PLANT CYTOGENETICS. Ram J. Singh Department of Agronomy University of Illinois Urbana, Illinois. CRC Press Boca Raton Ann Arbor London Tokyo

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1 f{ PLANT CYTOGENETICS Ram J. Singh Department of Agronomy University of Illinois Urbana, Illinois CRC Press Boca Raton Ann Arbor London Tokyo

2 TABLE OF CONTENTS Chapter 1. INTRODUCTION 1 Chapter 2. THE HANDLING OF PLANT CHROMOSOMES 7 I. Introduction 7 II. Mitotic and Meiotic Chromosomes 7 A. Collection of Roots 7 B. Pretreatments of Roots 8 1. Ice-Cold Water Hydroxyquinoline 8 3. Colchicine 8 4. oc-bromonaphthalene 8 5. Paradichlorobenzene 9 C. Fixation 9 D. Staining of Chromosomes 9 1. Aceto-Carmine Staining Feulgen Staining Alcoholic-Hydrochloric Acid-Carmine Lacto-Propionic-Orcein Giemsa Staining 13 a. Giemsa C-Banding Technique 13 i. Dehydration 13 ii. Denaturation 13 iii. Renaturation 14 iv. Staining 14 b. Giemsa N-Banding Technique 15 c. HCl-KOH-Giemsa (HKG) Technique 15 III. Smear Technique for Plant Chromosomes 16 A. Chromosome Preparation from the Roots 16 B. Chromosome Preparation from Cell Suspension and Callus 17 IV. In Situ Hybridization 18 A. Chromosome Preparation 18 B. In Situ Hybridization Procedure Solutions Hybridization Procedure 22 V. Pollen Staining 23 VI. Pollen-Stigma Incompatibility 23 Chapter 3. CELL DIVISION 25 I. Introduction 25 II. Mitosis 25 A. Process of Mitosis Interphase Prophase 25

3 3. Metaphase Anaphase Telophase Cytokinesis 27 B. Duration of Mitosis 28 C. Chromosome Orientation at Interphase and Prophase 29 D. Somatic Association 29 III. Meiosis 31 A. Process of Meiosis Cycle 1 32 a. Prophase-I.32 i. Leptonema 32 ii. Zygonema 32 iii. Pachynema 32 iv. Diplonema 33 v. Diakinesis 33 b. Metaphase-I 33 c. Anaphase-1 34 d. Telophase-I 34 e. Interkinesis Cycle II 35 B. Duration of Meiosis 35 C. Gametogenesis 36 Chapter 4. GENETIC CONTROL OF MEIOSIS 39 I. Introduction 39 II. Synaptic Mutants 39 A. Distribution of Synaptic Mutants 44 B. Origin of Synaptic Mutants 44 C. Cytological Behavior of Synaptic Mutants 46 D. Synaptic Mutants and Recombinations 49 E. Factors Influencing Pairing in Synaptic Mutants 50 III. Genes Responsible for Chromosome Disjunction 51 IV. Other Meiotic Mutants 53 V. Role of Heterochromatin in Chromosome Pairing 53 VI. Diploid-Like Meiosis in Allopolyploids...54 A. The 5-B System in Wheat (2«= 6x - 42)..54 B. Origin of Ph 56 VII. Haploidy 56 A. Mechanism of Chromosome Elimination 57 B. Genetics of Chromosome Elimination 57 C. Haploid-Initiator Gene in Barley 58 VIII. Male Sterility 61 A. Classification of Male Sterility 61 B. Mechanism of Male Sterility 61

4 Chapter 5. KARYOTYPE ANALYSIS 63 I. Introduction...: 63 II. Nomenclature of Chromosomes 64 III. Karyotype Analysis of Barley Chromosomes 65 A. Chromosome 1 66 B. Chromosome 2 66 C. Chromosome 3 70 D. Chromosome 4 70 E. Chromosome 5 70 F. Chromosome 6 70 G. Chromosome 7 70 Chapter 6a. CHROMOSOMAL ABERRATIONS STRUCTURAL CHROMOSOME CHANGES 71 I. Deficiencies 71 A. Introduction 71 B. Origin and Identification of Deficiencies 71 C. Transmission of Deficiencies 75 D. Genetic Studies 75 E. Use of Deficiencies in Hybrid Maize Breeding 76 F. Ring Chromosomes 78 II. Duplications 80 A. Introduction 80 B. Origin of Duplications and Deficiencies 80 C. Identification of Duplications and Deficiencies 81 D. Transmission of Duplications and Deficiencies 82 E. Use of Duplications and Deficiencies in Genetic Studies 82 III. Interchanges 83 A. Introduction 83 B. Identification of Interchanges 84 C. Interchanges in Genetic Studies : 88 D. Principles of Producing Interchange Testers 91 E. Identification of Interchanged Chromosomes 91 F. B-A Interchanges 93 G. Role of Interchanges in Evolution of Crops Oenothera Species 95 a. Gametophytic and Zygotic Lethals 96 b. Microspore and Megaspore Competition 96 c. Chromosome Designation in Oenothera Secale Species 97 IV. Inversions 101 A. Introduction 101 B. Types of Inversions Paracentric Inversion 101 a. Cytological Behavior 102

5 b. Fertility 105 c. Linkage studies Pericentric Inversion 107 a. Cytological Behavior 107 b. Fertility 109 Chapter 6b. CHROMOSOMAL ABERRATIONS NUMERICAL CHROMOSOME CHANGES (HETEROPLOIDY) 111 I. Euploidy Ill A. Introduction Ill B. Classification of Euploidy Ill 1. Autopolyploidy a. Autotriploids 113 i. Sources of Autotriploids 113 ii. Cytological Behavior in Autotriploids 116 iii. Fertility in Autotriploids 119 iv. Cytology in Hypertriploids 121 b. Autotetraploids 122 i. Sources of Autotetraploids 122 Colchicine 122 Nitrous Oxide 123 ii. Morphological Characteristics of Autotetraploids 125 iii. Cytological Behavior in Autotetraploids 125 iv. Fertility and Breeding Behavior in Autotetraploids 126 v. Genetic Segregation in Autotetraploids Allopolyploidy 129 a. Triticale (x Triticosecale Wittmack) 129 II. Aneuploidy Trisomics, 131 A. Primary Trisomics Introduction Sources of Primary Trisomics 132 a. Autotriploids 132 b. Synaptic Mutants (Asynaptic and Desynaptic) 137 c. Mutagen Treatments 137 d. Normal Diploids 138 e. Other Sources Identification of Primary Trisomics 139 a. Morphological Identification 139 i. Effect of the Length of Extra Chromosome on Plant Morphology 141 ii. Effect of a Nucleolus Organizer Chromosome on Plant Morphology 142 iii. Effect of Genetic Background 142

6 b. Cytological Identification 143 c. Identification of Primary Trisomics with Translocation Testers Transmission of Extra Chromosome in Primary Trisomics 147 a. Female Transmission 147 b. Pollen Transmission 150 c. Progenies of Primary Trisomics Genetic Segregation in Primary Trisomics 151 a. Association of a Recessive Gene 151 i. Random Chromosome Segregation 152 ii. Random Chromatid and Maximum Equational Segregation 152 b. Association of a Dominant Gene 154 c. Gene-Chromosome-Linkage Group Relationships 154 B. Secondary Trisomics Introduction Sources of Secondary Trisomics Identification of Secondary Trisomics 160 a. Morphological Identification 160 b. Cytological Identification Transmission of the Extra Chromosome in Secondary Trisomics Genetic Segregation in Secondary Trisomics 162 C. Tertiary Trisomics Introduction Sources of Tertiary Trisomics Identification of Tertiary Trisomics 166 a. Morphological Identification 166 b. Cytological Identification Transmission of the Extra Chromosome in Tertiary 1 Trisomics Genetic Segregation in Tertiary Trisomics Balanced Tertiary Trisomics (BTT) 169 D. Telotrisomics Introduction Sources of Telotrisomics Identification of Telotrisomics 174 a. Morphological Identification 174 b. Cytological Identification 175 c. Meiotic Behavior of Telotrisomics 177 i. Meiotic Abnormalities 180 ii. Stability of Telocentric Chromosomes Transmission of the Extra Chromosome in Telotrisomics Genetic Segregation in Telotrisomics 184

7 E. Acrotrisomics Introduction Sources of Acrotrisomics Identification of Acrotrisomics 191 a. Morphological Identification 191 b. Cytological Identification 191 c. Meiotic Behavior of Acrocentric Chromosomes Transmission of the Extra Chromosome in Acrotrisomics Genetic Segregation in Acrotrisomics 193 F. Compensating Trisomics Introduction Sources of Compensating Trisomics Identification of Compensating Trisomics 196 a. Morphological Identification 196 b. Cytological Identification Transmission of the Extra Chromosome in Compensating Trisomics Genetic Segregation in Compensating Trisomics 197 G. Novel-Compensating Diploids Introduction Sources of Novel-Compensating Diploids Identification of Novel-Compensating Diploids 199 a. Morphological Identification 199 b. Cytological Identification Meiotic Behavior in Novel-Compensating Diploids 199 a. Plants with In acro3l 3S + 1 telo3s 199 b. Plants with 2«= acro3l 3S + 2 telo3s Breeding Behavior of Novel-Compensating Diploids Usefulness of Novel-Compensating Diploids 203 III. Monosomics and Nullisomics ; 206 A. Introduction 206 B. Sources of Monosomics and Nullisomics Spontaneous Origin Chemical Treatments and X-rays Haploids, Polyploids, and Aneuploids Asynaptic and Desynaptic Lines Intra- and Interspecific Hybrids Genetic System 211 C. Identification of Monosomics and Nullisomics Morphological Identification Cytological Identification Meiosis in Monosomics and Nullisomics Behavior of Univalent Chromosomes at Meiosis 219 D. Fertility of Monosomics and Nullisomics 220 E. Breeding Behavior of Monosomics and Nullisomics 221

8 F. Genetic studies Locating'Recessive Genes Locating Dominant Genes Locating Duplicate Genes 225 IV. Alien Addition Lines 226 A. Introduction 226 B. Production of Alien Addition Lines (AALs) Hexaploid Species Tetraploid Species Diploid Species 231 C. Identification of Alien Addition Lines Morphological Identification Cytological Identification Meiosis in Alien Addition Lines Intercrossing Disomic Alien Addition Lines Biochemical Identification 237 D. Breeding Behavior of Alien Addition Lines Monosomic Alien Addition Lines (MAALs) Disomic Alien Addition Lines (DAALs) 238 E. Fertility in Alien Addition Lines 242 V. Alien Substitution Lines 243 A. Introduction 243 B. Types of Alien Substitutions Genomic substitution Chromosome Substitution and Translocation Lines 244 a. Production of Substitution and Translocation Lines b. Wheat-Rye Substitutions and Homoeologous Relationships 248 i. Chromosome 1R 248 ii. Chromosome 2R 248 iii. Chromosome 3R 249 iv. Chromosome 4R 252 v. Chromosome 5R vi. Chromosome 6R 253 vii. Chromosome 7R 253 C. Practical Application of Substitution Lines 254 Chapter 7. GENOME ANALYSIS I. Introduction 255 II. Classical Taxonomy and Genome Designations 255 III. Genome Relationships among Diploid Species 257 A. Crossing Affinity 257 B. Chromosome Pairing Intragenomic Chromosome Pairing Intergenomic Chromosome Pairing Variable and Minimum Chromosome Pairing 265

9 IV. Genomes of Glycine 269 V. Genomes of Gossypium 270 VI. Ancestors of Allopolyploid Species 272 A. Brassica (B. carinata, 2n = 4x= 34; B. juncea, 2n = 4x = 36; B. napus, 2n = 4x = 38) B. Glycine (G. tomentella, 2n = 4x = 80) 274 C. Gossypium (G. hirsutum; G. barbadense, 2n=4x=52) 277 D. Nicotiana(N. tabacum, 2n = 4x = 48) 279 E. Triticum (T. aestivum, 2n = 6x = 42) The Source of the A-Genome The Source of the B-Genome The Source of the D-Genome 283 Chapter 8. CHROMOSOMAL ABERRATIONS IN CELL AND TISSUE CULTURE DERIVED CALLUSES AND THEIR REGENERANTS 285 I. Introduction 285 II. Chromosomal Aberrations in Callus 285 A. Media Composition 285 B. Age of Callus 288 C. Nature of Callus (Morphogenic vs. Nonmorphogenic) 289 D. Genetic Background of the Explants 290 E. Kind of Media (Solid vs. Liquid) 293 III. Mechanism of Chromosomal Aberrations in Culture 293 IV. Chromosomal Aberrations in Regenerated Plants 295 A. Diploid vs. Polyploid Species Potato (Solanum tuberosum) Wheat {Triticum aestivum) Triticale 299 B. Age of Callus 299 C. Source of Explant Materials 300 D. Culture Conditions '. 301 V. Chromosomal Aberrations in Haploid Callus and Their Regenerants 301 VI. Chromosomal Aberrations in Somatic Hybrids 303 A. Stable Somatic Hybrids 304 B. Partially Stable Somatic Hybrids 304 C. Unstable Somatic Hybrids 304 References 309 Glossary 357 Appendix 365 Index 369

Chapter 11 Chromosome Mutations. Changes in chromosome number Chromosomal rearrangements Evolution of genomes

Chapter 11 Chromosome Mutations Changes in chromosome number Chromosomal rearrangements Evolution of genomes Aberrant chromosome constitutions of a normally diploid organism Name Designation Constitution