Cytogenetics in Plant Breeding

1 Cytogenetics in Genetics and Plant Breeding.- 1.1 Cytogenetics as a Subdiscipline of Genetics.- 1.1.1 The Two Functions of the Genetic Material.- 1.1.2 Cytogenetics Defined.- 1.2 Cytogenetics in Plant Breeding.- 2 Chromosome Composition, Structure and Morphology.- 2.1 DNA.- 2.1.1 The Chemical Basis.- 2.1.2 Heterogeneity of DNA; Unique and Repetitive DNA.- 2.1.3 Replication.- 2.2 Chromosome Structure; Histones and Other Chromosomal Proteins.- 2.3 Euchromatin, Heterochromatin.- 2.4 Special Functional Elements in Chromosomes.- 2.4.1 Nucleolus Organizing Region (NOR).- 2.4.2 Centromere.- 2.4.3 Telomeres.- 2.5 Microscopic Chromosome Morphology: the Karyotype, Standard and Variations.- 3 The Mechanisms of Genetic Transmission.- 3.1 The Somatic Cycle.- 3.1.1 Mitosis.- 3.1.2 Duration of Mitosis.- 3.1.3 Order and Disorder in the Somatic Spindle and Nucleus.- 3.1.3.1 Relative Position of Large and Small Chromosomes in the Spindle and in the Nucleus. Hollow Spindle.- 3.1.3.2 Rabl Orientation.- 3.1.3.1 Nucleolar Fusion.- 3.1.3.2 Somatic Pairing.- 3.1.3.3 Non-homologous Chromosome Association; Nuclear Compartmentalization.- 3.1.4 Mitotic Variants with Genetic Consequences.- 3.1.4.1 Intact Organism.- 3.1.4.1.1 Accidents.- 3.1.4.1.2 Systematic Deviations.- 3.1.4.1.2.1 Chromosome Doubling.- 3.1.4.1.2.2 Elimination.- 3.1.4.1.2.3 B-Chromosomes.- 3.1.4.2 In Vitro Culture.- 3.2 Generative Transmission: Fertilization - Meiosis.- 3.2.1 Fertilization.- 3.2.2 Meiosis.- 3.2.2.1 Prophase I.- 3.2.2.2 Metaphase 1.- 3.2.2.3 Anaphase I, Telophase I.- 3.2.2.4 Meiosis II.- 3.2.3 Systematic Variants of Meiotic Behaviour.- 3.2.3.1 Achiasmate Meiosis.- 3.2.3.2 Holokinetic Chromosomes.- 3.2.3.3 Neocentric Activity.- 3.2.3.4 Specialized Chromosomes.- 3.2.4 Recombination.- 3.2.4.1 Two Forms of Recombination.- 3.2.4.1.1 Chromosome Recombination.- 3.2.4.1.2 Exchange Recombination.- 3.2.4.1.2.1 Two and More Chiasmata in One Chromosome.- 3.2.4.1.2.2 Genetic Variation in Exchange Recombination.- 3.2.4.1.2.2.1 Genetic Variation in Frequency of Exchange.- 3.2.4.1.2.2.2 Genetic Variation in Pattern of Exchange.- 4 The Somatic Chromosome Complement: Karyotype Analysis.- 4.1 The Karyotype.- 4.1.1 Characteristics of the Karyotype.- 4.1.2 Applications of Karyotype Analysis.- 4.2 Approaches to Karyotype Analysis: Chromosome Number and Morphology.- 4.2.1 Number of Genomes Per Cell: Indirect Methods.- 4.2.2 Exact Chromosome Number; Chromosome Morphology.- 4.2.2.1 Techniques of Preparation.- 4.2.2.2 Observations; Measurements.- 4.2.1 Presenting the Karyotype.- 4.2.3.1 Karyogram and Idiogram.- 4.2.3.2 Idiogram Construction: Coping with Variation.- 4.2.3.3 Idiogram Construction: Plotting the Observations.- 4.2.2 Markers Within Chromosome Arms.- 4.2.4.1 Chromosome Banding.- 4.2.4.2 Molecular Markers.- 4.2.4.3 Genetic Markers.- 5 Karyotype Variants A: Chromosome Structural Variants.- 5.1 Deficiencies.- 5.1.1 Types.- 5.1.2 Origin.- 5.1.3 Relevance.- 5.1.4 Characteristics and Identification.- 5.1.5 Consequences.- 5.2 Duplications.- 5.2.1 Types.- 5.2.2 Origin.- 5.2.3 Relevance.- 5.2.4 Characteristics and Identification.- 5.2.5 Consequences.- 5.3 Inversions Ill.- 5.3.1 Types (Paracentric and Pericentric) and Origin Ill.- 5.3.2 Relevance Ill.- 5.3.3 Characteristics and Identification Ill.- 5.3.4 Consequences.- 5.4 Translocations.- 5.4.1 Reciprocal Translocation or Interchange and Simple Terminal Translocation.- 5.4.1.1 Types and Origin.- 5.4.1.2 Relevance.- 5.4.1.3 Characteristics and Identification.- 5.4.1.4 Consequences.- 5.4.2 Two or More Interchanges Combined: Translocation Tester Set; Balanced Complex Translocation Heterozygotes.- 5.4.2.1 Types and Origin.- 5.4.2.2 Relevance.- 5.4.2.3 Characteristics and Identification.- 5.4.2.4 Consequences.- 5.4.3 Simple Interstitial Translocations.- 1.2.1.1 Types, Origin and Relevance.- 1.2.1.2 Characteristics, Identification and Consequences.- 5.5 Other Rearrangements (Robertsonian Fission and Fusion; Isochromosome; Compound).- 5.5.1 Types and Origin.- 5.5.2 Relevance.- 5.5.3 Characteristics, Identification and Consequences.- 6 Karyotype Variants B: Chromosome Number Variants.- 6.1 Euploidy.- 6.1.1 Haploidy.- 6.1.1.1 Types and Terminology.- 6.1.1.2 Origin.- 6.1.1.3 Relevance.- 6.1.1.4 Characteristics and Identification.- 6.1.1.5 Consequences.- 6.1.2 Polyploidy.- 6.1.2.1 Types.- 6.1.2.2 Autopolyploidy; Types.- 6.1.2.2.1 Autotriploids.- 6.1.2.2.1.1 Origin.- 6.1.2.2.1.2 Relevance.- 6.1.2.2.1.3 Characteristics and Identification.- 6.1.2.2.1.4 Consequences.- 6.1.2.2.2 Autotetraploids.- 6.1.2.2.2.1 Origin.- 6.1.2.2.2.2 Relevance.- 6.1.2.2.2.3 Characteristics and Identification.- 6.1.2.2.2.4 Consequences.- 6.1.2.2.3 Higher Autopolyploids.- 6.1.2.3 Allopolyploidy.- 6.1.2.3.1 Types.- 6.1.2.3.2 Origin.- 6.1.2.3.3 Relevance.- 6.1.2.3.4 Characteristics and Identification.- 6.1.2.3.5 Consequences.- 6.1.2.4 Polyploid Hybrids.- 6.1.2.4.1 Types, Origin and Relevance.- 6.1.2.4.2 Characteristics, Identification and Consequences.- 6.2 Aneuploidy.- 6.2.1 Hypoploidy, Monosomy.- 6.2.1.1 Types of Monosomy.- 6.2.1.2 Origin.- 6.2.1.1 Relevance.- 6.2.1.2 Characteristics and Identification.- 6.2.1.3 Consequences.- 6.2.2 Hyperploidy.- 6.2.2.1 Primary Trisomy.- 6.2.2.1.1 Types.- 6.2.2.1.2 Origin.- 6.2.2.1.3 Relevance.- 6.2.2.1.4 Characteristics and Identification.- 6.2.2.1.5 Consequences.- 6.2.2.2 Secondary and Telocentric Trisomy.- 6.2.2.2.1 Types, Origin.- 6.2.2.2.2 Relevance.- 6.2.2.2.3 Characteristics and Identification.- 6.2.2.2.4 Consequences.- 6.2.2.3 Tertiary and Translocation Trisomy.- 6.2.2.3.1 Types, Origin.- 6.2.2.3.2 Relevance.- 6.2.2.3.3 Characteristics and Identification.- 6.2.2.3.4 Consequences.- 6.2.2.4 Other Trisomies and Higher Polysomies.- 6.2.2.4.1 Compensating Trisomies.- 6.2.2.4.2 Alien Additions.- 6.2.2.4.2.1 Types, Origin.- 6.2.2.4.2.2 Relevance.- 6.2.2.4.2.3 Characteristics, Identification and Consequences.- 7 Diagnosis: Identifying Cytogenetic Causes of Variants of the Karyotype and the Generative Cycle.- 7.1 Diagnosis: The Collection of Specific Information: Context, Objectives and Means.- 7.2 The Diagnostic Strategy.- 7.3 The Diagnostic Use of Meiotic Behaviour and Configurations: Types and Distribution;Causes and Consequences.- 7.3.1 Stages.- 7.3.2 Basic Configuration.- 7.3.3 Distribution of Configurations.- 7.4 The Diagnostic Protocol.- 7.4.1 No Chromosome Number Deviation.- 7.4.1.1 Meiosis: Diakinesis/Metaphase I: No Obvious Deviations.- 7.4.1.2 Univalents.- 7.4.1.1 Heteromorphic or Otherwise Abnormal Bivalents.- 7.4.1.2 Multivalents.- 7.4.1.4.1 Trivalents.- 7.4.1.4.2 Quadrivalents: Chromosome Number Normal; Karyotype Visibly Changed.- 7.4.1.4.3 Higher-Order Multivalents; Chromosome Number Normal, Chromosome Structure Normal or Deviant.- 7.4.1.3 Chromosome Number Normal; Diakinesis-Metaphase I Normal.- 7.4.1.5.1 Unequal Sister Chromatids.- 7.4.1.5.2 Chromatid Bridges.- 7.4.1.5.3 Chromatid Loops.- 7.4.1.5.4 Anaphase II Bridges.- 7.4.2 Chromosome Number Not Normal; Aneuploidy: Hyperploidy.- 7.4.2.1 Trisomies.- 7.4.2.1.1 Univalents.- 7.4.2.1.2 Heteromorphic Bivalents.- 7.4.2.1.3 Multivalents.- 7.4.2.1.4 Anaphase I and Anaphase II Aberrations.- 7.4.2.2 Two or More Extra Chromosomes.- 7.4.2.2.1 Only Normal Bivalents.- 7.4.2.2.2 Univalents.- 7.4.2.2.3 Heteromorphic Bivalents.- 7.4.2.2.4 Multivalents.- 7.4.3 Hypoploidy.- 7.4.3.1 Monosomies.- 7.4.3.1.1 Univalents.- 7.4.3.1.2 Heteromorphic or Otherwise Abnormal Bivalents.- 7.4.3.1.3 Multivalents.- 7.4.3.2 Hypoploids: Two Chromosomes Less than Normal.- 7.4.3.2.1 Only Normal Bivalents.- 7.4.3.2.2 Univalents.- 7.4.3.2.3 Heteromorphic Bivalents and Multivalents.- 7.4.4 Euploidy.- 7.4.4.1 Gametic Chromosome Number ("Haploidy").- 7.4.4.1.1 Only Normal Bivalents.- 7.4.4.1.2 Univalents.- 7.4.4.1.3 Heteromorphic or Otherwise Abnormal Bivalents.- 7.4.4.1.4 Multivalents, Anaphase and Cellular Abnormalities.- 7.4.4.2 Triploidy.- 7.4.4.2.1 Univalents.- 7.4.4.2.2 Heteromorphic and Otherwise Abnormal Bivalents.- 7.4.4.2.3 Multivalents.- 7.4.4.2.3.1 Trivalents.- 7.4.4.2.3.2 Higher Order Multivalents.- 7.4.4.1 The Doubled Chromosome Number.- 7.4.4.3.1 Only Normal Bivalents.- 7.4.4.3.2 Univalents.- 7.4.4.3.3 Heteromorphic or Otherwise Abnormal Bivalents.- 7.4.4.3.4 Multivalents.- 7.4.4.3.5 Anaphase and Cellular Irregularities.- 7.4.4.2 Aneuploidy in Combination with Doubled Chromosome Number.- 7.4.4.3 Higher Ploidy Levels.- 8 Estimating, Recording and Manipulating Recombination.- 8.1 Chromosome Recombination and Exchange Recombination.- 8.1.1 The Role of Chromosome Number in Recombination.- 8.1.1.1 Chromosome Recombination in Diploids as the Basis of Mendelian Inheritance.- 8.1.1.2 Variation in Chromosome Recombination.- 8.1.1.2.1 Ploidy Level.- 8.1.1.2.1.1 Haploids.- 8.1.1.2.1.2 Polyploids.- 8.1.1.2.2 Chromosome-Associated Restrictions of Chromosome Recombination.- 8.1.1.2.2.1 Affinity.- 8.1.1.2.2.2 Permanent Translocation Heterozygosity.- 8.1.1.3 The Relative Importance of Chromosome Recombination in Plant Breeding.- 8.2 Exchange Recombination: Crossing-Over.- 8.2.1 Estimates of Crossing-Over.- 8.2.1.1 Segregation of Genetic Markers.- 8.2.1.2 Chiasma Frequency, Recombination Nodules and Chiasmate Chromosome Arm Association Frequency..- 8.2.1.3 Mapping Functions.- 8.2.1.4 Models for Deriving Chiasmate Association Frequencies from Configuration Frequencies.- 8.2.1.5 Variation in Crossing-Over.- 8.3 Recording Recombination: Genetic Chromosome Maps.- 8.3.1 Recombinational Maps of Genes and Other Markers; Three-Point Test.- 8.3.2 The Location of Genes on Chromosomes.- 8.3.2.1 Aneuploids.- 8.3.2.1.1 Monosomies.- 8.3.2.1.2 Primary Trisomies.- 8.3.2.1.3 Telocentric Trisomies.- 8.3.2.1.4 Tertiary and Other Complex Trisomies.- 8.3.2.2 Chromosomal Rearrangements.- 8.3.2.2.1 Deficiencies and Inversions.- 8.3.2.2.2 Translocations, Duplications and Robertsonian Splits..- 8.3.1 The Physical and Recombinational Location of Genes Within Chromosomes.- 8.3.3.1 Natural Chromosome Morphological Markers.- 8.3.3.1.1 The Centromere.- 8.3.3.1.2 Heterochromatin, Chromosomes and Banding Polymorphisms.- 8.3.3.1.3 The NOR and Other Multigene Loci: In Situ Hybridization.- 8.3.3.2 The Break Points of Rearrangements as Genetic and Chromosomal Markers.- 8.3.3.2.1 Deficiencies.- 8.3.3.2.2 Translocations, Duplications and Inversions.- 8.3.3.3 Rearranged Aneuploids: Tertiary and Other Complex Monosomies and Trisomies.- 8.3.2 Recombinational Chromosome Maps: An Example.- 8.4 Manipulating Recombination.- 9 Genome Analysis: Identification of and Relations Between Genomes.- 9.1 Genome Analysis: Different Concepts.- 9.2 Genomic Composition of Allopolyploids.- 9.2.1 Identification of the Progenitors.- 9.2.2 Assigning Chromosomes to Genomes and Homoeologous Groups.- 9.3 Relations Between Genomes: Homology, Homoeology, Affinity.- 9.3.1 Diploid Hybrids.- 9.3.2 Quantitative Models for Polyploid Hybrids.- 9.3.2.1 Triploid Hybrids.- 9.3.2.2 Tetraploid Hybrids.- 9.3.2.2.1 Tetraploid Hybrids with Unmarked Chromosomes.- 9.3.2.2.2 Tetraploid Hybrids with Marked Chromosomes.- 9.3.2.3 Higher Polyploids and Aneuploids.- 10 Manipulation of Genome Composition: A. Gene Transfer.- 10.1 Objectives.- 10.2 Molecular Versus Generative Gene Transfer.- 10.1 Identification of Transferred Chromatin.- 10.2 Different Approaches to Generative Gene Transfer...- 10.4.1 Gene Transfer by Direct Recombination.- 10.4.2 Manipulation of Recombination.- 10.4.3 Modification of Chromosome Pairing Affinity.- 10.4.4 Indirect Gene Transfer Via Addition or Substitution.- 10.4.4.1 Isolation of Addition and Substitution Lines.- 10.4.4.2 Gene Transfer from Alien Addition or Substitution Chromosomes.- 10.4.4.2.1 Homoeologous Recombination.- 10.4.4.2.2 Translocations.- 10.4.4.2.2.1 Reciprocal Translocations.- 10.4.4.2.2.2 Centromere Translocations.- 11 Manipulation of Genome Composition. B. Gene Dose: Duplication, Polyploidy and Gametic Chromosome Number.- 11.1 Objectives.- 11.2 Duplications.- 11.2.1 Multiple Copy Genes.- 11.2.2 Duplication of Small Chromosome Segments.- 11.2.3 Addition of Entire Chromosomes.- 11.3 Increase in the Number of Genomes: Polyploidy.- 11.3.1 Autopolyploidy.- 11.3.1.1 Triploids.- 11.3.1.2 Autotetraploids.- 11.3.1.2.1 Induction.- 11.3.1.2.1.1 Somatic Induction.- 11.3.1.2.1.2 Meiotic Doubling.- 11.3.1.2.2 Effects of Autopolyploidy.- 11.3.1.2.2.1 Somatic Effects.- 11.3.1.2.2.2 Effects of the Tetrasomic Genetic System.- 11.3.1.2.3 Reproductive Stabilization of Autotetraploids.- 11.3.1.2.3.1 Reduced Fertility and Segregation of Aneuploids.- 11.3.1.2.3.2 Quadrivalent Formation in Relation to Chromosome Morphology.- 11.3.1.2.3.3 Quadrivalent Distribution.- 11.3.1.2.3.4 Preferential Pairing.- 11.3.1.2.3.5 Localization of Pairing Initiation and Chiasmata.- 11.3.1.2.3.6 Shift of Point of Pairing Partner Exchange.- 11.3.1.2.3.7 Other Effects: Interference, B-Chromosomes; Correlation with Diploid Meiotic.- 11.3.1.2.4 Autotetraploidy: Conclusion.- 11.3.2 Artificial Allopolyploidy.- 11.3.2.1 Objectives and Pitfalls.- 11.3.2.2 Construction of Allopolyploids.- 11.3.2.2.1 Adjusting Chromosome Pairing Differentiation.- 11.3.2.2.2 Adjusting Mitotic and Meiotic Chromosome Behaviour: the Heterochromatin Story of Triticale.- 11.3.2.2.3 Reconstruction of Existing Allopolyploids.- 11.4 Reduction in Genome Number: Gametic Chromosome Number.- 11.4.1 Objectives.- 11.4.2 Induction.- 11.4.2.1 Somatic Reduction.- 11.4.2.2 Parthenogenetic Origin of Haploidy.- 12 Manipulation of the Genetic System.- 12.1 Natural and Artificial Variation in Generative Genetic Systems.- 12.2 Allopolyploidization of Autopolyploids.- 12.2.1 Pairing Affinity Differentiation.- 12.2.2 Chromosomal Rearrangements as Pairing Affinity Differentiating Factors.- 12.2.2.1 Translocations.- 12.2.2.2 Inversions.- 12.2.2.3 Genes Enhancing Pairing Affinity Differentiation.- 12.3 Permanent Translocation Heterozygosity.- 12.4 Cytogenetic Approaches to Hybrid Breeding.- 12.4.1 Introduction.- 12.4.2 Chromosomal Self-Regulating Systems for the Maintenance of Homozygous ms. ms Lines.- 12.4.2.1 Duplications.- 12.4.2.2 Balanced Tertiary Trisomy and Variants.- 12.4.2.3 XYZ System in Wheat.- 12.5 Apomixis and Related Systems.- References.