The Genetical Analysis of Quantitative Traits

394 Pages·1996·10.978 MB·English

by  Michael J. Kearsey, Harpal S. Pooni (auth.)

The Genetical Analysis of Quantitative Traits
The Genetical Analysis of
Quantitative Traits
Michael J. Kearsey
and
Harpal S. Pooni
Plant Genetics Group
School of Biological Sciences
The University of Birmingham
Birmingham, UK
SPRINGER-SCIENCE+BUSINESS MEDIA, B.V.
First edition 1996
© Michael J. Kearsey and Harpal S. Pooni 1996
Originally published by Chapman & Hall in 1996
Typeset in 1 l/13pt Times by Academic & Technical Typesetting. Bristol
ISBN 978-0-412-60980-0 ISBN 978-1-4899-4441-2 (eBook)
DOI 10.1007/978-1-4899-4441-2
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Contents
Preface Xl
Dedication xiii
1 Introduction 1
1.1 Qualitative, single gene differences 2
1.2 What are quantitative traits? 4
1.3 Who studies quantitative traits? 6
1.4 Why are quantitative traits important? 8
1.5 What do we need to know about quantitative traits? 10
1.6 Historical development of quantitative genetics 13
Summary 16
References 16
Further reading 17
2 Basic generations - means 18
2.1 Single gene model with additive and dominance
effects 19
2.2 Two gene model with additive and dominance effects 21
2.3 Multiple gene model with additive and dominance
effects 22
2.4 Extension to other generations 25
2.5 Relationships between generation means 27
2.6 Estimating genetical parameters 30
2.7 Interpretation: heterosis and potence ratio 33
Summary 36
References 36
3 Basic generations - variances 38
3.1 Variation in the non-segregating generations 38
3.2 Environmental variation 39
3.3 Estimating environmental variance 41
3.4 Variation in the segregating generations 42
3.5 Estimation of genetical components 45
VI CONTENTS
3.6 Heritability, h2 48
3.7 Relationships between [a] and VA, and [d] and Vo 49
3.8 Dominance ratio 50
3.9 Variances and means 51
3.10 Conclusions from the analysis of basic generations 51
Summary 51
References 52
Further reading 52
4 Selfing and full-sib mating 53
4.1 Selfing: F 3 families 54
4.2 Selfing: F 4 families and beyond 57
4.3 Applications of se1fing theory 61
4.4 Variation between inbred lines derived from an F2 63
4.5 Sib-mating an F2 65
4.6 Sib-mating: regression of offspring onto the parents 70
4.7 Further inbreeding by full-sib mating 72
4.8 Estimation of variance components by weighted
least squares 73
4.9 Unequal family sizes 74
Summary 75
References 75
5 Half-sib mating designs 77
5.1 The North Carolina Experiment I: NCI 77
5.2 The North Carolina Experiment II: NCII 82
5.3 General and specific combining ability 84
5.4 Multiple NCIIs 85
5.5 The North Carolina Experiment III: NCIII 86
5.6 The Triple Test Cross: TTC 92
5.7 The diallel cross 95
5.8 HS designs using inbred lines from an F2 as parents 97
Summary 98
References 99
6 Genes, genetic markers and maps 101
6.1 Genetic markers 102
6.2 Structural and regulatory genes 102
6.3 Mutations in structural genes 103
6.4 Molecular genetic markers 107
6.5 Chiasmata, crossing over and genetic exchange 111
6.6 Chiasma frequency and recombination frequency 117
6.7 Estimation of recombination frequency 120
6.8 Mapping functions 127
6.9 Segregation distortion 130
CONTENTS VII
Summary 131
References 132
Further reading 133
7 Gene counting and location 133
7.1 Reasons for locating QTL 133
7.2 Background to methodology 134
7.3 QTL and marker loci in segregating generations 137
7.4 Handling more than one QTL on a chromosome 151
7.5 Biometrical methods of gene counting 156
7.6 General conclusions on QTL counting and locating 160
Summary 162
References 162
Further reading 164
8 Designer chromosomes 165
8.1 Chromosome engineering 165
8.2 Locating a QTL within the substituted region 168
8.3 Detecting substitution effects 170
8.4 Manipulating whole chromosomes 172
8.5 Chromosome substitution methods in different species 173
8.6 Use of chromosome substitution lines 182
Summary 184
References 184
9 Populations 186
9.1 Problems of studying populations 186
9.2 Solutions 187
9.3 Consequences of definitions of VA and V 189
D
9.4 Studies of human populations 192
9.5 The use of twins 194
9.6 Heritabilities of human traits 197
9.7 Genotype-environment correlation 198
9.8 Diallel crosses 200
9.9 Inbreeding in a population 201
Summary 203
References 204
10 The consequences of linkage 205
10.1 Genetic variation with linkage 205
10.2 Extension to more than two genes 208
10.3 Linkage and random mating an F2 210
10.4 Linkage and inbreeding an F2 212
10.5 Linkage disequilibrium in populations in general 212
10.6 Tests of linkage 213
10.7 Sex linkage 215
VIII CONTENTS
10.8 Basic generations of single crosses 216
10.9 Full-sib families 219
10.10 Half-sib designs 220
Summary 222
References 223
11 Epistasis 224
11.1 Definitions 225
11.2 Relationship with classical epistasis 226
11.3 What is parameter m? 228
11.4 The effects of association and dispersion on epistasis 228
11.5 Deriving the expectations of generation means 231
11.6 Estimates and tests of significance 232
11.7 Determining the type of epistasis for a multigene
case 234
11.8 Epistasis and scaling tests 234
11.9 Higher order interactions 235
11.10 Epistasis and variances 236
Summary 239
References 240
12 Genotype by environment interaction 241
12.1 The nature and causes of G x E 241
12.2 Tests of G x E 244
12.3 Macro-environmental variables 245
12.4 G x E with many lines 251
12.5 Interpretation of G x E analysis 252
12.6 Predictions in the presence of G x E 254
12.7 Conclusions from the genetic analysis of G x E 255
12.8 Selection in heterogeneous environments 257
12.9 Other methods of analysis 259
12.10 G x E - stability versus flexibility 262
Summary 263
References 263
Further reading 265
13 Maternal effects and non-diploids 266
13.1 Maternal effects 266
13.2 Models for generation means 267
13.3 Maternal effects and scaling tests 269
13.4 Generation variances 272
13.5 Maternal effects in FS and HS designs 273
13.6 Haploids and polyploids 274
13.7 Basic generations with haploids 274
13.8 Multiple mating designs with haploids 277
CONTENTS IX
13.9 Basic generations with polyploids 278
13.10 Multiple mating designs with polyploids 282
Summary 283
References 283
14 Correlated and threshold characters 285
14.1 Correlations between characters 285
14.2 Environmental correlations 287
14.3 Genetic correlations 288
14.4 Genetic covariation and design of experiment 291
14.5 Causes of covariation 292
14.6 General conclusions about correlations 294
14.7 Threshold traits 294
14.8 Handling threshold traits 296
14.9 Two or more thresholds 298
Summary 300
References 300
Further reading 301
15 Applications 302
15.1 Choice of breeding objective 302
15.2 The causes of heterosis 304
15.3 Predicting the breeding potential of crosses 308
15.4 Effects of failed assumptions on predictions of
RILsand SCHs 314
15.5 Predicting the response to selection 315
15.6 Correlated response to selection 321
15.7 Indirect selection 322
15.8 Multi-trait selection 323
15.9 Marker-based selection 324
15.10 Genetic architecture of populations 327
15.11 Human populations 329
Summary 332
References 333
Further reading 334
16 Experimental design 335
16.1 Replication 335
16.2 Power of experiments 339
16.3 Power of biometrical experiments based on ANOVA 342
16.4 Reliability of the additive genetic variance 346
16.5 Data analysis 347
Summary 348
References 349
Further reading 349
X CONTENTS
Appendix A Precision of h~ with FS families 350
Appendix B Precision of h~ with HS families 351
Appendix C Statistical tables; F, X2, t 352
Appendix D Normal deviate and intensity of selection (i) 354
Appendix E Area under the normal curve 355
Appendix F The weighted least squares procedure 356
Symbols 360
Problems 364
Answers to problems 370
Index 379