Genetic mapping and marker assisted selection: basics, practice and benefits / N. Manikanda Boopathi

Incluye bibliografía

1 Germplasm Characterisation: Utilising the Underexploited Resources.. Phenotyping for Morphological and Agronomic Characters.. Case Study in Rice Germplasm Characterisation for Drought Resistance.. Traits Useful for Characterisation.. Allele Mining.. Genetic Diversity and Clustering.. Software.. Principle Behind the Genetic Diversity Analysis.. Principle of Measuring Goodness of Fit of a Classification.. Genetic Diversity Analysis Using Molecular Markers.. Parental Selection.. Bibliography.. Literature Cited.. Further Readings.. 2 Mapping Population Development.. Mapping Population and Its Importance in Genetic Mapping.. Selfing and Crossing Techniques in Crop Plants.. F2 Progenies.. F2 -Derived F3 (F2:3 Populations.. F2 Intermating Populations or Immortalised F2 Populations.. DH Lines.. BC Progenies.. RILs.. NILs, Exotic Libraries and Advanced Backcross Populations.. Four-Way Cross Populations.. Multi-Cross Populations.. Nested Association Mapping Populations.. Natural Populations.. Chromosome-Specific Genetic Stocks for Linkage Mapping.. Bulk Segregant Analysis.. Combining Markers and Populations.. Characterisation of Mapping Populations.. Choice of Mapping Populations.. Challenges in Mapping Population Development and Solutions to These Challenges.. Bibliography.. Literature Cited.. Further Readings.. 3 Genotyping of Mapping Population.. Markers and Its Importance.. Morphological Markers.. Biochemical Markers or Isozymes.. Principle.. Electrophoresis.. Chromatography.. Gel Filtration.. Immunochemistry.. Catalysis.. Genome Structure and Organisation.. Chromosome Structure.. Mitochondrial DNA.. Chloroplast DNA.. Molecular Markers.. Restriction Fragment Length Polymorphism (RFLP.. PCR-Based Techniques.. Arbitrarily Primed PCR-Based Markers.. Random Amplified Polymorphic DNA (RAPD.. Arbitrarily Primed Polymerase Chain Reaction (AP-PCR and DNA Amplification Fingerprinting (DAF

Amplified Fragment Length Polymorphism (AFLP.. Sequence-Specific PCR-Based Markers.. Microsatellite-Based Marker Technique.. Inter-Simple Sequence Repeats (ISSR.. Single-Nucleotide Polymorphism (SNPs.. Single-Feature Polymorphism (SFP.. Sequence-Characterised Amplified Regions (SCAR.. Cleaved Amplified Polymorphic Sequences (CAPS.. Randomly Amplified Microsatellite.. Polymorphisms (RAMP.. Sequence-Related Amplified Polymorphism (SRAP.. Target Region Amplification Polymorphism (TRAP.. Single-Strand Conformation Polymorphism (SSCP.. Transposable Elements (TE-Based Molecular Markers.. Retrotransposon-Based Molecular Markers.. Diversity Array Technology (DArT.. Intron-Targeted Intron-Exon Splice Conjunction (IT-ISJ Marker.. Restriction Site Associated DNA (RAD Markers.. RNA-Based Molecular Markers.. cDNA-AFLP.. RNA Fingerprinting by Arbitrarily Primed PCR (RAP-PCR.. cDNA-SSCP.. Role of Genomics.. Selection of Marker Technology.. Research Problem.. The Number of Loci and/or Alleles.. Discrimination Level.. Mode of Inheritance.. Quality of DNA.. Expertise Required.. Costs.. Speed.. Reproducibility.. PCR Versus Non-PCR Techniques.. Marker Genotyping and Scoring.. Analysing the Genotype Score: Chi-Square Test.. c 2 Test to Analyse the Segregation Ratio Using the Program ANTMAP.. Bibliography.. Literature Cited.. Further Readings.. 4 Linkage Map Construction.. Basics of Genetic/Linkage Mapping: Mendelian Ratios, Meiosis, Crossing Over and Partial Linkage.. Mapping Functions.. Mapping of Genetic Markers: Practical Considerations.. Testing for Linkage: LOD Scores.. Grouping, Ordering and Spacing.. Sources of Error.. Chromosomal Assignment.. Allopolyploidy and Autopolyploidy.. Bridging Linkage Maps to Develop Unified.. Linkage Maps.. Bibliography.. Literature Cited.. Further Readings.. 5 Phenotyping.. Phenotyping Versus QTL Mapping.. Need for Precise Phenotyping.. Phenotyping for Biotic Stress.. Phenotyping for Abiotic Stress.. Heritability of Phenotypes

Statistical Analysis of Phenotypic Data: Simple Statistics, Heritability Estimation and Correlation.. Bibliography.. Literature Cited.. Further Readings.. 6 QTL Identification.. QTL: A Prelude.. Single-Marker Analysis (SMA.. Interval Mapping.. Multiple QTL and Methods to Detect Multiple QTL.. Composite Interval Mapping.. Multiple Trait Mapping.. Testing for Linked QTL Versus Pleiotropic QTL.. Multiple Interval Mapping (MIM or Multiple QTL Mapping.. Statistical Signi fi cance.. Permutation Testing.. Bootstrapping.. Permutation Versus Bootstrapping and Other Methods.. QTL × QTL Interaction: Impact of Epistasis.. QTL × Environment Interaction.. Congruence of QTL: Across the Environments and Across the Genetic Backgrounds Is the Key in MAS.. Meta-QTL Analysis.. Concluding Remarks on QTL Methods.. Alternatives in Classical QTL Mapping.. Bulked Segregant Analysis and Selective Genotyping.. Genomics-Assisted Breeding.. Array Mapping.. Association Mapping.. Nested Association Mapping.. EcoTILLING.. Challenges in QTL Mapping.. Confronts with Mapping Populations.. Markers and Its Implications.. Segregation Distortion.. Phenotyping.. Statistical Issues.. Practical Utility.. Bibliography.. Literature Cited.. Further Readings.. 7 Fine Mapping.. Need for Fine Mapping or High-Resolution Mapping.. Types of Molecular Markers Suitable for Fine Mapping.. Physical Mapping and Its Role in Fine Mapping.. Comparative Mapping.. Genetical Genomics/eQTL Mapping.. Map-Based Cloning.. Validation of QTLs.. Testing the Markers in Related Germplasm Accessions.. Bibliography.. Literature Cited.. Further Readings.. 8 Marker-Assisted Selection.. Advantages of MAS.. Limitations in MAS.. Prerequisites for an Efficient Marker-Assisted.. Selection Program.. Procedure for a Generalised MAS Program for Selection from Breeding Lines/Populations.. Marker-Assisted Backcross Breeding.. Gene Pyramiding or Stacking

Accelerated Methods of Gene Pyramiding.. Marker-Assisted Recurrent Selection (MARS).. Advanced Backcross (AB)-QTL Analysis.. Mapping-As-You-Go (MAYG).. Application of Markers in Germplasm Storage, Evaluation and Use.. Resources for MAS on the Web.. Bibliography.. Literature Cited.. Further Readings.. 9 Success Stories in MAS.. Tomato.. Maize.. Wheat.. Rice.. Barley.. Soybean.. Varieties Released Through MAS.. Hybrids Developed Through MAS.. MAS in Multinational Companies.. Contrasting Stories.. Conclusions and Future Prospects.. Bibliography.. Literature Cited.. Further Readings.. 10 Curtain Raiser to Novel MAS Platforms.. Current Techniques in Molecular, Biochemical and Physiological Studies and Its Integration into MAS.. Molecular Techniques.. Expression Profiling.. cDNA Library Construction.. Differential Display and Representational Difference Analysis.. Subtractive Hybridisation.. Microarray.. Types of DNA Chips and Their Production.. Hybridisation and Detection Methods.. 1. DNA Sequencing by Hybridisation.. 2. Single Nucleotide Polymorphisms and Point Mutations.. 3. Functional Genomics.. 4. Reverse Genetics.. 5. Diagnostics and Genetic Mapping.. 6. Genomic Mismatch Scanning.. 7. DNA Chips and Agriculture.. 8. Proteomics.. 9. Nucleic Acid Sequencing.. Second-Generation DNA Sequencing.. 454 Pyrosequencing.. Illumina Genome Analyser.. AB SOLiD.. Microchip-Based Electrophoretic Sequencing.. Sequencing by Hybridisation.. Sequencing in Real Time.. Targeted Capture of Genomic Subsets.. Handling and Storage of Sequence Information.. Predicting Function from Sequence.. Homology Searches.. Other Sequence Comparisons Strategies.. Serial Analysis of Gene Expression (SAGE).. cDNA-AFLP.. RFLP-Coupled Domain-Directed Differential Display (RC4D).. Gene Tagging by Insertional Mutagenesis.. T-DNA Tag.. Transposon Tags.. Post-transcriptional Gene Silencing.. MicroRNAs.. Biochemical Techniques.. Plant Proteomics spa

Why Proteomics?.. Types of Proteomics.. Protein Expression Proteomics.. Structural Proteomics.. Functional Proteomics.. Protein Analysis.. One- and Two-Dimensional Gel Electrophoresis.. Alternatives to Electrophoresis in Proteomics.. Acquisition of Protein Structure Information.. Edman Sequencing.. Mass Spectrometry.. Types of Mass Spectrometers.. Peptide Fragmentation.. De Novo Peptide Sequence Information.. Uninterpreted MS/MS Data Searching.. Proteomics Approach to Protein Phosphorylation.. Phosphoprotein Enrichment.. Phosphorylation Site Determination by Edman Degradation.. Phosphorylation Site Determination by Mass Spectrometry.. Metabolite Profiling Technologies.. Physiological Techniques.. Near-Infrared (NIR Spectroscopy.. Canopy Spectral Reflectance (SR and Infrared Thermography (IRT.. Estimation of Compatible Solutes.. Genomics-Assisted Breeding.. Functional Markers.. Comparative Genomics.. Identification of Novel Molecular Networks and Construction of New Metabolic Pathway.. Bioinformatics for MAS.. Bibliography.. Literature Cited.. Further Readings.. 11 Recent Advances in MAS in Major Crops.. Rice.. Rice and Drought.. Mechanisms of Drought Resistance in Rice.. Phenology.. Root System.. Osmotic Adjustment.. Dehydration Tolerance.. Shoot-Related Drought-Resistance Traits.. Genetic Linkage Map in Rice.. QTL Mapping of Drought-Resistance.. Traits in Rice.. Rice Subspecies and Habitat.. Marker-Aided Selection and Near-Isogenic Lines for Drought-Resistance Improvement.. Target Population of Environment and Molecular Breeding.. Concluding Remarks on MAS in Rice for Water-Limited Environments.. Cotton.. Status of Cotton Molecular Marker Technology.. Molecular Markers and Polymorphism in Cotton.. Simple Sequence Repeats (SSRs in Cotton.. Cotton Linkage Maps.. QTL Mapping for Yield and Fibre Quality.. Traits in Cotton.. Specific Challenges in Cotton MAS.. Confronts with Mapping Population.. QTL × Environme

QTL × Environment Analysis.. Incongruence Among QTL Studies.. Complexities in Integration of Functional.. Genomics with QTL.. Alternatives and Future Perspectives.. Meta-analysis of QTL: Synergy Through Networks.. Map-Based Cloning.. Cotton Genome Sequencing.. Advances in Functional Genomics.. System Quantitative Genetics: Bridging Subdisciplines.. Association Mapping and Alternatives.. Improved Databases.. Concluding Remarks for MAS in Cotton.. Mungbean.. Genetic Diversity and Linkage Mapping in Mungbean.. QTL Mapping in Mungbean.. Legume Comparative Genomics and Its Importance in Mungbean MAS.. Concluding Remarks for MAS in Mungbean.. Tomato.. Conventional Breeding and Tomato Improvement.. Biotechnology and Tomato Breeding.. MAS for Bacterial Spot Resistance.. MAS for Tomato Yellow Leaf Curl Virus Resistance.. MAS for Other Economic Traits.. MAS for Genetic Improvement of Fruit Quality Traits.. Fine Mapping and Characterisation of Fruit-Size QTL.. Concluding Remarks for MAS in Tomato.. Hot Pepper.. Progress in MAS in Hot Pepper.. Concluding Remarks on MAS in Hot Pepper.. Bibliography.. Literature Cited.. Further Reading.. 12 Future Perspectives in MAS.. MAS in Orphan Crops.. MAS in Developing Countries.. Community Efforts in Developing Countries and Their Implications in MAS.. Field and Laboratory Infrastructure Improvement.. Lessons Learnt and Concluding Remarks.. Bibliography.. Literature Cited.. Further Readings.. About the Author

Genetic mapping and marker assisted selection (MAS) is considered as one of the major tools in genetic improvement of crop plants in this genomics era. This book describes basics in linkage mapping, step-by-step procedure to perform MAS, achievements made so far in different crops, and limitations and prospects of MAS in plant breeding. It summarizes all this in a simple but comprehensive mode using suitable examples so as to explain the concept and its historical developments. To summarize, this book describes technologies for identification of genes of interest through genetic mapping, recaps the major applications of MAS to plant breeding; lists examples in which MAS is being applied to various breeding programs, and emphasizes the various difficulties that limit the application of MAS in plant breeding, providing possible solutions to overcome these difficulties, and finally tries to illustrate the future prospects. This book would be a valuable guide to the under-graduates and post-graduates of agricultural universities and institutes that are interested and/or involved in genetic improvement of crop plants using modern tools. Bibliography listed in this book constitutes two parts: literature cited and further reading. Literature cited contains references cited in the text and further information on the given concept/technique can be obtained from these references. Further reading provides a list of suggested readings for in-depth coverage of the topics. eng