Molecular Markers in Plants -- Contents -- Contributors -- Preface -- 1 Evolution of DNA Marker Technology in Plants -- Introduction -- Early Marker Technologies -- DNA-Based Methods -- Restriction Fragment Length Polymorphism -- PCR-Based Methods -- Arbitrary Methods -- Random Amplified DNA Polymorphism -- Amplified Fragment Length Polymorphism -- Diversity Array Technique -- Specific Sequence-Based PCR -- Sequence Characterized Amplified Region -- Reverse Transcription-Polymerase Chain Reaction -- Simple Sequence Repeat -- Single Nucleotide Polymorphism -- Discovery -- Analysis -- Impact of Advancing DNA Sequencing Technology -- Whole-Genome Sequencing -- Organellar Sequencing -- Transcriptome Sequencing -- Amplicon Sequencing -- Enriched Genome Sequencing -- Genotyping by Sequencing -- Evolving Range of Applications of DNA Markers in Plants -- Plant Identification for IP Protection -- Plant Variety Identification for Production and Quality Control -- Applications -- Biosecurity Applications -- Applications in Conservation Biology -- Application in Evolutionary Biology -- Applications in Understanding Biological Functions -- Application in Plant Improvement -- Food Industry Applications -- Future Developments -- References -- 2 Whole-Genome Sequencing for Marker Discovery -- Sequencing Strategies -- Sequencing Technologies -- Sanger Sequencing -- Second-Generation Sequencing Methods -- Major SGS Systems -- Third-Generation Sequencing Developments -- Epigenetic Markers -- Genome-Wide Selection -- Data Analysis Resources -- References -- 3 Amplicon Sequencing for Marker Discovery -- Introduction -- Background -- Maximizing Efficiency Through Sample Pooling -- Pooling of cDNA or Genomic DNA -- Pooling PCR Products -- Tissue Pooling -- Other Considerations for Pooling -- Barcoding Genotypes Prior to Amplification and MPS -- Haplotyping.

Limitations of Amplicon-Based MPS -- PCR-Based Limitations to Amplicon Sequencing -- Effects of End Bias in MPS Sequence Coverage -- Limitations Associated with Internal Coverage Nonuniformity -- Mitigating Problems Introduced During Sample Preparation -- Gene Paralogs -- Some Solutions to Obvious Pitfalls of MPS of Amplicons -- Bioinformatics -- Concluding Remarks -- Acknowledgments -- References -- 4 Transcriptome Sequencing for Marker Discovery -- Introduction -- Basic Approach -- Profiling Platforms -- Advantages -- Disadvantages -- Pipelines -- Applications -- Conclusions -- References -- 5 Molecular Markers in Plant Improvement -- Introduction -- Plant Domestication and Traditional Breeding -- Application of Molecular Markers to Breeding -- Next-Generation Approaches to QTL Discovery -- Conclusion -- References -- 6 Applications of Molecular Markers in Plant Conservation -- Introduction -- Traditional Approaches -- Maintaining Viable Populations-Quantifying Diversity -- Identifying Lineage Boundaries-Defining Provenances -- The Way Forward -- An Integrated Approach-Landscape Genetics -- The Future Is Here-Conservation Genomics -- Conclusion -- References -- 7 Molecular Markers for Plant Biosecurity -- Introduction -- The Present-PCR for Specific Diagnosis and for DNA Barcoding -- DNA Barcoding for Fungi -- DNA Barcoding for Bacteria -- DNA Barcoding for Viruses -- The Future-Next-Generation Sequencing Methods to Revolutionize Plant Quarantine Diagnostics -- Viral Metagenomics -- Genome-Based Diagnostic Marker Development -- Environmental Barcoding -- Conclusions -- Acknowledgments -- References -- 8 Molecular Markers for Harnessing Heterosis -- Introduction -- Molecular Markers for Understanding the Genetic Basis of Heterosis -- Molecular Diversity and Heterosis-Molecular Markers for Predicting Heterosis -- Maize -- Rice -- Wheat -- Brassica.

Cotton -- Soybean -- Conclusion -- References -- 9 Genetic Variant Discovery and Its Use in Genome Characterization of Agronomically Important Crop Species -- Introduction -- Sanger Resequencing -- Single Feature Polymorphisms -- Next-Generation Sequencing -- Early Wins -- Next-Generation Sequencing for SNP Discovery in Well-Characterized Species -- Next-Generation Sequencing for SNP Discovery in Underresourced Species -- High-Density Genotyping using the Illumina Golden Gate Platform -- Genotyping by Sequencing -- Genome Characterization and Haplotypes -- Conclusions and Perspectives -- References -- 10 Future Prospects of Molecular Markers in Plants -- Introduction -- Molecular Markers: The Past -- Molecular Markers: The Present -- Molecular Markers: The Future -- Reduced-Representation Sequencing (CRoPS and RRLs) -- RAD-Tag Sequencing (RAD-seq) -- Low-Coverage Sequencing for Genotyping (GBS and MSG) -- Novel Approaches or Platforms for Plant Breeding -- Genome-Wide Association Studies -- Genome-Wide Selection -- Conclusions -- Acknowledgments -- References -- Index -- Supplemental Images.