B.D. Singh. A.K. Singh. Marker-Assisted Plant. Breeding: Principles. and Practices. ^ Springer

Transcription

1 BD Singh AK Singh Marker-Assisted Plant Breeding: Principles and Practices ^ Springer

2 Contents Part I General 1 Introduction to Marker-Assisted Crop Improvement 3 11 Introduction 3 12 Domestication: The Evolution of Crop Plants 3 13 Plant Breeding Major Developments in Plant Breeding The Genotype and Phenotype Genetic Variation: Qualitative and Quantitative Inheritance Contributions: Pure Line Varieties Contributions: Hybrid Varieties Contributions: Clones Limitations of Phenotype-Based Plant Breeding 8 14 The Growing Food Needs 9 15 The Transgenic Technology: Lukewarm Social Response Molecular Markers: Selection Made Easy and More Reliable Designer Crops Some Notable Achievements of Marker-Assisted Plant Breeding Future Prospects of Marker-Assisted Plant Breeding 14 Part II Genetic Markers 2 Hybridization-Based Markers Introduction Genetic Markers Visible/Morphological Markers Protein-Based Markers DNA Markers Concluding Remarks on Genetic Markers Random, Gene-Based, and Functional Markers Isolation and Purification of DNA from Plants 26 xv

3 xvi Contents 25 Restriction Fragment Length Polymorphism Restriction Enzymes Southern Hybridization Probes Polymorphisms Detected by RFLP Markers Genetic Aspects of RFLPs Advantages of RFLPs Limitations of RFLPs Conversion of RFLP Markers into PCR-Based Markers Diversity Array Technology Variable Number of Tandem Repeats Single Feature Polymorphisms Restriction-Site-Associated DNA Markers Appendices Appendix 21: Isolation and Purification of DNA from Plants 42 Appendix 22: Genomic and cdna Libraries 44 Appendix 23: Microarrays 45 3 Polymerase Chain Reaction-Based Markers Introduction Oligonucleotides 33 Polymerase Chain Reaction Generalized Procedure for PCR Separation of PCR Amplification Products Multiplex PCR Applications of PCR Advantages and Limitations of PCR PCR-Based Markers Randomly Amplified Polymorphic DNAs DNA Amplification Fingerprinting Arbitrary-Primed PCR Sequence-Characterized Amplified Regions Amplified Fragment Length Polymorphisms The Procedure of AFLP Features of AFLP Modifications of the AFLP Technique Conversion of AFLP Markers Sequence-Tagged Sites Microsatellites or Simple Sequence Repeats Simple Sequence Repeat Markers Discovery of SSR Markers Increasing the Throughput of SSR Markers Merits of SSR Markers Limitations of SSR Marker System Inter-Simple Sequence Repeats Modifications of ISSR Merits and Limitations of ISSR Markers 64

4 Contents xvii 314 Cleaved Amplified Polymorphic Sequences Single-Strand Conformation Profile/Polymorphism 316 Denaturing/Temperature Gradient Gel Electrophoresis Sequence-Related Amplification Polymorphism Target Region Amplification Polymorphism Transposable Element-Based Markers Conserved Orthologous Set of Markers Start Codon-Targeted Polymorphism CAAT Box-Derived Polymorphism Conserved DNA-Derived Polymorphism Conserved Region Amplification Polymorphism Intron-Targeting Polymorphism RNA-Based Molecular Markers 74 Appendices 74 Appendix 31: The Number of RAPD Bands Theoretically Expected from a DNA Sample 74 Appendix 32: Polymerase Chain Reaction and Randomly Amplified Polymorphic DNAs 75 4 Sequence-Based Markers Introduction DNA Sequencing First-Generation DNA Sequencing Methods Next-Generation DNA Sequencing Methods 423 The Third-Generation DNA Sequencing 79 Methods Comparison Between NGS and TGS Sequencers RNA Sequencing RNA-Seq Single-Molecule Direct RNA Sequencing Single-Nucleotide Polymorphisms Types of SNPs Methods for Discovery of SNPs Amplicon Sequencing SNP Mining Transcriptome Sequencing Whole-Genome Sequencing Reduced Representation Approaches Sequence Capture Validation of Discovered SNPs Methods for SNP Genotyping Allele-Specinc PCR '-Nuclease Assay (TaqMan Assay) Molecular Beacons Microarray-Based SNP Genotyping Bead-Based Techniques Primer Extension 108

5 xviii Contents 467 Pyrosequencing Oligonucleotide Ligation Assay Dynamic Allele-Specific Hybridization Ill 4610 Denaturing High-Performance Liquid Chromatography Ill 4611 InDels as Molecular Markers Epigenetic Markers Use of Genomics, Transcriptomics, Proteomics, and Metabolomics in Marker Development Polymorphic Information Content of Marker Loci Marker System Selection 118 Part III Linkage Maps 5 Mapping Populations Introduction Mapping Populations Selection of Parents for Developing a Mapping Population F2 Population F2-Derived F3 Population Backcross Population Doubled Haploids Recombinant Inbred Lines Immortalized F2 Population Near-Isogenic Lines Chromosomal Segment Substitution Lines Backcross Inbred Lines Advanced Intercross Lines Recurrent Selection Backcross Population Interconnected Mapping Populations Multiparent Advanced Generation Intercross Populations Nested Association Mapping Population Mapping Populations for Cross-Pollinated Species Linkage Mapping in Polyploid Species Chromosome-Specific Genetic Stocks Natural Populations and Germplasm/Breeding Lines Segregation Ratios in Mapping Populations Characterization of Mapping Populations Problems in Mapping Studies Size of Mapping Population Choice of Mapping Population Linkage Mapping of Molecular Markers and Oligogenes Introduction Genetic Maps Linkage Maps Cytogenetic Maps Physical Maps 152

6 63 Estimation of Recombination Rates Genetic Distance The Haldane Distance The Kosambi Distance Variation in Genetic Distance Relationship Between Genetic and Physical Distances General Procedure for Linkage Mapping of Molecular Markers and Oligogenes Mapping of the Loci Present in a Chromosome Strategies for Mapping of Oligogenes Use of Near-Isogenic Lines Bulked Segregant Analysis Mapping of Recessive Morphological Mutants by a Two-Step Procedure Bulked Segregant RNA-Seq The MutMap Technique LOD Score and LOD Score Threshold A Complete Linkage Map Integration or Merger of Linkage Maps Confirmation and Validation Comparative Mapping Fine Mapping (High-Resolution Mapping) Software for Mapping of Oligogenes/Molecular Markers MapMaker/Exp RI Plant Manager G-MENDEL MultiMap AntMap JoinMap MergeMap ActionMap TetraploidMap for Windows MultiPool Mutation Mapping Analysis Pipeline for Pooled RNA-Seq MapPop Next-Generation Mapping Selective Mapping and Selective Genotyping Pooled DNA Analysis Physical Mapping of Molecular Markers Sources of Errors in Linkage Mapping The Significance of Genetic Maps 182 Mapping of Quantitative Trait Loci Introduction Quantitative Trait Loci The General Procedure for QTL Mapping 186

7 xx Contents Marker and Quantitative Trait Data Structure Methods for QTL Detection and Mapping Single QTL Mapping Multiple QTL Mapping Some Remarks on QTL Mapping Bulked Segregant Analysis for QTL Mapping Multiple Trait QTL Mapping LOD Score and LOD Score Threshold QTL Confidence/Support Interval Confirmation and Validation of QTL Mapping Results QTL Fine Mapping Homozygous Lines Derived from Near-Isogenic Lines Intercross Recombinant Inbred Lines Recurrent Selection Backcross QTL Mapping Genetically Heterogeneous Stocks Multiparent Advanced Generation Intercross Population Reverse QTL Mapping Combination of QTL Mapping and Transcriptome Profiling QTL Meta-Analysis Inconsistent Estimates of QTL Effects Segregation of Different QTLs in Different Populations QTLx Genetic Background Interaction QTLx Environment Interaction The Beavis Effect QTL Detection Power and Precision of QTL Mapping 715 Factors Affecting Results from QTL Mapping Genetic Properties of QTLs Genetic Background Type and Size of Mapping Population Environmental Effects on QTL Expression Experimental Error Advantages of QTL Linkage Mapping Limitations of QTL Mapping Nature and Function of Polygenes Software for QTL Mapping MapMaker/QTL PLABQTL QTL Cartographer MapManager QT/QTX R/QTL R/QTLBIM QTL Express 214

8 Contents xxi 7198 FlexQTL INTERQTL MCQTL QGene Some Other Software Programs Association Mapping Introduction The General Procedure for Association Mapping Phenotyping Genome-Wide and Candidate Gene Approaches for Association Mapping Populations Used for Association Mapping in Plants Population-Based Association Panels Family-Based Association Panels: NAM Population Family-Based Association Panels: MAGIC Population Linkage Disequilibrium for Biallelic Loci Measures of Linkage Disequilibrium Two Biallelic Loci Two Loci with Multiple Alleles Multiple Locus Methods Graphic Representation of LD Useful LD The Extent of LD in Plant Species Uses of LD in Plant Molecular Biology Experimental Designs and Models for Association Mapping Case and Control Approach Family-Based Designs Structured Association Model Mixed Linear Models Joint Linkage-Association Mapping Multilocus Mixed Model Multitrait Mixed Model Significance Tests for Marker-Trait Associations Controlling "False Discovery" Rate Relevance of Marker Systems in LD Estimation Factors Affecting LD and Association Mapping Mating Pattern in the Population Selection Population Structure Admixture Genomic Region Kinship Genetic Drift and Bottleneck 248

9 xxii Contents 8168 Gene Conversion Ascertainment Bias Marker Mutation Rate Errors in Genotyping Conclusions About LD Patterns in Plant Species LD Maps Mapping of Expression Quantitative Trait Loci Power of Association Mapping Confirmation of Marker-Trait Associations Through Replication Studies The tagsnp Strategy of SNP Genotyping Software for LD Studies Conclusions from Association Mapping Studies Current Issues in Association Mapping Future Perspectives Merits of Association Mapping Limitations of Association Mapping 255 Part IV Applications 9 Marker-Assisted Selection Introduction Marker-Assisted Characterization of Germplasm and Genetic Purity Marker-Assisted Backcrossing Foreground Selection Background Selection Recombinant Selection A Four-Step Comprehensive Selection Strategy A Theory for Background Selection During MABC MABC for Transfer of Oligogenic Traits MABC for Transfer of Quantitative Trait Loci MABC for Gene Pyramiding Strategy for Gene Pyramiding Pyramiding of Oligogenes Pyramiding of QTLs with Oligogenes Governing the Same Trait Transgene Pyramiding Multitrait Introgression Combined Marker-Assisted Selection Marker-Assisted Recurrent Selection MARS in Cross-Pollinated Crops F2 Enrichment and MARS in Self-Pollinated Crops 279

10 911 Innovative Breeding Schemes for Effective Use of MAS Inbred Enhancement and QTL Mapping Advanced Backcross QTL Analysis Single Large-Scale MAS Pedigree MAS Single Backcross-Doubled Haploid Scheme Breeding by Design Mapping as You Go Marker-Evaluated Selection for Adaptation and Agronomic Performance Integration of MAS in Breeding Programs Advantages of MAS Limitations of MAS Present Constraints and Future Directions Achievements Genomic Selection Introduction Genome-Wide Selection A Generalized Procedure for Genomic Selection Training Population Genetic Composition Population Size Marker Density Computation of Genomic Estimated Breeding Values Stepwise Regression Ridge Regression Bayesian Approach Semi-parametric Regression Methods Machine Learning Methods Factors Affecting the Accuracy of GEBV Estimates 1061 The Method of Estimation of Marker Effects The Polygenic Effect Term Based on Kinship The Method of Phenotypic Evaluation of Training Population The Marker Type and Density Trait Heritability and the Number of QTLs Affecting the Trait The Breeding Population Effects of Genomic Selection on Genetic Diversity Integration of Genomic Selection in Breeding Programs 305

11 xxiv Contents 109 Effectiveness of Genomic Selection Advantages of Genomic Selection Limitations of Genomic Selection Future Directions Phylogenetic Relationships and Genetic Diversity Introduction Estimation of Genetic Distance/Similarity Estimation of Genetic Distance from Morphological Trait Data Estimation of Genetic Distance from Molecular Marker Data Estimation of Genetic Distance from Populations Choice of the Genetic Distance Measure 113 Genetic Diversity Analysis: Phylogenetic 315 Relationships Cluster Analysis Principal Component Analysis Principal Coordinate Analysis Multidimensional Scaling Determination of the Optimal Number of Clusters Choice of Clustering Method Use of Diverse Datasets Resampling Techniques Genetic Diversity Analysis: Conservation of Genetic Resources Germplasm Conservation Applications of Molecular Markers in Germplasm Conservation Conservation of Wild Species Genetic Diversity Analysis: Prediction of Heterotic Pools and Heterotic Combinations Genetic Basis of Heterosis Molecular Basis of Heterosis Identification/Prediction of Heterotic Pools and Heterotic Cross Combinations Molecular Markers in Resolution of the Genetic Basis of Heterosis Molecular Markers for Identification/Prediction of Heterotic Pools and Heterotic Cross Combinations Fingerprinting and Gene Cloning Introduction DNA Fingerprinting 341

12 Contents xxv 123 Characterization of Lines and Hybrids for Intellectual Property Rights Protection Plant Breeder's Rights Description of Plant Varieties Limitations of Molecular Markers Assessment of Genetic Purity of Lines and Hybrids In Silico Gene Prediction Chromosome Walking Chromosome Jumping Positional Gene Cloning The Three Steps of Positional Cloning Positional Cloning of Some Plant Genes Some Useful Tips for Positional Gene Cloning Problems in Positional Cloning Chromosome Landing Positional Cloning of Quantitative Trait Loci cdna Sequencing in Positional Cloning Achievements High-Throughput SNP Genotyping Introduction High-Throughput Genotyping of Known SNP Loci The Invader Technology Pyrosequencing KASP Genotyping Assay TaqMan OpenArray Genotyping System 1325 SNP Analysis by MALDI-TOF MS (The Homogeneous MassEXTEND Assay) Nanofluidic Dynamic Array-Based Assays 1327 The Array Tape Technology The Illumina GoldenGate SNP Genotyping Platform Molecular Inversion Probe Technology Whole-Genome-Based Microarray Platforms High-Throughput SNP Discovery and Genotyping Reduced Representation Sequencing Reduced Representation Libraries Complexity Reduction of Polymorphic Sequences Restriction Site-Associated DNA Sequencing Low-Coverage Genotyping Genotyping by Sequencing Multiplexed Shotgun Genotyping Applications of NGS-Based Marker Discovery and Genotyping Methods 396

13 xxvi Contents 138 A Comparison of NGS and Other SNP Genotyping Approaches Reduced Representation Versus Whole-Genome Sequencing SNP Discovery in Polyploids Bioinformatics Tools for Marker Discovery from NGS Sequence Data PoPoolation RADtools Stacks TASSEL SAMtools/BCFtools Future Directions Bioinformatics Tools and Databases for Genomics Research Introduction Representation of Nucleotide and Amino Acid Sequences Bioinformatics Tools AutoSNP SNP2CAPS TASSEL STRUCTURE Microarray Software A C Elegans Database (AceDB) MAPMAN GenScan ClustalW Bioinformatics Databases GenBank Phytozome European Molecular Biology Laboratory Nucleotide Sequence Database Swiss-Prot UniProt Knowledgebase (UniProtKB) Gramene GrainGenes MaizeGDB RiceGeneThresher Microarray Databases (ArrayExpress and Gene Expression Omnibus) HarvEST Sources of Multiple Databases and Tools National Center for Biotechnology Information Kyoto Encyclopedia of Genes and Genomes 416

14 1453 Molecular Biology Database Collection Architecture for Metabolomics (ArMet) Database Search and Analysis Tools Genamics SoftwareSeek Sequence Manipulation Suite PHYL1P 428 Phenomics Introduction Phenomics The Imaging Technology Advantages of Image-Based Phenotyping Reflectance Imaging Visual Imaging Near Infrared Imaging Infrared Imaging Fluorescence Imaging Chlorophyll Fluorescence Green Fluorescence Protein Magnetic Resonance Imaging Multi-sensor Monitoring Approaches Field-Based Phenomics Morphological and Growth Analyses Dynamic Measurement of Leaf Area Plant Biomass Estimation Basic Plant Growth Analysis Assessment of Structure/Development Measurement of Senescence/Necrosis Analysis of Root Systems Seed and Fruit Phenotyping Laser Scanning: 3-D Plant Morphology Analyses of Chemical and Physiological Parameters Estimation of Relative Chlorophyll Content Monitoring Photosynthesis Assessment of Water Use Estimation of Soil Water Content Analysis of Chemical Composition Biotic Stress Detection Monitoring Drought Stress Stomatal Conductance Leaf/Canopy Temperature Visible Imaging IR Thermography Chlorophyll Fluorescence Estimation of Tissue Water Content 454

15 xxviii Contents 1515 Molecular Biomarkers Image Analysis Image Analysis Software ImageJ HTPheno Rosette Tracker MartrackLeaf HPGA (High-throughput Plant Growth Analysis) Root System Analyzer SmartRoot RootReader2D RootReader3D Applications of Phenomics Achievements Future Directions 460 Glossary 463 References 485 Author Index 501 Subject Index 507