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Table of Contents
Preface to the Volume; Contents; 1 The Economic Evolution of the Soybean Industry; Abstract; 1.1 Introduction; 1.2 Production Economics; 1.3 Marketing; References; 2 Botany and Cytogenetics of Soybean; Abstract; 2.1 Introduction; 2.2 Botany; 2.2.1 Taxonomy; 2.2.2 Morphology; 2.3 Cytology; 2.3.1 Handling of Soybean Chromosomes; 2.3.1.1 Mitotic Chromosomes; 2.3.1.2 Meiotic Chromosomes; 2.3.1.3 Karyotype Analysis; 2.4 Cytogenetics; 2.4.1 Genomes of the Glycine Species; 2.4.1.1 Classical Taxonomy; Crossing Affinity; 2.4.1.2 Meiotic Chromosome Pairing.
2.4.1.3 Genomic Affinity by Molecular Techniques2.4.2 Origin of Polyploid Complexes of Glycine tabacina and G. tomentella; 2.4.2.1 Glycine tabacina (2n = 80); 2.4.2.2 Glycine tomentella (2n = 78, 80); 2.4.3 Chromosomal Aberrations-Structural Aberrations; 2.4.4 Chromosomal Aberrations-Numerical Changes; 2.4.4.1 Autopolyploidy; 2.4.4.2 Aneuploidy-Trisomics; Primary Trisomics; Monosomics; Tetrasomics; 2.4.5 Chromosome Mapping; 2.4.5.1 Chromosome Map; 2.4.5.2 Classical Linkage Groups; 2.4.5.3 Cytogenetic Map; 2.5 Wide Hybridization; 2.5.1 Genetic Resources; 2.5.1.1 Soybean GP-1.
2.5.1.2 Soybean GP-22.5.1.3 Soybean GP-3; 2.5.2 Intersubgeneric Hybridization; References; 3 Classical and Molecular Genetic Mapping; Abstract; 3.1 Introduction; 3.2 Classical Genetic Maps; 3.3 RFLP-Based Genetic Maps; 3.4 Genetic Maps Based on RAPD and AFLP Markers; 3.5 Simple Sequence Repeat (SSR) or Microsatellite Markers; 3.6 An SSR-Based Soybean Genome Map; 3.7 Integration of Classical and Molecular Linkage Groups; 3.8 Single Nucleotide Polymorphisms (SNPs); 3.9 SNPs in Soybean; 3.10 Soybean SNP-Based Maps; References; 4 Structural Variation and the Soybean Genome; Abstract.
4.1 Introduction4.2 Functional Structural Variants in Soybean; 4.3 Genome Scans for SV; 4.4 Understanding the Limitations of a Reference Genome; 4.5 Diversity and Structural Variation Within and Between Glycine soja and Glycine max; 4.6 Evolving R-gene Clusters; 4.7 Evolutionary Dynamics of Structural Variation; 4.8 Whole-Genome Duplication; 4.9 Mapping Using SVs as a Marker; 4.10 Inducing SVs; 4.11 Conclusions; Acknowledgements; References; 5 Sequencing, Assembly, and Annotation of the Soybean Genome; Abstract; 5.1 Introduction; 5.2 Genome Sequencing Platform.
5.3 Plant Genomes and Assemblies5.4 Soybean Genome Assembly and Annotation; 5.4.1 Soybean Genome Before Whole Genome Sequencing; 5.4.2 Soybean Whole Genome Sequencing; 5.4.2.1 Cultivated Soybean Genome Version 1; 5.4.2.2 Cultivated Soybean Genome Version 2; 5.4.2.3 Wild Soybean Whole Genome Sequencing; 5.5 Conclusion and Future Perspectives; Acknowledgements; References; 6 Comparative Genomics of Soybean and Other Legumes; Abstract; 6.1 Introduction; 6.2 Big Data and Comparative Genomics; 6.2.1 Availability of Sequenced Legumes and Current Polyploid Knowledge; 6.3 Gene-by-Gene Analyses.
2.4.1.3 Genomic Affinity by Molecular Techniques2.4.2 Origin of Polyploid Complexes of Glycine tabacina and G. tomentella; 2.4.2.1 Glycine tabacina (2n = 80); 2.4.2.2 Glycine tomentella (2n = 78, 80); 2.4.3 Chromosomal Aberrations-Structural Aberrations; 2.4.4 Chromosomal Aberrations-Numerical Changes; 2.4.4.1 Autopolyploidy; 2.4.4.2 Aneuploidy-Trisomics; Primary Trisomics; Monosomics; Tetrasomics; 2.4.5 Chromosome Mapping; 2.4.5.1 Chromosome Map; 2.4.5.2 Classical Linkage Groups; 2.4.5.3 Cytogenetic Map; 2.5 Wide Hybridization; 2.5.1 Genetic Resources; 2.5.1.1 Soybean GP-1.
2.5.1.2 Soybean GP-22.5.1.3 Soybean GP-3; 2.5.2 Intersubgeneric Hybridization; References; 3 Classical and Molecular Genetic Mapping; Abstract; 3.1 Introduction; 3.2 Classical Genetic Maps; 3.3 RFLP-Based Genetic Maps; 3.4 Genetic Maps Based on RAPD and AFLP Markers; 3.5 Simple Sequence Repeat (SSR) or Microsatellite Markers; 3.6 An SSR-Based Soybean Genome Map; 3.7 Integration of Classical and Molecular Linkage Groups; 3.8 Single Nucleotide Polymorphisms (SNPs); 3.9 SNPs in Soybean; 3.10 Soybean SNP-Based Maps; References; 4 Structural Variation and the Soybean Genome; Abstract.
4.1 Introduction4.2 Functional Structural Variants in Soybean; 4.3 Genome Scans for SV; 4.4 Understanding the Limitations of a Reference Genome; 4.5 Diversity and Structural Variation Within and Between Glycine soja and Glycine max; 4.6 Evolving R-gene Clusters; 4.7 Evolutionary Dynamics of Structural Variation; 4.8 Whole-Genome Duplication; 4.9 Mapping Using SVs as a Marker; 4.10 Inducing SVs; 4.11 Conclusions; Acknowledgements; References; 5 Sequencing, Assembly, and Annotation of the Soybean Genome; Abstract; 5.1 Introduction; 5.2 Genome Sequencing Platform.
5.3 Plant Genomes and Assemblies5.4 Soybean Genome Assembly and Annotation; 5.4.1 Soybean Genome Before Whole Genome Sequencing; 5.4.2 Soybean Whole Genome Sequencing; 5.4.2.1 Cultivated Soybean Genome Version 1; 5.4.2.2 Cultivated Soybean Genome Version 2; 5.4.2.3 Wild Soybean Whole Genome Sequencing; 5.5 Conclusion and Future Perspectives; Acknowledgements; References; 6 Comparative Genomics of Soybean and Other Legumes; Abstract; 6.1 Introduction; 6.2 Big Data and Comparative Genomics; 6.2.1 Availability of Sequenced Legumes and Current Polyploid Knowledge; 6.3 Gene-by-Gene Analyses.