INTRODUCTION TO

GENETIC ANALYSIS M~.JTERNATIONAl TENTH EDITION

Anthony j. F. Griffiths University of British Columbia

Susan R. Wessler University of California, Riverside

Sean B. Carroll Howard Hughes Medica/Institute University of Wisconsin-Madison

john Doebley University of Wisconsin-Madison

II W. H. Freeman and Company • New York

pal grave macmillan

>

Contents • Brief Contents 1n Preface xiii Preface xiii

1 The Genetics Revolution in the g-The Genet-icsRevolution in the Life Sciences 1 life Sciences 1

ART I TRANSMISSION GENETICS I

1.1 The Nature of Biological Information 2

2 Single-Gene Inheritance 27 The molecular structure of DNA 3

3 Independent Assortment of Genes 77 DNA is organized into genes and chromosomes 4

4 Mapping Eukaryote Chromosomes 1.2 How Information Becomes Biological Form 9

by Recombination 115 Transcription 9

5 The Genetics of Bacteria and Translation 10

Their Viruses 159 How does life replicate itself? 17

6 Gene Interaction 199 Change at the DNA level 12

PART II FROM DNA TO PHENOTYPE 1.3 Genetics and Evolution 14

Natural selection 14 7 Large-Scale Chromosomal Changes 235 Constructing evolutionary lineages 15 8 DNA: Structure and Replication 279 1.4 Genetics Has Provided a Powerful New 9 RNA: Transcription and Processing 311 Approach to Biological Research 17 10 Proteins and Their Synthesis 337 Forward genetics 17

11 Gene Isolation and Manipulation 367 Reverse genetics 17

12 Regulation of Gene Expression in Manipulating DNA 18

Bacteria and Their Viruses 407 Detecting specific sequences of DNA, RNA,

13 Regulation of Gene Expression in and protein 18

Eukaryotes 439 1.5 Model Organisms Have Been Crucial in the 14 The Genetic Control of Development 473 Genetics Revolution 21

15 Genomes and Genomics 509 1.6 Genetics Changes Society 23 1.7 Genetics and the Future 24

PART Ill MUTATION, VARIATION, AND EVOLUTION PART I TRANSMISSION GENETICS

16 The Dynamic Genome: Transposable Elements 545 Single-Gene Inheritance 27

17 Mutation, Repair, and Recombination 575 2.1 Single-Gene Inheritance Patterns 29 18 Population Genetics 609 Mendel's pioneering experiments 29

19 The Inheritance of Complex Traits 655 Mendel's law of equal segregation 32

20 Evolution of Genes and Traits 699 2.2 The Chromosomal Basis of Single-Gene Inheritance Patterns 34

A Brief Guide to Model Organisms 731 Single-gene inheritance in diploids 34

Appendix A: Genetic Nomenclature 747 Single-gene inheritance in haploids 39

Appendix 8: Bioinformatics Resources for 2.3 The Molecular Basis of Mendelian

Genetics and Genomics 748 Inheritance Patterns 40

Glossary Structural differences between alleles at the

751 molecular level 40 Answers to Selected Problems 769 Molecular aspects of gene transmission 41

Index 779 Alleles at the molecular level 44

v

vi CONTENTS

2.4 Some Genes Discovered by Observing Mapping Eukaryote Chromosomes Segregation Ratios 46

by Recombination 115 A gene active in the development of flower color 47 4.1 Diagnostics of Linkage 117 A gene for wing development 47 Using recombinant frequency to estimate linkage 7 7 7

A gene for hypha/ branching 48 How crossovers produce recombinants for

Forward genetics 49 linked genes 179

Predicting progeny proportions or parental Linkage symbolism and terminology 779

genotypes by applying the principles of Evidence that crossing over is a breakage-and-single-gene inheritance 49 rejoin!ng process 720

2.5 Sex-Linked Single-Gene Inheritance Evidence that crossing over takes place at the

Patterns 50 four-chromatid stage 7 2 7

Sex chromosomes 50 Multiple crossovers can include more than

Sex-linked patterns of inheritance 57 two chromatids 72 7

X-linked inheritance 57 4.2 Mapping by Recombinant Frequency 122

2.6 Human Pedigree Analysis 54 Map units 722

Autosomal recessive disorders 55 Three-point testcross 726

Autosomal dominant disorders 56 Deducing gene order by inspection 728

Autosomal polymorphisms 58 Interference 729

X-linked recessive disorders 60 Using ratios as diagnostics 7 31

X-linked dominant disorders 62 4.3 Mapping with Molecular Markers 131

Y-linked inheritance 63 Single nucleotide polymorphisms 732

Calculating risks in pedigree analysis 63 Simple sequence length polymorphisms 732

Detecting simple sequence length polymorphism 733

Recombination analysis using molecular Independent Assortment of Genes 77 markers 733

3.1 Mendel's law of Independent Assortment 78 4.4 Centromere Mapping with Linear Tetrads 136

3.2 Working with Independent Assortment 82 4.5 Using the Chi-Square Test for Testing

Predicting progeny ratios 82 linkage Analysis 137

Using the chi-square test on monohybrid and 4.6 Accounting for Unseen Multiple Crossovers 139

dihybrid ratios 85 A mapping function 740

Synthesizing pure lines 87 The Perkins formula 74 7

Hybrid vigor 89 4.7 Using Recombination-Based Maps in

3.3 The Chromosomal Basis of Independent Conjunction with Physical Maps 142

Assortment 90 4.8 The Molecular Mechanism of Crossing Over 144

Independent assortment in diploid organisms 97

Independent assortment in haploid organisms 92 The Genetics of Bacteria and Independent assortment of combinations of Their Viruses 159 autosomal and X-/inked genes 93

Recombination 95 5.1 Working with Microorganisms 161

3.4 Polygenic Inheritance 97 5.2 Bacterial Conjugation 163

3.5 Organelle Genes: Inheritance Independent Discovery of conjugation 763

of the Nucleus 99 Discovery of the fertility factor (F) 765

Patterns of inheritance in organelles 700 Hfr strains 766

Cytoplasmic segregation 701 Mapping of bacterial chromosomes 770

Cytoplasmic mutations in humans 103 F plasmids that carry genomic fragments 774

MtDNA in evolutionary studies 705 R plasm ids 174

CONTENTS VII

5.3 Bacterial Transformation 177 DNA: Structure and Replication 279 The nature of transformation 177

Chromosome mapping using transformation 8.1 DNA: The Genetic Material 280

778

Bacteriophage Genetics 178 Discovery of transformation 280

5.4 Infection of bacteria by phages 178

Hershey-Chase experiment 282

Mapping phage chromosomes by using phage crosses 780 8.2 The DNA Structure 284

DNA structure before Watson and Crick 284 Transduction 182 5.5 The double helix 286 Discovery of transduction 782

Generalized transduction 783 8.3 Semiconservative Replication 289

Specialized transduction 785 Meselson-Stahl experiment 290

Mechanism of specialized transduction 786 The replication fork 297

5.6 Physical Maps and Linkage Maps Compared 187 DNA polymerases 292

8.4 Overview of DNA Replication 294

Gene Interaction 199 8.5 The Replisome: A Remarkable Replication

6.1 Interactions Between the Alleles of a Machine 296

Single Gene: Variations on Dominance 200 Unwinding the double helix 297

Complete dominance and recessiveness 200 Assembling the replisome: replication initiation 298

Incomplete dominance 202 8.6 Replication in Eukaryotic Organisms 299

Codominance 202 The eukaryotic replisome 299

Recessive lethal alleles 204 Eukaryotic origins of replication 300

6.2 Interaction of Genes in Pathways 207 DNA replication and the yeast cell cycle 307

Biosynthetic pathways in Neurospora 207 Replication origins in higher eukaryotes 302

Gene interaction in other types of pathways 209 8.7 Telomeres and Telomerase: Replication

6.3 Inferring Gene Interactions 210 Termination 303

Sorting mutants using the complementation test 270

Analyzing double mutants of random mutations 274 RNA: Transcription and Processing 311

6.4 Penetrance and Expressivity 221 9.1 RNA 313 Early experiments suggest an RNA intermediate 373

PARTH FROM DNA TO PHENOTYPE Properties of RNA 373

Large-Scale Chromosomal Changes 235 Classes of RNA 375

7.1 Changes in Chromosome Number 9.2 Transcription 316

237 Overview: DNA as transcription template 377

Aberrant Euploidy 237

Aneuploidy Stages of transcription 377

245

The concept of gene balance 9.3 Transcription in Eukaryotes 320

249

7.2 Changes in Chromosome Structure 252 Transcription initiation in eukaryotes 322

Deletions 255 Elongation, termination, and pre-mRNA processing in eukaryotes 323

Duplications 258 9.4 lntron Removal and Exon Splicing 326 Inversions 260 Small nuclear RNAs (snRNAs): The mechanism Reciprocal translocations 263 of exon splicing 326

Robertsonian translocations 265 Self-splicing introns and the RNA world 328

Applications of inversions and translocations 266 9.5 Small Functional RNAs that Regulate and

Rearrangements and cancer 267 Protect the Eukaryotic Genome 328

Identifying chromosome mutations by genomics 268 miRNAs are important regulators of gene expression 328

7.3 Overall Incidence of Human Chromosome siRNAs ensure genome stability 330

Mutations 268 Similar mechanisms generate siRNA and miRNA 333

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viii CONTENTS

.:ar-rroteins and Their Synthesis 337 11.6 Genetic Engineering 395

Genetic engineering in Saccharomyces cerevisiae 396 10.1 Protein Structure 339

Genetic engineering in plants 397 10.2 The Genetic Code 342

Overlapping versus nonoverlapping codes Genetic engineering in animals 399

342

Number of letters in the codon 343

Use of suppressors to demonstrate a Regulation of Gene Expression in

triplet code 343 Bacteria and Their Viruses 407 Degeneracy of the genetic code 345 12.1 Gene Regulation 409 Cracking the code 345 The basics of prokaryotic transcriptional

Stop codons 346 regulation: genetic switches 410

10.3 tRNA: The Adapter 347 A first look at the lac regulatory circuit 411

Codon translation by tRNA 347 12.2 Discovery of the lac System:

Degeneracy revisited 349 Negative Control 414

10.4 Ribosomes 350 Genes controlled together 414

Ribosome features 352 Genetic evidence for the operator and repressor 415

Translation initiation, elongation, and Genetic evidence for allostery 417

termination 353 Genetic analysis of the lac promoter 418

Nonsense suppressor mutations 356 Molecular characterization of the Lac

10.5 The Proteome 357 repressor and the lac operator 418

Alternative splicing generates protein isoforms 357 Polar mutations 419

Posttranslational events 358 12.3 Catabolite Repression of the lac Operon:

Positive Control 420 The basics of lac catabolite repression: choosing

Gene Isolation and Manipulation 367 the best sugar to metabolize 420

11.1 Overview: Isolating and Amplifying The structure of DNA target sites 421

Specific DNA Fragments 368 A summary of the lac operon 422

11.2 Generating Recombinant DNA Molecules 370 12.4 Dual Positive and Negative Control: Genomic DNA can be cut up before cloning 370 The Arabinose Operon 423 The polymerase chain reaction amplifies 12.5 Metabolic Pathways and Additional Levels selected regions of DNA in vitro 371 of Regulation: Attenuation 424 DNA copies of mRNA can be synthesized 373 12.6 Bacteriophage Life Cycles: More Regulators, Attaching donor and vector DNA 374 Complex Operons 428

Amplification of donor DNA inside a Molecular anatomy of the genetic switch 431

bacterial cell 377 Sequence-specific binding of regulatory

Making genomic and eDNA libraries 380 proteins to DNA 432

11.3 Finding a Specific Clone of Interest 381 12.7 Alternative Sigma Factors Regulate Large

Finding specific clones by using probes 381 Sets of Genes 433

Finding specific clones by functional complementation 384 Regulation of Gene Expression in Southern- and Northern-blot analysis of DNA 385 Eukaryotes 439

11.4 Determining the Base Sequence of a 13.1 Transcriptional Regulation in Eukaryotes: DNA Segment 387 An Overview 440

11.5 Aligning Genetic and Physical Maps to 13.2 Lessons from Yeast: The GAL System 444 Isolate Specific Genes 390 Gal4 regulates multiple genes through upstream Using positional cloning to identify a activation sequences 445 human-disease gene 391 The Gal4 protein has separable DNA-binding Using fine-mapping to identify genes 393 and activation domains 446

CONTENTS ix

Gal4 activity is physiologically regulated 446 14.3 Defining the Entire Toolkit 485

Gal4 functions in most eukaryotes 447 The anteroposterior and dorsoventral axes 486

Activators recruit the transcriptional machinery 447 Expression of toolkit genes 487

The control of yeast mating type: 14.4 Spatial Regulation of Gene Expression in combinatorial interactions 448 Development 490

13.3 Dynamic Chromatin 450 Maternal gradients and gene activation 490

Chromatin-remodeling proteins and gene Drawing stripes: integration of gap-protein inputs 492 activation 452 Making segments different: integration of Histones and chromatin remodeling 452 Hox inputs 495

The inheritance of histone modifications and 14.5 Posttranscriptional Regulation of Gene chromatin structure 454 Expression in Development 497 DNA methylation: another heritable mark that RNA splicing and sex determination in influences chromatin structure 455 Drosophila 497

13.4 Short-Term Activation of Genes in a Regulation of mRNA translation and eel/lineage Chromatin Environment 456 in C. elegans 499

The ~-interferon enhanceosome 457 Translational control in the early embryo 499

Enhancer-blocking insulators 458 miRNA control of developmental timing in

13.5 Long-Term Inactivation of Genes in a C. elegans and other species 502

Chromatin Environment 459 14.6 From Flies to Fingers, Feathers, and Floor Plates:

Mating-type switching and gene silencing 459 The Many Roles of Individual Toolkit Genes 503

Heterochromatin and euchromatin compared 461 14.7 Development and Disease 504

Position-effect variegation in Drosophila reveals Polydactyly 504

genomic neighborhoods 467 Holoprosencephaly 505

Genetic analysis of PEV reveals proteins Cancer as a developmental disease 505 necessary for heterochromatin formation 463

13.6 Gender-Specific Silencing of Genes and Genomes and Genomics 509 Whole Chromosomes 465

Genomic imprinting explains some unusual 15.1 The Genomics Revolution 511

patterns of inheritance 465 15.2 Obtaining the Sequence of a Genome 512

But what about Dolly and other cloned Turning sequence reads into an assembled

mammals? 467 sequence 572

Silencing an entire chromosome: Whole-genome sequencing 574

X-chromosome inactivation 467 Traditional WGS 574

13.7 Post-Transcriptional Gene Repression Next-generation whole-genome shotgun by miRNAs 468 sequencing 575

Whole-genome-sequence assembly 577

The Genetic Control of Toward the personalized genome 579

Development 473 15.3 Bioinformatics: Meaning from Genomic

14.1 The Genetic Approach to Development 474 Sequence 519

14.2 The Genetic Toolkit for Drosophila The nature of the information content of DNA 520

Development 476 Deducing the protein-encoding genes from

Classification of genes by developmental genomic sequence 520

function 411 15.4 The Structure of the Human Genome 524

Homeotic genes and segmental identity 478 15.5 Comparative Genomics 527

Organization and expression of Hox genes 479 Phylogenetic inference 527

The homeobox 481 Of mice and humans 529

Clusters of Hox genes control development in Comparative genomics of chimpanzees and

most animals 482 humans 531

X CONTENTS

Comparative genomics of humans 53 7 17.2 The Molecular Basis of Spontaneous

Conserved and ultraconserved noncoding Mutations 580 elements 532 Luria and Delbruck fluctuation test 580

Comparative genomics of nonpathogenic and Mechanisms of spontaneous mutations 582 pathogenic E. coli 533

Spontaneous mutations in humans: 15.6 Functional Genomics and Reverse trinucleotide-repeat diseases 584

Genetics 534 17.3 The Molecular Basis of Induced Mutations 586 Ome, sweet ome 535 Mechanisms of mutagenesis 586 Reverse genetics 538 The Ames test: evaluating mutagens in our

environment 589

PART Ill MUTATION, VARIATION, 17.4 Biological Repair Mechanisms 591 AND EVOLUTION Direct reversal of damaged DNA 597

l[flhe Dynamic Genome: Base-excision repair 597

Transposable Elements 545 Nucleotide-excision repair 593

Postreplication repair: mismatch repair 596 16.1 Discovery of Transposable Elements

Error-prone repair: translesion DNA synthesis 591 in Maize 546 McClintock's experiments: the Ds element 546

Repair of double-strand breaks 599

Autonomous and nonautomous elements 549 The involvement of DSB repair in meiotic recombination 607

Transposable elements: only in maize? 550 17.5 Cancer: An Important Phenotypic

16.2 Transposable Elements in Prokaryotes 550 Consequence of Mutation 602 Bacterial insertion sequences 557 How cancer cells differ from normal cells 602 Prokaryote transposons 552 Mutations in cancer cells 603 Mechanism of transposition 552

16.3 Transposable Elements in Eukaryotes 555 Population Genetics 609 Class 7: retrotransposons 555 18.1 Detecting Genetic Variation 610 Class 2: DNA transposons 559 Single nucleotide polymorphisms (SNPs) 6 7 7 Utility of DNA transposons for gene discovery 562 Microsatellites 672

16.4 The Dynamic Genome: More Transposable Haplotypes 672 Elements Than Ever Imagined 564

Other sources and forms of variation 674 Large genomes are largely transposable elements 564

The HapMap project 615 Transposable elements in the human genome 565

The Gene-Pool Concept and the 18.2 The grasses: LTR retrotransposons thrive in Hardy-Weinberg law 616 large genomes 561

18.3 Mating Systems 620 Safe havens 567

Assortative mating 621 16.5 Epigenetic Regulation of Transposable

Isolation by distance 621 Elements by the Host 569 Inbreeding 622

Mutation, Repair, and The inbreeding coefficient 623

Recombination 575 Population size and inbreeding 625

The Phenotypic Consequences of 18.4 Genetic Variation and Its Measurement 627 17.1

The Modulation of Genetic Variation DNA Mutations 576 18.5 630

Types of point mutation 516 New alleles enter the population: mutation and migration 630

The molecular consequences of point Recombination and linkage disequilibrium 631 mutations in a coding region 578

The molecular consequences of point Gene drift and population size 633

mutations in a noncoding region 579 Selection 638

> CONTENTS xi

Forms of selection 641 Evolution of Genes and Traits 699 Balance between mutation and drift 644

Evolution by Natural Selection 20.1 702 Balance between mutation and selection 645

18.6 Biological and Social Applications 646 20.2 Molecular Evolution: The Neutral Theory 704

Conservation genetics 646 The development of the neutral theory 704

Calculating disease risks 647 The rate of neutral substitutions 706

DNA forensics 648

Googling your DNA mates 649 The signature of purifying selection on DNA 706

The Inheritance of Complex Traits 655 20.3 Natural Selection in Action: An Exemplary Case 707

19.1 Measuring Quantitative Variation 657 The selective advantage of HbS 709

Types of traits and inheritance 657 The molecular origins of HbS 710

The mean 658 20.4 Cumulative Selection and the Multistep The variance 659 Paths to Functional Change 712

The normal distribution 660 Multistep pathways in evolution 712

19.2 A Simple Genetic Model for Quantitative The signature of positive selection on DNA

Variation 661 sequences 716

Genetic and environmental deviations 661 20.5 Morphological Evolution 716

Genetic and environmental variances 663 Adaptive changes in a pigment-regulating

Correlation between variables 665 protein 711

19.3 Broad-Sense Heritability: Nature Versus Gene inactivation 7 18

Nurture 667 Regulatory-sequence evolution 719

Measuring heritability in humans using twin studies 668 Loss of characters through regulatory-sequence

19.4 Narrow-Sense Heritability: Predicting evolution 72 1

Phenotypes 671 Regulatory evolution in humans 722

Gene action and the transmission of genetic variation 671 20.6 The Origin of New Genes and Protein

The additive and dominance effects 672 Functions 724

A model with additivity and dominance 674 Expanding gene number 724

Narrow-sense heritability 676 The fate of duplicated genes 725

Predicting offspring phenotypes 679

Selection on complex traits 680

19.5 Mapping QTL in Populations with Known A Brief Guide to Model Organisms 731

Pedigrees 682

The basic method 683 Appendix A: Genetic Nomenclature 747

From QTL to gene 687 Appendix 8: Bioinformatics Resources

19.6 Association Mapping in Random-Mating for Genetics and Genomics 748

Populations 689 Glossary 751

The basic method 690 Answers to Selected Problems 769

GWA, genes, disease, and heritability 692 Index 779