATIONS OF GENETIC MAPPING -- 4.1 Marker-Assisted Crop Improvement -- 4.2 Map-Based Cloning of Genes and QTLs -- 4.3 Elucidation of Phylogenetic Relationships and Evolutionary Pathways -- 4.4 Construction of Third Generation Chromosome Maps -- 4.5 Role of Genetic Mapping in Genomics Arena -- 5. CONTRIBUTORY DISCIPLINES AND BENEFICIARIES -- 6. CONCERNS AND CAUTIONS -- 6.1 Selection of Crop -- 6.2 Selection of Traits -- 6.3 Selection of Base Materials -- 6.4 Converging Approach -- References -- 2. Molecular Markers-History, Features and Applications -- 1. INTRODUCTION -- 1.1 Genetic Markers -- 1.2 Molecular Markers -- 2. THE MAJOR CATEGORIES OF MOLECULAR MARKERS -- Restriction Fragment Length Polymorphism (RFLP) -- Dot Blot Assay -- PCR-based Markers -- Random Amplified Polymorphic DNA (RAPD) -- Amplified Fragment Length Polymorphism (AFLP) -- Sequence Characterized Amplified Region (SCAR) -- Simple Sequence Repeat (SSR) -- Expressed Sequence Tag-derived SSR (EST-SSR) -- Inter-Simple Sequence Repeat (ISSR) -- Cleaved Amplified Polymorphic Sequence (CAPS) -- Sequence-Specific Amplified Polymorphism (S-SAP).

Inter-Retrotransposon Amplified Polymorphism (IRAP) -- Retrotransposon-Microsatellite Amplified Polymorphism (REMAP) -- Retrotransposon-Based Insertional Polymorphism (RBIP) -- Sequence Related Amplification Polymorphism (SRAP) -- Target Region Amplification Polymorphism (TRAP) -- Single Nucleotide Polymorphism (SNP) -- 3. FEATURES OF MOLECULAR MARKERS -- 4. FUTURE PERSPECTIVES -- References -- 3. Mapping Populations: Development, Descriptions and Deployment -- 1. INTRODUCTION -- 2. MAPPING POPULATIONS -- 3. SELECTION OF PARENTS -- 4. POPULATIONS DERIVED FROM HOMOZYGOUS PARENTS -- 4.1 F2, Population -- Advantages -- Disadvantages -- 4.2 F2-derived F3 (F2:3) Population -- Advantages -- Disadvantages -- 4.3 Backcross (BC) Population -- Advantages -- Disadvantages -- 4.4 Doubled Haploid Lines (DHL) -- Aduantages -- Disadvantages -- 4.5 Recombinant Inbred Lines (RIL) -- Advantages -- Disadvantages -- 4.6 Near-lsogenic Lines (NIL) -- Advantages -- Disadvantages -- 5. CONSIDERATIONS FOR QTL MAPPING FROM HETEROZYGOUS PARENTS -- 5.1 Genetic Load, Heterozygosity and Mating Type -- 6. ESTIMATION OF ADDITIVITY AND DOMINANCE -- 7. MAPPING ACCURACY -- 7.1 Segregation Distortion in Linkage Mapping -- 8. COMBINING MARKERS AND POPULATIONS -- Conclusions -- References -- 4. Construction of Genetic Linkage Maps -- Overview -- 1. INTRODUCTION -- 2. FROM MARKERS TO LINKAGE MAPPING -- 2.1 Basic Concepts -- 2.2 Two- and Three-point Analysis -- 2.3 Genetic Distance and Mapping Functions -- 2.4 Estimating Genetic Distance from Experimental Data -- 2.5 Formation of Linkage Groups -- 2.6 Ordering of Markers within a Linkage Group -- 2.7 Special Considerations -- 3. MAPPING OUTBREEDING SPECIES -- 4. MAPPING WITH A REDUCED POPULATION SIZE -- 4.1 The Deterministic Approach -- Greedy Algorithm -- 4.2 The Stochastic Approach -- Application.

5. HIGH- AND ULTRA HIGH-DENSITY MAPS -- 5.1 Construction of High-Density Linkage Maps -- 5.2 Ultra High-Density Maps (UHD-maps) -- Construction of UHD maps -- 6. LINKAGE MAPS IN POLYPLOIDS -- 7. CONCLUDING REMARKS -- References -- 5. Mapping and Tagging of Genes Controlling Simple-inherited Traits -- 1. INTRODUCTION -- 1.1 Simple-Inherited Traits -- 1.2 The Early History of Genetic Maps -- 1.3 The Evolution of Genetic Maps -- 1.4 Integrated Cytogenetic Maps -- 1.5 Generating Cytogenetic Maps -- 2. IDENTIFICATION OF MARKERS LINKED TO TRAITS OF INTEREST -- 2.1 Use of NILs to Identify Linkage with Molecular Markers -- 2.2 Use of Bulked Segregant Analysis (BSA) to Identify Linkage with Molecular Markers -- 2.3 Targeting Disease Resistance Genes by NBS Profiling -- 3. CONVERSION OF DOMINANT TO CO-DOMINANT MARKERS -- 4. USE OF GENOMICS TOOLS FOR MAPPING -- 5. STATISTICAL CONSIDERATIONS -- 6. APPLICATION OF GENETIC MAPPING -- References -- 6. Genetic Mapping of Quantitative Trait Loci -- 1. INTRODUCTION -- 2. NATURE OF QUANTITATIVE VARIATION -- 3. MAPPING POPULATIONS -- 3.1 Controlled Crosses -- 3.2 Structured Pedigrees -- 3.3 Natural Populations -- 3.4 Joint linkage and linkage disequilibrium mapping -- 4. STATISTICAL MODELS, METHODS AND ALGORITHMS -- 4.1 Models -- 4.2 The QTL. Model -- 4.3 The Marker Model -- 4.4 Marker-conditional QTL. Model -- 4.5 Methods and Algorithms -- 4.5.1 Marker Analysis -- 4.5.1.1 Testing -- 4.5.1.2 Linkage analysis -- 4.5.2 Interval Mapping -- 4.5.2.1 Mixture model -- 4.5.2.2 Conditional probabilities -- 4.5.2.3 Likelihood and algorithm -- 4.5.2.4 Hypothesis testing -- 4.5.2.5 Example -- 4.5.3 Composite and Multiple Interval Mapping -- 5. CONCLUDING REMARKS -- Acknowledgements -- References -- 7. Comparative Mapping -- 1. INTRODUCTION -- 2. METHODOLOGY AND HISTORY -- 3. APPLICATIONS OF COMPARATIVE MAPPING.

3.1 Development of Linkage Maps -- 3.2 Predicting Gene Location and Function -- 3.3 Gene Cloning -- 3.4 Analysis of Genome Evolution -- 4. COMPARATIVE MAPPING IN GRASSES (POACEAE) -- 5. THE SOLANACEAE -- 6. THE BRASSICACEAE -- 7. THE FABACEAE -- 8. COMPARATIVE MAPPING BEYOND FAMILIES -- Conclusions -- References -- 8. Map-based Cloning of Genes and Quantitative Trait Loci -- 1. INTRODUCTION -- 2. DETAILED PROCEDURE OF W-BASED CLONING -- 2.1 Genetic Mapping or Tagging of the Targeted Genes or QTLs with DNA Markers -- 2.1.1 Genome-wide Interval Mapping -- Bulked Segregant Analysis (BSA) -- Near-Isogenic Line (NIL) Analysis -- 2.2 Physical Mapping of the Targeted Region -- 2.3 High-Resolution or Fine-Mapping of Targeted Gene Locus -- 2.4 Chromosome Walking or Landing -- 2.5 Gene Identification -- BLAST Search -- Comparative Sequence Analysis -- Gene Expression Analysis -- Genomic DNA Transformation -- cDNA Transformation -- RNA Interference (RNAi) -- 3. EXAMPLES OF MAP-BASED CLONING IN PLANTS -- 3.1 Map-based Cloning of Genes Controlling Mendelian Traits -- 3.2 Map-based Cloning of QTLs -- 4. NOTES OF MAP-BASED CLONING -- 4.1 Phenotyping Accuracy -- 4.2 Variation of Genetic Recombination Rate along a Chromosome -- 4.3 Use of Plant-Transformation-Competent BIBAC and TAC Libraries -- 4.4 Chromosome Walking versus Whole-Genome Physical Mapping and Sequencing -- 4.5 Targeted Gene Source Genotypes and Source Libraries -- 5. CONCLUDING REMARKS -- References -- 9. Bioinformatics: Fundamentals and Applications in Plant Genetics, Mapping and Breeding -- 1. WHAT IS BIOINFORMATICS? -- 2. UNDERSTANDING THE GENOME -- 3. GENE AND GENOME SEQUENCE DATABASES -- 4. GENE EXPRESSION INFORMATION -- 5. GENE EXPRESSION DATABASES -- 6. THE PROTEOME AND METABOLOME -- 7. THE PHENOME -- 8. FROM GENETICS AND GENOMICS TO PHENOMICS -- 9. MOLECULAR GENETIC MARKERS: SSRs AND SNPs.

10. MOLECULAR MARKER DATABASES -- 11. MOLECULAR MARKER APPLICATIONS -- 12. POPULATION GENETIC SOFTWARE PACKAGES -- 13. GENETIC DIVERSITY -- 14. HARDY-WEINBERG EQUILIBRIUM (HWE) -- 15. LINKAGE DISEQUILIBRIUM -- 16. POPULATION SUBDIVISION -- 17. PHYLOGENETIC ANALYSIS -- 17.1 Phylogenetic Analysis Software Packages -- 18. APPLICATION OF GENOTYPIC DATA TO GENETIC MAPPING ANALYSIS -- 19. QTL ANALYSIS -- 20. GENETIC MAPPING AND QTL SOFTWARE PACKAGES -- 21. INTEGRATED BIOINFORMATICS FOR CROP BREEDING -- References -- 10. An Overview on Plant Genome Initiatives -- 1. INTRODUCTION -- 1.1 What is a Plant Genome Initiative? -- 1.2 Plant Nuclear DNA Content -- 1.3 Molecular Maps -- 1.4 Molecular Markers -- 2. GENOME SEQUENCING INITIATIVES -- 3. EXAMPLES OF GENOME INITIATIVES -- 3.1 The Maize Sequencing Project -- 3.2 Wheat Genome Initiative -- 4. NON-GENOME SEQUENCING ACTIVITIES -- 4.1 The Identification of Genes -- 4.2 The Identification of Gene Function -- 5. FUTURE EXTENDED SEQUENCING OF PLANT GENOMES -- 6. CONCLUDING REMARKS -- References -- 11. Computing Strategies and Software for Gene Mapping -- 1. INTRODUCTION -- 2. QTL ANALYSIS WITH INBRED LINES -- 2.1 Single QTL Mapping -- 2.1.1 Missing Genotypes -- 2.1.2 Detection of QTL -- 2.1.3 Model Selection for Multiple QTL -- 2.1.4 Multiple QTL Estimation Approaches -- 2.1.5 Detailed Analysis of Multiple QTL Simulated Cross -- 2.1.6 Covariates and Gene-Environment Interactions -- 2.1.7 Overview of Available Packages -- 2.1.8 QTL Analysis with Outbred Lines -- 3. ASSOCIATION ANALYSIS -- 3.1 Association Analysis Examples -- Acknowledgements -- References -- Index.