Monographs on 17 Theoretical and Applied Genetics

Edited by

R. Frankel (Coordinating Editor), Bet-Dagan

M. Grossman, Urbana· H.F. Linskens, Nijmegen

P. Maliga, Piscataway . R. Riley, London

Monographs on Theoretical and Applied Genetics

Volume 1 Meiotic Configurations A Source of Information for Estimating Genetic Parameters By J. Sybenga (1975)

Volume 2 Pollination Mechanisms, Reproduction and Plant Breeding By R. Frankel and E. Galun (1977)

Volume 3 Incompatibility in Angiosperms By D. de Nettancourt (1977)

Volume 4 Gene Interactions in Development By L.1. Korochkin (1981)

Volume 5 The Molecular Theory of Radiation Biology By K.H. Chadwick and H.P. Leenhouts (1981)

Volume 6 Heterosis Reappraisal of Theory and Practice Editor: R. Frankel (1983)

Volume 7 Induced Mutations in Plant Breeding By W. Gottschalk and G. Wolff (1983)

Volume 8 Protoplast Fusion Genetic Engineering in Higher Plants By Y.Y. Gleba and K.M. Sytnik (1984)

Volume 9 Petunia Editor: K.C. Sink (1984)

Volume 10 Male Sterility in Higher Plants By M.L.H. Kaul (1988)

Volume 11 Tree Breeding: Principles and Strategies By G. Namkoong, H.C. Kang, and J.S. Brouard (1988)

Volume 12 The Wheat Rusts - Breeding for Resistance By D.R. Knott (1989)

Volume 13 Population Dynamics and the Tribolism Model Genetics and Demography By R.F. Costantino and R.A. Desharnais (1991)

Volume 14 Genetic Improvement of Tomato Editor: G. Kalloo (1991)

Volume 15 Evolution and Function of Heterostyly Editor: S.C.H. Barrett (1992)

Volume 16 Distant Hybridization of Crop Plants Editors: G. Kalloo and J.B. Chowdhury (1992)

Volume 17 Cytogenetics in Plant Breeding By J. Sybenga (1992)

1. Sybenga

Cytogenetics in Plant Breeding

With 74 Figures

Springer-Verlag Berlin Heidelberg New York London Paris Tokyo Hong Kong Barcelona Budapest

Prof. I>r. J. Sybenga I>epartment of Genetics Wageningen Agricultural University I>reijenlaan 2 6703 HA Wageningen The Netherlands

ISBN-13 :978-3-642-84085-2 e-ISBN-13 :978-3-642-84083-8 DOl: 10.1007/978-3-642-84083-8

Library of Congress Cataloging-in-Publication Data. Cytogenetics in plant breeding I [edited by] J. Sybenga. p. cm. - (Monographs on theoretical and applied genetics; 17) Includes bibliographical references (p. ) and index. ISBN-13:978-3-642-84085-2

I. Plant breeding. 2. Plant cytogenetics. 3. Crops-Cytogenetics. I. Sybenga, J. (Jacob), 1926-SBI23.C98 1992 631.5'23-dc20 92-9632

. II. Series.

This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting. reuse of illustrations. recitation. broadcasting. repro~uction on microfilm or in any other way. and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer-Verlag. Violations are liable for prosecution under the German Copyright Law.

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Preface

The role of cytogenetics in plant breeding is varied. It provides methods for manipulating the composition of the genome and the genetic character­istics of the reproductive system. It also provides methods for extracting information from the material used in various stages of a breeding pro­gram, for instance the frequency of recombination between homologous and homoeologous genomes, the presence of abnormalities in normal, treated or hybrid material, the possible causes of irregularities in segrega­tion, fertility etc. It also provides information of a more general nature on genetic transmission systems, general consequences of abnormalities etc.

Many of the techniques, approaches and concepts of cytogenetics have been available for a long time, but there has been continuous, gradual and occasionally rapid progress in the quantity and quality of techniques, knowl­edge and understanding of cytogenetics and their application to plant breed­ing. After a period of declining interest, mainly a consequence of the rapid development of cell biological and molecular techniques of manipulation, and the expectation that these would rapidly replace the more tedious, difficult and old-fashioned generative approaches, interest in cytogenetics is increasing again. This is due in part to cytogenetic developments in their own right and in part to the growing insight that the combination of cytogenetic and cell biological and molecular techniques can be very fruitful in both directions. In addition, experience is accumulating that molecular genetic manipulation after all does not produce results as rapidly and as easily as hoped earlier, and that cytogenetics might provide good alterna­tives. It should be noted, however, that cytogenetics, although often requir­ing less sophisticated techniques, is often conceptually more complicated than cell and molecular biology.

The long history of cytogenetic research (of which many of the reports are as relevant now as at the time of publication) and its varied potential for application in plant breeding have resulted in very extensive literature. It is not possible to be aware of, and even less possible to refer to, all relevant publications. The reader will find that the choices made in this book are personal and that many important references have been missed or for various other reasons not included. It is hoped that the most serious omis­sions will be brought to the attention of the author.

VI Preface

There are several reviews and proceedings of meetings dealing entirely or partly with the cytogenetics of different crop species, and cytogenetics in plant breeding in general, for example:

- Cytogenetics of Crop Plants, MS Swaminathan, PK Gupta, U Sinha (eds) (1983); MacMillan India Ltd., Delhi-Bombay; - Chromosome Engineering in Plants, Part A. PK Gupta, T. Tsuchiya, eds. Elsevier, Amsterdam 1991; - Chromosome Engineering in Plants, Part B. T. Tsuchiya, PK Gupta eds. Elsevier, Amsterdam 1991; - Proceedings of the International Wheat Genetics Symposia, at 5 year intervals held at different locations; - Proceedings of the Barley Genetics Symposia: published as Barley Genetics I, II, III etc. Held and published at varying intervals at dif­ferent locations. - Maize cytogenetics, Carlson W.R., in: Corn and Corn Improvement,

G.F. Sprague and I.W. Dudley, editors; "Agronomy", Madison, WI, USA (1988). New editions will appear in the future.

Several chapters on papers from these books and proceedings have been referred to in the present text.

The approach to the subject and the decision which chapters to include are the choice of the author. For instance, a separate chapter on inter­specific hybrids could have been included, but it was preferred to deal with them in the chapters where their use is discussed (especially Chap. 9 on genome analysis, Chap. 10 on gene transfer and Chap. 11 on manipulation of genome number). A general introduction to chromosomes and their behaviour is given, as it may be useful to be able to look up the most general principles in the book itself. However, for details the reader is referred to the literature. Such choices will not be argumented.

Many colleagues have contributed to this book by providing figures and special information. Without mentioning each personally, I wish to express my gratitude to all of them here. I am especially grateful to Dr. I.H. de long and Dr. l. N. de Vries, who took the trouble of going through much of the manuscript, giving many valuable comments and suggestions. I also thank Dr. de long and Ms. lannie van Eden for drawing or plotting several of the figures.

Contents

Chapter 1 Cytogenetics in Genetics and Plant Breeding

1.1 1.1.1 1.1.2 1.2

Cytogenetics as a Subdiscipline of Genetics ........... . The Two Functions of the Genetic Material ........... . Cytogenetics Defined .............................. . Cytogenetics in Plant Breeding ..................... .

1 1 3 4

Chapter 2 Chromosome Composition, Structure and Morphology

2.1 DNA............................................ 7 2.1.1 The Chemical Basis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.1.2 Heterogeneity of DNA; Unique and Repetitive DNA. . . 8 2.1.3 Replication ....................................... 9 2.2 Chromosome Structure; Histones and Other

Chromosomal Proteins ............................. 10 2.3 Euchromatin, Heterochromatin. . . . . . . . . . . . . . . . . . . . . . 13 2.4 Special Functional Elements in Chromosomes. . . . . . . . . 14 2.4.1 Nucleolus Organizing Region (NOR) . . . . . . . . . . . . . . . . . 14 2.4.2 Centromere. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 2.4.3 Telomeres . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.5 Microscopic Chromosome Morphology: the Karyotype,

Standard and Variations. . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Chapter 3 The Mechanisms of Genetic Transmission

3.1 3.1.1 3.1.2 3.1.3

3.1.3.1

3.1.3.2

The Somatic Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Mitosis .......... '" ... '" . . . ... . . ... . ..... . .... . . 23 Duration of Mitosis ................................ 29 Order and Disorder in the Somatic Spindle and Nucleus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 Relative Position of Large and Small Chromosomes in the Spindle and in the Nucleus. Hollow Spindle. . . . . . . . 31 RablOrientation .................................. 31

VIII

3.1.3.3 3.1.3.4 3.1.3.5

3.1.4 3.1.4.1 3.1.4.1.1 3.1.4.1.2 3.1.4.1.2.1 3.1.4.1.2.2 3.1.4.1.2.3 3.1.4.2 3.2 3.2.1 3.2.2 3.2.2.1 3.2.2.2 3.2.2.3 3.2.2.4 3.2.3 3.2.3.1 3.2.3.2 3.2.3.3 3.2.3.4 3.2.4 3.2.4.1 3.2.4.1.1 3.2.4.1.2 3.2.4.1.2.1 3.2.4.1.2.2 3.2.4.1.2.2.1 3.2.4.1.2.2.2

Contents

Nucleolar Fusion Somatic Pairing ................................... . Non-homologous Chromosome Association; Nuclear Compartmentalization ............................. . Mitotic Variants with Genetic Consequences .......... . Intact Organism .................................. . Accidents ........................................ . Systematic Deviations ............................. . Chromosome Doubling ............................ . Elimination ...................................... . B-Chromosomes .................................. . In Vitro Culture .................................. . Generative Transmission: Fertilization - Meiosis ...... . Fertilization ...................................... . Meiosis .......................................... . Prophase I ....................................... . Metaphase I ...................................... . Anaphase I, Telophase I ........................... . Meiosis II .... .................................... . Systematic Variants of Meiotic Behaviou~ ............ . Achiasmate Meiosis ............................... . Holokinetic Chromosomes ......................... . Neocentric Activity ............................... . Specialized Chromosomes .......................... . Recombination ................................... . Two Forms of Recombination ...................... . Chromosome Recombination ....................... . Exchange Recombination .......................... . Two and More Chiasmata in One Chromosome ....... . Genetic Variation in Exchange Recombination ........ . Genetic Variation in Frequency of Exchange ......... . Genetic Variation in Pattern of Exchange ............ .

32 32

32 34 34 34 36 36 37 37 39 42 43 45 45 54 54 56 56 56 57 57 58 58 58 58 60 60 61 61 63

Chapter 4 The Somatic Chromosome Complement: Karyotype Analysis

4.1 4.1.1 4.1.2 4.2

4.2.1 4.2.2

4.2.2.1

The Karyotype .................................... 65 Characteristics of the Karyotype ..................... 65 Applications of Karyotype Analysis .................. 66 Approaches to Karyotype Analysis: Chromosome Number and Morphology . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 Number of Genomes Per Cell: Indirect Methods .. . . . . . 68 Exact Chromosome Number; Chromosome Morphology .......................... 72 Techniques of Preparation .......................... 72

Contents

4.2.2.2 4.2.3 4.2.3.1 4.2.3.2 4.2.3.3 4.2.4 4.2.4.1 4.2.4.2 4.2.4.3

IX

Observations; Measurements. . . . . . . . . . . . . . . . . . . . . . . . 74 Presenting the Karyotype . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 Karyogram and Idiogram ........................... 76 Idiogram Construction: Coping with Variation. . . . . . . . . 80 Idiogram Construction: Plotting the Observations ... . . . 86 Markers Within Chromosome Arms . . . . . . . . . . . . . . . . . . 92 Chromosome Banding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 Molecular Markers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 Genetic Markers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 100

Chapter 5 Karyotype Variants A: Chromosome Structural Variants

5.1 5.1.1 5.1.2 5.1.3 5.1.4 5.1.5 5.2 5.2.1 5.2.2 5.2.3 5.2.4 5.2.5 5.3 5.3.1 5.3.2 5.3.3 5.3.4 5.4 5.4.1

5.4.1.1 5.4.1.2 5.4.1.3 5.4.1.4 5.4.2

5.4.2.1 5.4.2.2 5.4.2.3 5.4.2.4 5.4.3

Deficiencies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 101 Types.. . . .... ..... . . .... . . .... . .... ..... . .... . . .. 101 Origin ............................... , . . .... ...... 101 Relevance ........................................ 101 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 103 Consequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 105 Duplications ...................................... 105 Types............................................ 105 Origin.. . . .... . . ... . . ..... . .... . .... . . ........ . ... 107 Relevance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 107 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 108 Consequences. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 109 Inversions ........................................ 111 Types (Paracentric and Pericentric) and Origin. . . . . . . .. 111 Relevance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 111 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 111 Consequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 115 Translocations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 116 Reciprocal Translocation or Interchange and Simple Terminal Translocation . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 117 Types and Origin .................................. 117 Relevance ........................................ 117 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 118 Consequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 126 Two or More Interchanges Combined: Translocation Tester Set; Balanced Complex Translocation Heterozygotes ........................ 130 Types and Origin .................................. 130 Relevance ........................................ 130 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 132 Consequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 135 Simple Interstitial Translocations. . . . . . . . . . . . . . . . . . . .. 135

x

5.4.3.1 5.4.3.2 5.5

5.5.1 5.5.2 5.5.3

Contents

Types, Origin and Relevance. . . . . . . . . . . . . . . . . . . . . . .. 135 Characteristics, Identification and Consequences . . . . . .. 136 Other Rearrangements (Robertsonian Fission and Fusion; Isochromosome; Compound) . . ... ..... . .. 136 Types and Origin .................................. 136 Relevance ........................................ 138 Characteristics, Identification and Consequences . . . . . .. 139

Chapter 6 Karyotype Variants B: Chromosome Number Variants

6.1 6.1.1 6.1.1.1 6.1.1.2 6.1.1.3 6.1.1.4 6.1.1.5 6.1.2 6.1.2.1 6.1.2.2 6.1.2.2.1 6.1.2.2.1.1 6.1.2.2.1.2 6.1.2.2.1.3 6.1.2.2.1.4 6.1.2.2.2 6.1.2.2.2.1 6.1.2.2.2.2 6.1.2.2.2.3 6.1.2.2.2.4 6.1.2.2.3 6.1.2.3 6.1.2.3.1 6.1.2.3.2 6.1.2.3.3 6.1.2.3.4 6.1.2.3.5 6.1.2.4 6.1.2.4.1 6.1.2.4.2 6.2 6.2.1 6.2.1.1 6.2.1.2

Euploidy ......................................... 141 Haploidy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 141 Types and Terminology. . . . . . . . . . . . . . . . . . . . . . . . . . . .. 141 Origin. . . ..... . .... . .... . . .... . . ..... . . ....... . . .. 142 Relevance ........................................ 142 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 142 Consequences. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 143 Polyploidy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 144 Types............................................ 144 Autopolyploidy; Types. . . . . . . . . . . . . . . . . . . . . . . . . . . .. 144 Autotriploids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 145 Origin. .... . . .... . ..... . .... . . ..... . ..... ... . . .... 145 Relevance ........................................ 145 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 147 Consequences. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 148 Autotetraploids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 149 Origin. . . . . ... . . ... . . .... . ..... . . ..... . ... .... . . .. 149 Relevance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 149 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 149 Consequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 155 Higher Autopolyploids ............................. 160 Allopolyploidy .................................... 161 Types. . . . .... . .... . .... . . .... . . . ... . . .... .... . . .. 161 Origin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 162 Relevance ........................................ 162 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 163 Consequences. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 165 Polyploid Hybrids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 165 Types, Origin and Relevance . . . . . . . . . . . . . . . . . . . . . . .. 165 Characteristics, Identification and Consequences . . . . . .. 165 Aneuploidy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 166 Hypoploidy, Monosomy . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 166 Types of Monosomy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 166 Origin... . . . .... . .... . . .... . . .... . . ..... . ... . . .... 167

Contents

6.2.1.3 6.2.1.4 6.2.1.5 6.2.2 6.2.2.1 6.2.2.1.1 6.2.2.1.2 6.2.2.1.3 6.2.2.1.4 6.2.2.1.5 6.2.2.2 6.2.2.2.1 6.2.2.2.2 6.2.2.2.3 6.2.2.2.4 6.2.2.3 6.2.2.3.1 6.2.2.3.2 6.2.2.3.3 6.2.2.3.4 6.2.2.4 6.2.2.4.1 6.2.2.4.2 6.2.2.4.2.1 6.2.2.4.2.2 6.2.2.4.2.3

XI

Relevance ........................................ 168 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 169 Consequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 170 Hyperploidy ...................................... 172 Primary Trisomy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 172 Types............................................ 172 Origin.... . . .... . .... . . . .... . . ... . . .... . .... . ..... 172 Relevance ........................................ 173 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 173 Consequences. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 174 Secondary and Telocentric Trisomy .................. 178 Types, Origin ..................................... 178 Relevance ........................................ 179 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 179 Consequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 180 Tertiary and Translocation Trisomy .................. 182 Types, Origin ..................................... 182 Relevance ........................................ 182 Characteristics and Identification. . . . . . . . . . . . . . . . . . . .. 183 Consequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 185 Other Trisomies and Higher Polysomies .............. 185 Compensating Trisomics . . . . . . . . . . . . . . . . . . . . . . . . . . .. 185 Alien Additions ................................... 187 Types, Origin ..................................... 187 Relevance ........................................ 189 Characteristics, Identification and Consequences . . . . . .. 190

Chapter 7 Diagnosis: Identifying Cytogenetic Causes of Variants of the Karyotype and the Generative Cycle

7.1

7.2 7.3

7.3.1 7.3.2 7.3.3 7.4 7.4.1 7.4.1.1

7.4.1.2

Diagnosis: The Collection of Specific Information: Context, Objectives and Means. . . . . . . . . . . . . . . . . . . . .. 191 The Diagnostic Strategy ............................ 194 The Diagnostic Use of Meiotic Behaviour and Configurations: Types and Distribution; Causes and Consequences. . . . . . . . . . . . . . . . . . . . . . . . . .. 197 Stages .. , ...... : . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 197 Basic Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 197 Distribution of Configurations. . . . . . . . . . . . . . . . . . . . . .. 198 The Diagnostic Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . .. 198 No Chromosome Number Deviation. . . . . . . . . . . . . . . . .. 199 Meiosis: Diakinesis/Metaphase I: No Obvious Deviations. . . . . . . . . . . . . . . . . . . . . . . . . . . .. 199 Univalents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 200

XII

7.4.1.3 7.4.1.4 7.4.1.4.1 7.4.1.4.2

7.4.1.4.3

7.4.1.5

7.4.1.5.1 7.4.1.5.2 7.4.1.5.3 7.4.1.5.4 7.4.2

7.4.2.1 7.4.2.1.1 7.4.2.1.2 7.4.2.1.3 7.4.2.1.4 7.4.2.2 7.4.2.2.1 7.4.2.2.2 7.4.2.2.3 7.4.2.2.4 7.4.3 7.4.3.1 7.4.3.1.1 7.4.3.1.2 7.4.3.1.3 7.4.3.2 7.4.3.2.1 7.4.3.2.2 7.4.3.2.3 7.4.4 7.4.4.1 7.4.4.1.1 7.4.4.1.2 7.4.4.1.3 7.4.4.1.4 7.4.4.2 7.4.4.2.1 7.4.4.2.2 7.4.4.2.3 7.4.4.2.3.1 7.4.4.2.3.2

Contents

Heteromorphic or Otherwise Abnormal Bivalents . . . . .. 203 Multivalents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 207 Trivalents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 207 Quadrivalents: Chromosome Number Normal; Karyotype Visibly Changed ......................... 208 Higher-Order Multivalents; Chromosome Number Normal, Chromosome Structure Normal or Deviant. . .. 210 Chromosome Number Normal; Diakinesis-Metaphase I Normal. . . . . . . . . . . . . . . . . . . . .. 211 Unequal Sister Chromatids. . . . . . . . . . . . . . . . . . . . . . . . .. 211 Chromatid Bridges. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 212 Chromatid Loops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 213 Anaphase II Bridges ............................... 213 Chromosome Number Not Normal; Aneuploidy: Hyperploidy ...................................... 214 Trisomies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 214 Univalents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 214 Heteromorphic Bivalents ........................... 216 Multivalents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 216 Anaphase I and Anaphase II Aberrations . . . . . . . . . . . .. 219 Two or More Extra Chromosomes ................... 220 Only Normal Bivalents ............................. 220 Univalents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 221 Heteromorphic Bivalents ........................... 221 MuItivalents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 222 Hypoploidy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 222 Monosomics ...................................... 223 Univalents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 223 Heteromorphic or Otherwise Abnormal Bivalents . . . . .. 223 Multivalents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 224 Hypoploids: Two Chromosomes Less than Normal ..... 224 Only Normal Bivalents ..... . . . . . . . . . . . . . . . . . . . . . . .. 224 Univalents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 224 Heteromorphic Bivalents and Multivalents ............ 225 Euploidy ......................................... 225 Gametic Chromosome Number ("Haploidy") . . . . . . . . .. 225 Only Normal Bivalents ............................. 225 Univalents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 225 Heteromorphic or Otherwise Abnormal Bivalents . . . . .. 226 Multivalents, Anaphase and Cellular Abnormalities .... 226 Triploidy ......................................... 226 Univalents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 227 Heteromorphic and Otherwise Abnormal Bivalents . . . .. 227 MuItivalents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 228 Trivalents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 228 Higher Order Multivalents . . . . . . . . . . . . . . . . . . . . . . . . .. 228

Contents

7.4.4.3 7.4.4.3.1 7.4.4.3.2 7.4.4.3.3 7.4.4.3.4 7.4.4.3.5 7.4.4.4

7.4.4.5

XIII

The Doubled Chromosome Number. . . . . . . . . . . . . . . . .. 229 Only Normal Bivalents ............................. 229 Univalents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 230 Heteromorphic or Otherwise Abnormal Bivalents . . . . .. 230 Multivalents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 230 Anaphase and Cellular Irregularities. . . . . . . . . . . . . . . . .. 231 Aneuploidy in Combination with Doubled Chromosome Number.. . . .... . . ... . ... . . ... 231 Higher Ploidy Levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 232

Chapter 8 Estimating, Recording and Manipulating Recombination

8.1

8.1.1 8.1.1.1

8.1.1.2 8.1.1.2.1 8.1.1.2.1.1 8.1.1.2.1.2 8.1.1.2.2

8.1.1.2.2.1 8.1.1.2.2.2 8.1.1.3

8.2 8.2.1 8.2.1.1 8.2.1.2

8.2.1.3 8.2.1.4

8.2.1.5 8.3

8.3.1

8.3.2 8.3.2.1 8.3.2.1.1 8.3.2.1.2 8.3.2.1.3

Chromosome Recombination and Exchange Recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 233 The Role of Chromosome Number in Recombination... 233 Chromosome Recombination in Diploids as the Basis of Mendelian Inheritance. . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 233 Variation in Chromosome Recombination. . . . . . . . . . . .. 234 Ploidy Level ...................................... 234 Haploids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 234 Polyploids ........................................ 234 Chromosome-Associated Restrictions of Chromosome Recombination. . . . . . . . . . . . . . . . . . . . . . .. 235 Affinity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 235 Permanent Translocation Heterozygosity. . . . . . . . . . . . .. 235 The Relative Importance of Chromosome Recombination in Plant Breeding . . . . . . . . . . . . . . . . . . .. 235 Exchange Recombination: Crossing-Over. . . . . . . . . . . .. 236 Estimates of Crossing-Over ......................... 236 Segregation of Genetic Markers. . . . . . . . . . . . . . . . . . . . .. 236 Chiasma Frequency, Recombination Nodules and Chiasm ate Chromosome Arm Association Frequency . .. 237 Mapping Functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 239 Models for Deriving Chiasmate Association Frequencies from Configuration Frequencies. . . . . . . . . .. 240 Variation in Crossing-Over. . . . . . . . . . . . . . . . . . . . . . . . .. 243 Recording Recombination: Genetic Chromosome Maps . . . . . . . . . . . . . . . . . . . . . . . .. 244 Recombinational Maps of Genes and Other Markers; Three-Point Test. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 244 The Location of Genes on Chromosomes ............. 247 Aneuploids ....................................... 247 Monosomics ...................................... 247 Primary Trisomics ................................. 250 Telocentric Trisomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 251

XIV

8.3.2.1.4 8.3.2.2 8.3.2.2.1 8.3.2.2.2 8.3.3

8.3.3.1 8.3.3.1.1 8.3.3.1.2

8.3.3.1.3

8.3.3.2

8.3.3.2.1 8.3.3.2.2 8.3.3.3

Contents

Tertiary and Other Complex Trisomics ............... 254 Chromosomal Rearrangements . . . . . . . . . . . . . . . . . . . . .. 255 Deficiencies and Inversions. . . . . . . . . . . . . . . . . . . . . . . . .. 255 Translocations, Duplications and Robertsonian Splits . .. 256 The Physical and Recombinational Location of Genes Within Chromosomes .............................. 258 Natural Chromosome Morphological Markers. . . . . . . .. 258 The Centromere . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 258 Heterochromatin, Chromosomes and Banding Polymorphisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . .. 261 The NOR and Other Multigene Loci: In Situ Hybridization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 262 The Break Points of Rearrangements as Genetic and Chromosomal Markers. . . . . . . . . . . . . . . . . . . . . . . . .. 263 Deficiencies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 263 Translocations, Duplications and Inversions . . . . . . . . . .. 264 Rearranged Aneuploids: Tertiary and Other Complex Monosomics and Trisomics . . . . . . . . . . . . . . . . . . . . . . . . .. 267

8.3.4 Recombinational Chromosome Maps: An Example ...................................... 268

8.4 Manipulating Recombination . . . . . . . . . . . . . . . . . . . . . . .. 268

Chapter 9 Genome Analysis: Identification of and Relations Between Genomes

9.1 9.2 9.2.1 9.2.2

9.3

9.3.1 9.3.2 9.3.2.1 9.3.2.2 9.3.2.2.1 9.3.2.2.2 9.3.2.3

Genome Analysis: Different Concepts . . . . . . . . . . . . . . .. 271 Genomic Composition of Allopolyploids . . . . . . . . . . . . .. 271 Identification of the Progenitors. . . . . .. . . . . . . . . . . . . . .. 271 Assigning Chromosomes to Genomes and Homoeologous Groups ......................... 273 Relations Between Genomes: Homology, Homoeology, Affinity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 277 Diploid Hybrids .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 277 Quantitative Models for Polyploid Hybrids . . . . . . . . . . .. 279 Triploid Hybrids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 279 Tetraploid Hybrids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 288 Tetraploid Hybrids with Unmarked Chromosomes ..... 288 Tetraploid Hybrids with Marked Chromosomes. . . . . . .. 298 Higher Polyploids and Aneuploids ................... 300

Chapter 10 Manipulation of Genome Composition: A. Gene Transfer

10.1 Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 301 10.2 Molecular Versus Generative Gene Transfer. . . . . . . . . .. 302

Contents

10.3 10.4 10.4.1 10.4.2 10.4.3 10.4.4 10.4.4.1 10.4.4.2

10.4.4.2.1 10.4.4.2.2 10.4.4.2.2.1 10.4.4.2.2.2

Identification of Transferred Chromatin .............. . Different Approaches to Generative Gene Transfer ... . Gene Transfer by Direct Recombination ............. . Manipulation of Recombination .................... . Modification of Chromosome Pairing Affinity ......... . Indirect Gene Transfer Via Addition or Substitution ... . Isolation of Addition and Substitution Lines .......... . Gene Transfer from Alien Addition or Substitution Chromosomes .................................... . Homoeologous Recombination ..................... . Translocations .................................... . Reciprocal Translocations .......................... . Centromere Translocations ......................... .

Chapter 11 Manipulation of Genome Composition. B. Gene Dose: Duplication, Polyploidy and Gametic Chromosome Number

11.1 11.2 11.2.1 11.2.2 11.2.3 11.3 11.3.1 11.3.1.1 11.3.1.2 11.3.1.2.1 11.3.1.2.1.1 11.3.1.2.1.2 11.3.1.2.2 11.3.1.2.2.1 11.3.1.2.2.2 11.3.1.2.3 11.3.1.2.3.1 11.3.1.2.3.2

11.3.1.2.3.3 11.3.1.2.3.4 11.3.1.2.3.5 11.3.1.2.3.6 11.3.1.2.3.7

11.3.1.2.4 11.3.2

Objectives ....................................... . Duplications ..................................... . Multiple Copy Genes .............................. . Duplication of Small Chromosome Segments ......... . Addition of Entire Chromosomes ................... . Increase in the Number of Genomes: Polyploidy ...... . Autopolyploidy ................................... . Triploids ......................................... . Autotetraploids ................................... . Induction ........................................ . Somatic Induction ................................ . Meiotic Doubling ................................. . Effects of Autopolyploidy .......................... . Somatic Effects ................................... . Effects of the Tetrasomic Genetic System ............ . Reproductive Stabilization of Autotetraploids ......... . Reduced Fertility and Segregation of Aneuploids ...... . Quadrivalent Formation in Relation to Chromosome Morphology ...................................... . Quadrivalent Distribution .......................... . Preferential Pairing ............................... . Localization of Pairing Initiation and Chiasmata ....... . Shift of Point of Pairing Partner Exchange ............ . Other Effects: Interference, B-Chromosomes; Correlation with Diploid Meiotic .................... . Autotetraploidy: Conclusion ....................... . Artificial Allopolyploidy ........................... .

xv

302 305 305 309 312 317 317

319 320 321 321 322

327 328 328 329 331 332 332 332 334 334 334 336 341 341 343 344 344

347 348 349 349 350

352 353 354

XVI

11.3.2.1 11.3.2.2 11.3.2.2.1 11.3.2.2.2

11.3.2.2.3 11.4

11.4.1 11.4.2 11.4.2.1 11.4.2.2

Contents

Objectives and Pitfalls. . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 354 Construction of Allopolyploids ...................... 355 Adjusting Chromosome Pairing Differentiation ........ 355 Adjusting Mitotic and Meiotic Chromosome Behaviour: the Heterochromatin Story of Triticale. . . . . . . . . . . . . . .. 357 Reconstruction of Existing Allopolyploids . . . . . . . . . . . .. 362 Reduction in Genome Number: Gametic Chromosome Number .......................................... 364 Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 364 Induction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 365 Somatic Reduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 365 Parthenogenetic Origin of Haploidy . . . . . . . . . . . . . . . . .. 368

Chapter 12 Manipulation of the Genetic System

12.1

12.2 12.2.1 12.2.2

12.2.2.1 12.2.2.2 12.2.2.3 12.3 12.4 12.4.1 12.4.2

12.4.2.1 12.4.2.2 12.4.2.3 12.5

Natural and Artificial Variation in Generative Genetic Systems .......................................... 373 Allopolyploidization of Autopolyploids . . . . . . . . . . . . . .. 374 Pairing Affinity Differentiation ...................... 375 Chromosomal Rearrangements as Pairing Affinity Differentiating Factors ............................. 378 Translocations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 378 Inversions ........................................ 382 Genes Enhancing Pairing Affinity Differentiation ...... 386 Permanent Translocation Heterozygosity. . . . . . . . . . . . .. 386 Cytogenetic Approaches to Hybrid Breeding .......... 392 Introduction ...................................... 392 Chromosomal Self-Regulating Systems for the Maintenance of Homozygous ms.ms Lines. . . ... ...... 394 Duplications ...................................... 396 Balanced Tertiary Trisomy and Variants. . . . . . . . . . . . .. 398 XYZ System in Wheat. . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 400 Apomixis and Related Systems ...................... 402

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 409

Subject Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 439