Cytogenetics in Plant Breeding

An introductory discussion of basic chromosome structure and function preceeds the main text on the application of cytogenetic approaches to the analysis of the manipulation of both the genetic make-up and the genetic transmission system of plant breeding material. Analysis using light and electron microscopy, segregations and molecular techniques, yields information for assessing the material before and after manipulation. Much attention is given to quantitative methods. Manipulation not only involves the construction of specific genotypes, but also chromosomal transmission systems. Although analysis and manipulation in the somatic cycle are considered, the focus is on the generative cycle, with emphasis on analysis and subsequent segregation of specifically constructed material. The book is intended for plant breeders and other scientists interested in the analysis and manipulation of breeding material at the chromosomal level. Comparisons with molecular and cell biological approaches are made, and the potential of the various methods is evaluated.

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.