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SEV ENTH E D ITI O N
Genetics
From Genes to Genomes
Michael L. Goldberg
CORNELL UNIVERSITY
Janice A. Fischer
THE UNIVERSITY OF TEXAS AT AUSTIN
Leroy Hood
THE INSTITUTE FOR SYSTEMS BIOLOGY
Leland H. Hartwell
FRED HUTCHISON CANCER CENTER
GENETICS
Published by McGraw Hill LLC, 1325 Avenue of the Americas, New York, NY 10121. Copyright ©2021
by McGraw Hill LLC. All rights reserved. Printed in the United States of America. No part of this publication
may be reproduced or distributed in any form or by any means, or stored in a database or retrieval system,
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United States.
1 2 3 4 5 6 7 8 9 LWI 24 23 22 21 20
ISBN 978-1-260-57582-8
MHID 1-260-57582-9
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mheducation.com/highered
About the Authors
Dr. Janice Fischer is a Professor at The University of Texas at Austin, where she
is an award-winning teacher of genetics and Director of the Biology Instructional
Office. She received her Ph.D. in biochemistry and molecular biology from Harvard
University, and did postdoctoral research at The University of California at Berkeley,
Harvard University, and The Whitehead Institute at MIT. In her research, Dr. Fischer
used Drosophila first to study how tissue-specific transcription works, and then to
examine the roles of ubiquitin and endocytosis in cell signaling during development.
©Janice Fischer
Dr. Lee Hood received an M.D. from The Johns Hopkins University School of
Medicine and a Ph.D. in biochemistry from the California Institute of Technology.
His current research interests include cancer biology, the development of biological
instrumentation (for example, the protein sequencer and the automated fluorescent
DNA sequencer), genomics, systems biology and systems medicine. His early research
played a key role in unraveling the mysteries of antibody diversity. More recently he
has pioneered systems approaches to biology and medicine and has pioneered scien-
tific (quantitative) wellness and the analyses of individuals with genomics/phenomics.
©Lee Hood
Dr. Hood has taught molecular evolution, immunology, molecular biology,
genomics, biochemistry, and systems biology and has coauthored textbooks in
biochemistry, molecular biology, immunology, and systems biology and medicine, as
well as The Code of Codes—a monograph about the Human Genome Project. He was
one of the first advocates for the Human Genome Project and directed one of the
federal genome centers that sequenced the human genome. Dr. Hood is currently a
Professor and cofounder of the cross-disciplinary Institute for Systems Biology in
Seattle, Washington.
Dr. Hood is also Senior Vice President and Chief Science Officer of Providence
St. Joseph Health. Dr. Hood has received a variety of awards, including the Albert
Lasker Award for Medical Research (1987), the Distinguished Service Award from
the National Association of Teachers (1998), and the Lemelson/MIT Award for
Invention (2003). He is the 2002 recipient of the Kyoto Prize in Advanced
Biotechnology—an award recognizing his pioneering work in developing the protein
and DNA synthesizers and sequencers that provided the technical foundation of mod-
ern biology. He received the Medal of Science from President Obama in 2011. He is
deeply involved in K–12 science education. His hobbies include running, exercise,
and reading.
iii
Brief Contents
Preface ix
chapter 6
chapter 4 DNA Structure, Replication, and
Sex Chromosomes 91 Recombination 165
4.1 Sex Chromosomes and Sex 6.1 Experimental Evidence for DNA as the Genetic
Determination 92 Material 166
v
vi Contents
chapter 10
chapter 7
Digital Analysis of DNA 303
Mutation 203
10.1 Fragmenting DNA 304
7.1 Mutations: Primary Tools of Genetic 10.2 Cloning DNA Fragments 309
Analysis 204
10.3 Sequencing DNA 313
7.2 Molecular Mechanisms that Alter DNA
10.4 Sequencing Genomes 317
Sequence 209
■ Tools of Genetics: Serendipity in Science: The
7.3 DNA Repair Mechanisms 218
Discovery of Restriction Enzymes 306
■ Fast Forward: Trinucleotide Repeat
Diseases 216
chapter 11
chapter 8 Genome Annotation 327
Using Mutations to Study Genes 229 11.1 Finding the Genes in Genomes 328
11.2 Genome Architecture and Evolution 333
8.1 What Mutations Tell Us About Gene
Structure 230 11.3 Bioinformatics: Information Technology and
Genomes 341
8.2 What Mutations Tell Us
About Gene Function 238 11.4 A Comprehensive Example: The Hemoglobin
Genes 342
8.3 A Comprehensive Example: Mutations that
Affect Vision 245
chapter 12
chapter 9 Analyzing Genomic Variation 352
Gene Expression: The Flow of 12.1 Variation Among Genomes 353
Information from DNA to RNA 12.2 Genotyping a Known Disease‑Causing
to Protein 257 Mutation 357
9.1 The Genetic Code 258 12.3 Sampling DNA Variation in
a Genome 362
9.2 Transcription: From DNA
to RNA 267 12.4 Positional Cloning 368
9.3 Translation: From mRNA to Protein 275 12.5 The Era of Whole-Genome
Sequencing 374
9.4 Differences in Gene Expression
■ Fast Forward: Genetic Genealogy 366
Between Prokaryotes and
Eukaryotes 283 ■ Tools of Genetics: The Lod Score
9.5 The Effects of Mutations on Gene Expression Statistic 372
and Function 286
■ Genetics and Society: HIV and Reverse
Transcription 271
Contents vii
chapter 17
(left): Texas A&M University/FEMA/HandoutGetty Images; Organellar Inheritance 511
(right): ©Alpha/ZUMAPRESS/Newscom
17.1 Mitochondria and Their Genomes 512
chapter 13 17.2 Chloroplasts and Their Genomes 515
The Eukaryotic Chromosome 395 17.3 The Relationship Between Organellar and
Nuclear Genomes 517
13.1 Chromosomal DNA and Proteins 396
17.4 Non-Mendelian Inheritance of Mitochondria
13.2 Chromosome Structure and Compaction 397 and Chloroplasts 519
13.3 Chromosomal Packaging and Gene 17.5 Mutant Mitochondria and Human Disease 524
Expression 402 ■ Fast Forward: Mitochondrial Eve 524
13.4 Replication of Eukaryotic Chromosomes 408
13.5 Chromosome Segregation 411
13.6 Artificial Chromosomes 414 PART V
How Genes Are
chapter 14 Regulated 535
Chromosomal Rearrangements 425
14.1 Rearrangements of Chromosomal DNA 426
14.2 The Effects of Rearrangements 430 ©Courtesy of Mattias Ormsestad
and Eric Roettinger/Kahi Kai
14.3 Transposable Genetic Elements 440
14.4 Genome Restructuring and Evolution 447 chapter 18
■ Fast Forward: Programmed DNA Rearrangements Gene Regulation in Prokaryotes 535
and the Immune System 428 18.1 The Elements of Prokaryotic Gene
Expression 536
chapter 15 18.2 Regulation of Transcription Initiation via DNA-
Binding Proteins 537
Ploidy 460
18.3 RNA-Mediated Mechanisms of Gene
15.1 Aberrations in Chromosome Number: Regulation 549
Aneuploidy 461 18.4 Discovering and Manipulating Bacterial Gene
15.2 Variation in Number of Chromosome Sets: Regulatory Mechanisms 553
Euploidy 464 18.5 A Comprehensive Example: Control of
15.3 Whole-Genome Duplication as a Driver of Bioluminescence by Quorum Sensing 558
Evolution 470
chapter 19
chapter 16 Gene Regulation in Eukaryotes 570
Bacterial Genetics 478 19.1 Overview of Eukaryotic Gene Regulation 571
16.1 The Enormous Diversity of Bacteria 479 19.2 Control of Transcription Initiation Through
Enhancers 571
16.2 Bacterial Genomes 480
19.3 Regulation After Transcription 582
16.3 Bacteria as Experimental Organisms 485
19.4 A Comprehensive Example: Sex Determination
16.4 Gene Transfer in Bacteria 487
in Drosophila 587
16.5 Using Genetics to Study Bacterial Life 499
■ Tools of Genetics: The Gal4/UASG Binary Gene
Expression System 578
viii Contents
chapter 20 chapter 23
Epigenetics 599 The Genetics of Cancer 683
20.1 Genomic Imprinting 600 23.1 Characteristics of Cancer Cells 684
20.2 Inheritance of Programmed Gene Repression 23.2 The Genetic Basis of Cancers 686
Through Cell Division 604 23.3 How Cell Division Is Normally Controlled 689
20.3 Transgenerational Epigenetic 23.4 How Mutations Cause Cancer 695
Inheritance 607 23.5 Personalized Cancer Treatment 701
20.4 A Comprehensive Example: Epigenetic ■ Tools of Genetics: Analysis of Cell-Cycle
Inheritance in Mice 609 Mutants in Yeast 693
chapter 21 chapter 24
Manipulating the Genomes of Variation and Selection in Populations 714
Eukaryotes 619
24.1 The Hardy-Weinberg Law: Predicting
21.1 Creating Transgenic Organisms 620 Genetic Variation in “Ideal” Populations 715
21.2 Uses of Transgenic Organisms 623 24.2 What Causes Allele Frequencies to
21.3 Targeted Mutagenesis 627 Change in Real Populations? 721
21.4 Human Gene Therapy 634 24.3 Ancestry and the Evolution of Modern
■ Tools of Genetics: Cloning by Somatic Cell Humans 731
Nuclear Transfer 625
■ Tools of Genetics: How Bacteria Use CRISPR/
chapter 25
Cas9 to Vaccinate Themselves Against
Viruses 633 Genetic Analysis of Complex Traits 747
■ Genetics and Society: Should We Alter Human 25.1 Heritability: Genetic Versus Environmental
Germ-Line Genomes? 638 Influences on Complex Traits 748
25.2 Mapping Quantitative Trait Loci (QTLs) 757
■ Tools of Genetics: The Chi-Square Test for
chapter 22
Independence 764
Genetic Analysis of Development 648
22.1 Model Organisms: Prototypes for Guidelines for Gene Nomenclature A-1
Developmental Genetics 649 Brief Answer Section B-1
22.2 Mutagenesis Screens 650 Glossary G-1
22.3 Determining Where and When Genes Index I-1
Act 656
22.4 Ordering Genes in a Pathway 659
22.5 A Comprehensive Example: Body Plan
Development in Drosophila 661
Preface
Last A-Head ix
A Note from the Authors ∙∙ Human genetics: how genes contribute to health and
diseases, including cancer.
The science of genetics is less than 150 years old, but its ∙∙ The unity of life-forms: the synthesis of information
accomplishments within that short time have been aston- from many different organisms into coherent models.
ishing. Gregor Mendel first described genes as abstract ∙∙ Molecular evolution: the molecular mechanisms by
units of inheritance in 1865; his work was ignored and which biological systems, whole organisms, and
then rediscovered in 1900. Thomas Hunt Morgan and his populations have evolved and diverged.
students provided experimental verification of the idea
that genes reside within chromosomes during the years The strength of this integrated approach is that students
1910–1920. By 1944, Oswald Avery and his coworkers who complete the book will have a strong command of
had established that genes are made of DNA. James genetics as it is practiced today by both academic and cor-
Watson and Francis Crick published their pathbreaking porate researchers. These scientists are rapidly changing
structure of DNA in 1953. Remarkably, less than 50 years our understanding of living organisms, including ourselves.
later (in 2001), an international consortium of investiga- Ultimately, this vital research may create the ability to re-
tors deciphered the sequence of the 3 billion nucleotides in place or correct detrimental genes—those “inborn errors of
the h uman genome. Twentieth-century genetics made it metabolism,” as researcher Archibald Garrod called them
possible to identify individual genes and to understand a in 1923, as well as the later genetic alterations that lead to
great deal about their functions. the many forms of cancer.
Today, scientists are able to access the enormous
amounts of genetic data generated by the sequencing of
many organisms’ genomes. Analysis of these data will re- The Genetic Way of Thinking
sult in a deeper understanding of the complex molecular Modern genetics is a molecular-level science, but an under-
interactions within and among vast networks of genes, pro- standing of its origins and the discovery of its principles is
teins, and other molecules that help bring organisms to life. a necessary context. To encourage a genetic way of think-
Finding new methods and tools for analyzing these data will ing, we begin the book by reviewing Mendel’s principles
be a significant part of genetics in the twenty-first century. and the chromosomal basis of inheritance. From the outset,
Our seventh edition of Genetics: From Genes to Genomes however, we aim to integrate organism-level genetics with
emphasizes both the core concepts of genetics and the fundamental molecular mechanisms.
cutting-edge discoveries, modern tools, and analytical meth- Chapter 1 ties Mendel’s studies of pea trait inheritance
ods that will keep the science of genetics moving forward. to the actions of enzymes that determine whether a pea is
The authors of the seventh edition have worked to- round or wrinkled, yellow or green, etc. In the same chapter,
gether in revising every chapter in an effort not only to we point to the relatedness of the patterns of heredity in all
provide the most up-to-date information, but also to pro- organisms. Chapters 2 through 5 cover extensions to
vide continuity and the clearest possible explanations of Mendel, chromosomes and inheritance, and the fundamen-
difficult concepts in one voice. tals of gene linkage and mapping. Starting in Chapter 6, we
focus on the physical characteristics of DNA, on mutations,
Our Focus—An Integrated Approach and on how DNA encodes, copies, and transmits biological
information.
Genetics: From Genes to Genomes represents a new approach
Beginning in Chapter 10, we move into the digital rev-
to an undergraduate course in genetics. It reflects the way
olution in DNA analysis with a look at modern genetic
we, the authors, currently view the molecular basis of life.
techniques, including gene cloning, PCR, microarrays, and
We integrate:
high-throughput genome sequencing. We explore how
∙∙ Formal genetics: the rules by which genes are bioinformatics, an emergent analytical tool, can aid in dis-
transmitted. covery of genome features. This section concludes in
∙∙ Molecular genetics: the structure of DNA and how it Chapter 12 with case studies leading to the discovery of
directs the structure of proteins. human disease genes.
∙∙ Digital analysis and genomics: recent technologies The understanding of molecular and computer-based
that allow a comprehensive analysis of the entire gene techniques carries into our discussion of chromosome
set and its expression in an organism. specifics in Chapters 13 through 17, and also informs our
ix
x Preface
analysis of gene regulation in Chapters 18 through 20. Figure illustrations break down complex processes
Chapter 21 describes the most recent technology that sci- into step-by-step illustrations that lead to greater
entists can use to manipulate genomes at will—for research student understanding. All illustrations are rendered
and practical purposes including gene therapy. Chapter 22 with a consistent color theme—for example, all
explains the use of genetic tools at the molecular level to presentations of phosphate groups are the same color,
uncover the complex interactions of eukaryotic develop- as are all presentations of mRNA.
ment. In Chapter 23, we explain how our understanding of ∙∙ Accessibility Our intention is to bring cutting-edge
genetics and the development of molecular genetic tech- content to the student level. A number of more
nologies is enabling us to comprehend cancer and in some complex illustrations are revised and segmented to
cases to cure it. help the student follow the process. Legends have been
Chapters 24 and 25 cover population genetics, with a streamlined to highlight only the most important ideas,
view of how molecular tools have provided information on and throughout the book, topics and examples have
species relatedness and on genome changes at the molecular been chosen to focus on the most crucial information.
level over time. In addition, we explain how bioinformatics ∙∙ Problem Solving Developing strong problem-solving
can be combined with population genetics to trace human skills is vital for every genetics student. The authors
ancestry and to identify the genes that control complex traits. have carefully created problem sets at the end of each
Throughout our book, we present the scientific reason- chapter that allow students to improve their problem-
ing of some of the ingenious researchers of the field—from solving abilities, often in the context of current
Mendel, to Watson and Crick, to the collaborators on the discoveries in genetics.
Human Genome Project. We hope student readers will see ∙∙ Solved Problems These cover topical material with
that genetics is not simply a set of data and facts, but also a complete answers that provide insight into the step-
human endeavor that relies on contributions from excep- by-step process of problem solving.
tional individuals. ∙∙ Problems More than 700 questions involving a variety
of levels of difficulty develop excellent problem-
solving skills. The problems are organized by chapter
Student-Friendly Features section and in order of increasing difficulty within
each section for ease of use by instructors and
As digital components of the text become more and more
students. The companion online Study Guide and
crucial, we are very excited that Janice Fischer, a textbook
Solutions Manual, completely revised for the seventh
author, will continue in the seventh edition in a dual role as
edition by Michael Goldberg and Janice Fischer,
Digital Editor! Janice will ensure the important consistency
provides detailed analysis of strategies to solve all of
between text and digital.
the end-of-chapter problems. Many of the more
We have taken great pains to help the student make the
difficult problems could be adapted easily for use
leap to a deeper understanding of genetics. Numerous
as case studies in the classroom. Solved Problems 223
features of this book were developed with that goal in mind.
∙∙ One Voice
Genetics Genes to Genomes S O LV E D P R O B L E M S
has a friendly, engaging
reading style that helps Solved Problem I Depending on its tautomeric state, 5-BU can some-
students master the concepts The DNA sequence of one strand of a gene from three in- times behave like thymine and sometimes like cyto-
throughout this book. The dependently isolated mutants is given here (5′ ends are at sine. 5-BU is a two-way mutagen. A reversion (C⋮G
left). Using this information, what is the sequence of the → T:A) can occur if 5-BU is incorporated into DNA
writing style provides the wild-type gene in this region? in the C-like state (the DNA will have a 5-BU⋮G)
student with the focus and mutant 1 ACCGTAATCGACTGGTAAACTTTGCGCG
base pair, and then 5-BU acts like a T during the next
round of replication, resulting in a 5-BU:A base pair.
continuity required to make mutant 2 ACCGTAGTCGACCGGTAAACTTTGCGCG Following the next round of DNA replication, the
the book successful in the mutant 3 ACCGTAGTCGACTGGTTAACTTTGCGCG result will be T:A.
classroom. b. Hydroxylamine changes C to hydroxylated C (C* in
Answer Fig. 7.13b), and C* can pair only with A. As shown in
∙∙ Visualizing Fig. 7.13b, hydroxylamine can cause a C⋮G →T:A
Each independently derived mutation will be caused by a
Genetics The highly different single base change. When you find a base that dif- substitution. Because it cannot modify a T:A base
specialized art program fers in only one of the three sequences, that different base pair, hydroxylamine is a one-way mutagen.
is the mutation. Determine the wild-type sequence by find- c. Ethylmethane sulfonate (EMS) modifies (ethylates)
developed for this book ing the base that is present at that position in the other two G within a DNA molecule. Figure 7.13b shows that if
integrates photos and line art sequences (underlined in the following). The wild-type ethylated G (G*) pairs with T during replication, a
sequence is therefore: G⋮C → A:T substitution results in the next round of
in a manner that provides replication. Because it cannot modify an A:T base
the most engaging visual 5′ ACCGTAGTCGACTGGTAAACTTTGCGCG 3′
pair, EMS is a one-way mutagen.
presentation of genetics Solved Problem II
d. Nitrous acid changes C to U and also A to hypoxan-
thine (H), a base that pairs C. Figure 7.13b shows
available. Our Feature So-called two-way mutagens can induce both a particular how these nitrous acid-induced alterations can cause
mutation and (when added subsequently to cells whose (after DNA replication) both C⋮G → T:A and
chromosomes carry this mutation) a true reversion of the T:A → C⋮G substitutions; either of these changes
mutation that restores the original DNA sequence. In con- can revert the other. Thus, nitrous acid is a two-way
trast, one-way mutagens can induce mutations but not exact mutagen.
reversions of these mutations. Based on Fig. 7.13, which of e. Proflavin can add any single base pair or delete any
Changes in the Seventh Edition:
A Chapter-by-Chapter Summary
The seventh edition has been revised and modernized sig- Chapter 11 Genome Annotation
nificantly as compared with the sixth edition. We scruti- ∙∙ Clarified overview of DNA sequence organization of
nized the entire text and clarified the language wherever chromosomes.
possible. In total, we created more than 30 new figures and Chapter 12 Analyzing Genomic Variation
tables, and revised many more in addition. We also wrote ∙∙ New coverage of genetic genealogy.
more than 100 new end-of-chapter problems, and revised ∙∙ New explanation of Illumina high-throughput DNA
many other problems for clarity. sequencing technology.
Based on user feedback, we eliminated Chapter 1 in the sev- Chapter 13 The Eukaryotic Chromosome
enth edition, which allowed space to split three long chapters ∙∙ New coverage of the role of condensins in shaping
in the sixth edition into two separate chapters, and to create a chromosomes.
new chapter. Chapter 4 in the sixth edition became Chapter 3 ∙∙ Updated information about the mechanism of
(Chromosomes and Inheritance) and Chapter 4 (Sex X-chromosome inactivation.
Chromosomes) in the seventh edition. Chapter 7 in the sixth ∙∙ Updated coverage of yeast synthetic chromosomes.
edition became Chapter 7 (Mutation) and Chapter 8 (Using
Chapter 19 Gene Regulation in Eukaryotes
Mutations to Study Genes) in the seventh edition. Chapter 13
∙∙ New coverage of topologically associating domains
in the sixth edition became Chapter 14 (Chromosomal
(TADs) and chromatin conformation capture
Rearrangements) and Chapter 15 (Ploidy) in the seventh edi-
technology.
tion. And a new Chapter 20 (Epigenetics) contains expanded
∙∙ Epigenetics section moved in revised form into new
coverage of this fast-moving field. The entire Solutions
Chapter 20.
Manual and Study Guide was corrected and revised for clarity.
Chapter 20 Epigenetics (New!)
Along with the numerous text changes, Janice Fischer spent ∙∙ Genomic imprinting in mammals.
a great deal of time helping to update the test bank and ques- ∙∙ Transmission of programmed gene repression through
tion bank content to align with the new edition. Author cell division.
Janice Fischer recorded video tutorials for the sixth edition ∙∙ Transgenerational epigenetic inheritance.
that will be included with the seventh edition. These tutori- ∙∙ Intergenerational inheritance of acquired traits in
als explain topics that are often difficult to understand. mammals.
Every chapter of the seventh edition was improved signifi- Chapter 21 Manipulating the Genomes of Eukaryotes
cantly from the sixth edition. The most important changes in ∙∙ Updated coverage of CRISPR/Cas9 technology.
the seventh edition are summarized below: ∙∙ Updated material on transgenic animals for human
drug production and consumption.
Chapter 4 Sex Chromosomes ∙∙ Updated coverage of human gene therapy.
∙∙ New section Human Intersexuality.
Chapter 23 The Genetics of Cancer
Chapter 5 Linkage, Recombination, and Gene Mapping ∙∙ Coverage of new cancer therapies that strengthen the
∙∙ Clarified analysis of three-point testcrosses. body’s immune surveillance (CAR-T cell therapy and
Chapter 9 Gene Expression PD-1/PD-L1 antibody treatment).
∙∙ Updated Wobble rules. Chapter 25 Genetic Analysis of Complex Traits
Chapter 10 Digital Analysis of DNA ∙∙ Clarified and updated material on human GWAS
∙∙ Clarified explanation of whole-genome shotgun analysis.
sequencing.
xi
of20
Guided Tour
chapterMammalian Cells Retain Memories
Inactivated X Chromosomes
ze
In Chapters 4 and 13, you saw that when early embryos of
t is
Epigenetics
mammalian females contain approximately 500–1000
cells, a random one of the two X chromosomes becomes
ere. facultative heterochromatin—a Barr body—in each cell.
With the exception of a few genes (mostly in the pseudoau-
e
tosomal regions), the entire Barr body chromosome is
en Integrating
silenced. Genetic Concepts
Genetics:You will From recall
Genesthat totheGenomes
long noncoding takes anRNA (lncRNA)
integrated approach in its presentation of genetics, thereby giving students a
Courtesy Randy L. Jirtle, Ph.D. Originally published in B. Weinhold,
Xist is command
strong key to Barr body formation.
of genetics The Xist
as it is practiced lncRNA
today
“Color byby is Linkedand
Soy:academic
Genistein corporate
to Epigenetic Effects,” researchers.
Environ Health Principles are related through-
transcribed
out the text from the one essays,
in examples, X chromosome that Perspect.
case histories, will
andbecome
2006 Apr., 114(4): A240. Environews, Science Selections
connections sections toVYmake sure students fully understand the rela-
the Barr body.
tionships between Thetopics.
Xist lncRNA binds the X chromosome Despite having the same agouti genotype (A a), the coat
colors of these mice differ. In the yellow (mutant) mouse, the AVY
from which it was transcribed, spreads along its length,
epiallele and
is unmethylated, while in the gray (normal) mouse, AVY
recruits histone modifying enzymes to the chromatin (re-
is hypermethylated.
call Fig. 13.16). Consequently, the chromatin of the inac-
tiveChapter
X is covered Outline
with histone marks such as H3K9me c h a pt e r o u t l i n e
and
H3K27me
Every chapter thatopens
closewith chromatin and recruit DNMTs
a brief outline ● 20.1 Genomic that Imprinting
THE SEQ methylate
U EofN the O FCpG
C E chapter DNA islands.
contents.
base pairs in genes is the ● 20.2 Inheritance of Programmed Gene
ultimate, but Remarkably,
not only, carrierinofallgenetic information. of each ofRepression
the descendants those Through Cell Division
Geneticists have known for a long time that somatic cells 20.3 Transgenerational Epigenetic Inheritance
original 500–1000 female embryonic cells, the same
●
or gametes can also transmit information between genera- 20.4 A Comprehensive Example: Epigenetic
X chromosome (either the maternal X or the paternal X) at the A Locus in Mice
●
bodies of 242 healthy individuals. This analysis revealed tracrRNA Scientists also cas9
analyzeFthe
A Smetagenomes
T F O R WA of Rbacteria
D that
more than 10,000 different bacterial species in total, and as live in extreme environments (extremophiles) because they
many as 1000 on a single individual. The most striking cas9 mRNAof genes for proteins that work under
harbor an abundance 3′
conclusion from this study is that individuals vary widely3′ unusual 5′conditions. These Genetic Genealogy
proteins
5′ can sometimes be use- Pre-crRNA
in the species of bacteria that they carry. ful in the laboratory. For example,
Between 1976 and DNA
Taq1986, the polymerase,
so-called “Golden State Killer” The degree of genetic relatedness between any two individ-
committed at least 50 rapes and 12 murders in California. This uals can be estimated by the fraction of their (autosomal) DNA
A major current goal of the microbiome project is to the enzyme usedCas9
for PCR because it can withstand the hot
40-year-old cold case was reopened in 2018 as a consequence that they share (Fig. B). For example, your DNA comes from half
determine how human microbiomes affect important traits temperatures that denature DNA, comes from the bacterial
of people’s natural fascination with their genealogy; that is, in- of your mother’s DNA (in an egg) and half of your father’s DNA (in
RNase III
of their hosts. Strong evidence already exists that human species Thermus aquaticus,
formation first
aboutdiscovered
their ancestryinand thecurrent-day
hot relatives. a sperm); therefore, you share 50% of your DNA with each of your
Genealogy companies—the largest and best known of these parents. You also share 50% of your DNA with each of your sib-
being 23andMe and Ancestry.com—use microarray technology lings, on average: Each parent has two alleles of each SNP, and
similar to that shown in Fig. 12.15 to analyze the genomic DNA each child inherits a random one of those two SNP alleles.
submitted in the saliva of their clients to determine which alleles The power of genetic genealogy comes from two sources:
3′ 3′ Pre-crRNA processing
of many3′SNP loci they carry. 3′ First, microarrays look at a very large number of SNPs; and
5′ 5′ The basis of genetic 5′ genealogical analysis
5′ is that relatives second, companies performing genetic genealogy have de-
5′ share haplotype blocks. You will see in Chapter 25 that haplotype 3′ veloped giant databases that catalog the SNP analysis of mil-
blocks are segments of DNA with particular sets of linked SNP lions of people. If you think about it, this information is more
alleles that tend to travel together from one generation to another massive than that in the CODIS database, which is restricted to
because they are flanked by recombination hotspots. (In other a small number of SSR loci in a smaller sample of people (indi-
words, the DNA within the haplotype block contains no hotspots
crRNAs viduals arrested for or convicted of crimes). It is therefore not
for crossing-over.) You learned in Chapter 5 that during spermato- surprising that law enforcement agencies are very interested
genesis in humans, on average one crossover occurs per chromo- in employing the power of genealogical databases.
some, and during oogenesis about two crossovers per In the case of the Golden State Killer, when investigators
chromosome (Fig. A, left). It therefore makes sense that the more compared samples of the suspect’s DNA taken from the crime
closely related two
tracrRNA people are, the more haplotype blocks they scenes with the database of a small genealogy company called
share, andcrRNA
the longer are their uninterrupted shared DNA seg- GEDmatch, they found matches with two individuals. The degree
ments (Fig. A, right). of relatedness indicated that these two people were likely the
Figure A Shared segments of autosomes among relatives. One pair of autosomes are shown for each individual. At left, the
colors indicate segments of chromosomes that could be passed down through two generations. Because of crossing-over during gamete
formation, one of your homologs
Viralcan contain segments from all four of your maternal grandparents’ homologs, and your other homolog can
chromosome
contain segments from all four of your paternal grandparents’ homologs. At right, the same information is presented in a different way;
5′ NGGblack indicates chromosomal segments shared by you and each of your relatives. Note that long stretches of shared haplotypes are the
PAM site
best evidence of genetic relatedness.
Homologous chromosomes can recombine You share more SNP alleles and longer DNA segments
in each
Viralgeneration.
DNA cleavage with closer relatives.
Fast Forward
Grandmother Grandfather Grandmother Grandfather Grandmother Grandfather Grandmother Grandfather
Visualizing Genetics
Full-color illustrations and photographs bring the printed word to life. These visual reinforcements support and further
clarify the topics discussed throughout the text.
F E AT U R E F I G U R E 1 0 . 7
O O O 4′ 1′
CH HC
H G DNA fragments
HC C2′
G C T C A G T G G 3′ electrophorese
5′ H 3′ A down the gel
H H
– Purple dye C No 3′–OH, Photomultiplier
H so terminates chain tube
G C T C A G T G G C
5′ H 3′ G dATP
Filter
– Green dye Adenine Output to wheel
H computer
G–
G C T C A G T G G C A O O– O– CH2
5′ H 3′ –O
5′
Scanning
P O P O P O CH2
O laser excites
T
O O O 4′
CH 1′ fluorescent dye
H HC
Detector HC C2′
G C T C A G T G G C A G 3′
5′ H 3′
5′ OH H
Primer Complementary to
(Sequence of 3′–OH needed
template strand of
newly synthesized for chain elongation
insert
DNA)
(continued)
314
(f) A DNA sequence trace from one gel lane. Yellow is pseudocolored as black for easier visualization. Base-calling software reads
out the sequence of the newly synthesized DNA strand.
5′ T G G C A G C T C A G C G G C T G G G C A A G C G C G T G 3′
315
Guided Tour xv
3.3 Meiosis: Cell Divisions that Halve Chromosome Number 85
TABLE 3.2 How Chromosome Behavior During Meiosis Explains Mendel’s Laws
(a) The Law of Segregation (b) The Law of Independent Assortment
R R r r R R r r
Meiosis I
Anaphase
R R r r
Meiosis I Comparative Figures
Anaphase
OR
Comparison illustrations lay out the basic
Solved Problems 471
XY XY XY
Meiosis I
(2 chromatids
per chromosome) X Y XY X Y
Meiosis II
Gametes
(1 chromatid
X X Y Y XY XY X X YY
per chromosome)
The creation of a project of this scope is never solely the ∙∙ Debra Nero, Cornell University
work of the authors. We are grateful to our colleagues who ∙∙ Kristin Patterson, The University of Texas at Austin
answered our numerous questions, or took the time to share ∙∙ Leslie Pick, University of Maryland
with us their suggestions for improvement of the previous ∙∙ Hong Qiao, The University of Texas at Austin
edition. Their willingness to share their expertise and ∙∙ Maureen Sanz, Molloy College
expectations was a tremendous help to us. ∙∙ Inder Saxena, The University of Texas at Austin
∙∙ Len Seligman, Pomona College
∙∙ Eric Alani, Cornell University ∙∙ Heidi Sleister, Drake University
∙∙ Preston Aldrich, Benedictine University ∙∙ Sebastian M. Spencer, Pensacola Christian College
∙∙ Charles Aquadro, Cornell University ∙∙ Sibum Sung, The University of Texas at Austin
∙∙ James T. Arnone, William Paterson University ∙∙ James Thompson, University of Oklahoma
∙∙ Daniel Barbash, Cornell University ∙∙ Steve Vokes, The University of Texas at Austin
∙∙ Christine M. Beatty, Loyola University Chicago ∙∙ Alain Bopda Waffo, Alabama State University
∙∙ Andrew Clark, Cornell University ∙∙ Blerta Xhemalce, The University of Texas at Austin
∙∙ Steven Fenster, Fort Lewis College
∙∙ Wayne Forrester, Indiana University Janice Fischer and Michael Goldberg would also like to
∙∙ Tom Fox, Cornell University thank their genetics students at The University of Texas at
∙∙ Kathryn Gardner, University of Pittsburgh Austin and Cornell University for their amazing questions.
∙∙ Jamie S. Lyman Gingerich, University of Wisconsin– Many of their ideas have influenced the seventh edition. A
Eau Claire special thank-you to Mike McGee for his extensive feed-
∙∙ Shubha Govind, The City College of City University back on this seventh edition. We would also like to thank
of New York the highly skilled publishing professionals at McGraw-Hill
∙∙ Nancy Hollingsworth, Stony Brook University who guided the development and production of the seventh
∙∙ Enamul Huq, The University of Texas at Austin edition of Genetics: From Genes to Genomes: Ian
∙∙ Vishy Iyer, The University of Texas at Austin Townsend and Michelle Vogler for their support; Elizabeth
∙∙ Alyssa Johnson, Louisiana State University Sievers for her organizational skills and tireless work to tie
∙∙ Mark Kirkpatrick, The University of Texas at Austin up all loose ends; and Vicki Krug and the entire production
∙∙ Henry Lerner, Harvard Medical School team for their careful attention to detail and ability to move
∙∙ Paul Macdonald, The University of Texas at Austin the schedule along.
∙∙ Kyle Miller, The University of Texas at Austin
xvi
Guided Tour xvii
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Genetics
From Genes to Genomes
PART I B asic P rinciple s: How Traits Are Transmitted
chapter
1
Mendel’s Principles
of Heredity
Lawrence Manning/Corbis
chapter outline
●● 1.1 The Puzzle of Inheritance
●● 1.2 Genetic Analysis According to Mendel
●● 1.3 Mendelian Inheritance in Humans
A Q U I C K G L A N C E at a family portrait reveals children
who resemble one parent or the other, or who look like
a combination of the two. Some children, however, look and traits are bewilderingly complex. One example is that
unlike any of the assembled relatives and more like a many genes interact to generate the characteristics we rec-
great-great-grandparent. What causes the similarities ognize as a friend’s face.
and differences of appearance and the skipping of Gregor Mendel (1822–1884; Fig. 1.1), an Augustinian
generations? monk and expert plant breeder, discovered the basic prin-
The answers lie in our genes, the basic units of bio- ciples of genetics in the mid-nineteenth century. He pub-
logical information, and in heredity, the way genes trans- lished his findings in 1866, just seven years after Darwin’s
mit traits from parents to offspring. Each of us starts out On the Origin of Species appeared in print. Mendel worked
as a single fertilized egg cell that develops, by division in a monastery in Austria (Fig. 1.2), where he examined
and differentiation, into a mature adult made up of 1014 the inheritance of clear-cut alternative traits in pea plants,
(a hundred trillion) cells that carry out all of our body’s such as purple versus white flowers or yellow versus green
functions and control our outward appearance. Genes, seeds. In so doing, he inferred genetic laws that allowed
passed from one generation to the next, underlie the for- him to make verifiable predictions about which traits
mation of every heritable trait. Your genome—all the would appear, disappear, and then reappear, and in which
genes you possess—controls traits as diverse as a cleft generations.
chin; balding as you age; your hair, eye, and skin color; Mendel’s laws are based on the hypothesis that
and even your susceptibility to certain diseases. All such observable traits are determined by independent units of
traits run in families in predictable patterns that impose inheritance that we now call genes. Today, a gene is rec-
some possibilities and exclude others. ognized as a region of DNA that specifies a particular
Genetics, the science of heredity, pursues an expla- protein or RNA. To Mendel, however, a gene was an
nation of the mechanisms that determine inheritance. abstraction—an imagined particle that worked by an
Sometimes the relationship between gene and trait is unknown mechanism.
remarkably simple. A single change in a single gene, for Four general themes emerge from our detailed dis-
example, results in sickle-cell disease, a condition in cussion of Mendel’s work. First, variation in traits is
which the hemoglobin molecule found in red blood cells widespread in nature, reflecting immense genetic diver-
is defective. In other cases, the correlations between genes sity that provides the raw material for the continuous
1
2 Chapter 1 Mendel’s Principles of Heredity
evolution of life on the earth. Sec- Figure 1.1 Gregor Mendel. Figure 1.2 Mendel’s garden.
ond, variation is essential for fol- Photographed around 1862 Biophoto Associates/Science Source
holding one of his experimental
lowing genes from one generation plants. Science Source
to the next. Third, variation is
inherited according to patterns—
Mendel’s genetic laws—that explain
why individuals in the same fam-
ily are similar in some traits but
different in others. Fourth, the laws
Mendel discovered about heredity
apply equally well to all sexually
reproducing organisms, whether
they are peas or people.
Figure 1.3 The homunculus: A misconception. Well into the flower color, yellow versus green pea color. He could trace
nineteenth century, many prominent microscopists believed they saw unambiguously the transmission of such either-or traits, be-
a fully formed, miniature fetus crouched within the head of a sperm.
Klaus Guldbrandsen/SPL/Science Source
cause no intermediate forms existed. (The opposite of these
so-called discrete traits are continuous traits, such as
height and skin color in humans. Continuous traits show
many intermediate forms.)
Third, Mendel collected and perpetuated lines of peas
that bred true. Matings within such pure-breeding
(or true-breeding) lines produce offspring carrying spe-
cific parental characteristics that remain constant from
generation to generation. These lines are also called
inbred because they have been mated only to each other
for many generations. Plants with white flowers always
produced offspring with white flowers; plants with purple
flowers produced only offspring with purple flowers.
Mendel called constant but mutually exclusive alterna-
tives, such as purple versus white flowers or yellow versus
green seeds antagonistic pairs, and he settled on seven
such pairs for his study (Fig. 1.5). In his experiments,
Mendel cross-fertilized pairs of plants to produce hybrids,
offspring of genetically dissimilar parents, for each an-
tagonistic pair. Figure 1.5 shows the a ppearance of the
hybrids he studied.
Fourth, Mendel made reciprocal crosses, in which
(to prevent selfing), and then he brushed pollen from the he reversed the characteristics of the male and female
other plant onto the female organs of the first plant parents, thus controlling whether a particular characteris-
(Fig. 1.4c). Peas offered yet another advantage. For each tic was transmitted via the egg cell within the ovule or via
successive generation, Mendel could obtain large numbers a sperm cell within the pollen. For example, he could use
of individuals within a relatively short growing season. pollen from a purple flower to fertilize the eggs of a white
Second, Mendel examined the inheritance of clear-cut flower and also use pollen from a white flower to fertilize
alternative states of particular traits—purple versus white the eggs of a purple flower. Because the progeny of these
Figure 1.4 Mendel’s experimental organism: The garden pea. (a) Pea plants with white flowers. (b) The anthers produce pollen,
which generates sperm. Mature pollen lands on the stigma, a structure connected to the ovary (which becomes the pea pod). The pollen
then grows a tube that extends through the stigma to one of the ovules (immature seeds), allowing fertilization. (c) To prevent self-fertilization,
breeders remove the anthers from the female parents (here, the white flower) before the plant produces mature pollen. A paintbrush is used
to transfer pollen from the anthers of the male parent (here, the purple flower) to the female parent’s stigma. Each fertilized ovule becomes
an individual pea (mature seed) that can grow into a new pea plant. All of the peas produced from one flower are encased in the same pea
pod, but these peas form from different pollen grains and ovules. (a): Andrea Jones Images/Alamy
Cross-
fertilization:
pollen
transferred Anthers
onto stigma removed
Stigma of recipient previously
Anthers
( )
Seed
Ovules formation
( ) within
ovary
Seed
germination
Figure 1.5 The mating of parents with antagonistic reciprocal crosses were similar, Mendel demonstrated
characteristics produces hybrids. Note that each of the hybrids that the two parents contribute equally to inheritance.
for the seven antagonistic pairs studied by Mendel resembles only Fifth, Mendel worked with large numbers of plants,
one of the parents. The parental characteristic that shows up in the
hybrid is the dominant characteristic.
counted all offspring, subjected his findings to numerical
Antagonistic Pairs Appearance of Hybrid
analysis, and then compared his results with predictions
(dominant characteristic) based on his models. He was the first person to study in-
heritance in this quantitative manner. Mendel’s careful
Seed color (interior) numerical analysis revealed patterns of transmission that
reflected basic laws of heredity.
Finally, Mendel was a brilliant practical experimental-
Yellow Green Yellow ist. When comparing tall and short plants, for example, he
made sure that the short ones were out of the shade of the
Seed shape tall ones so their growth would not be stunted. In short,
Mendel purposely set up a simplified black-and-white ex-
perimental system and then figured out how it worked. He
Round
looked at discrete traits that came in two mutually exclu-
Round Wrinkled
sive forms and asked questions that could be answered by
observation and computation.
Flower color
In 1866, Gregor Mendel published in an obscure journal a but hidden in these F1 yellow peas, Mendel planted them to
paper titled “Experiments on Plant Hybrids.” In it, Mendel obtain mature F1 plants that he allowed to self-fertilize.
describes the transmission of visible characteristics in pea Such experiments involving hybrids for a single trait are
plants, defines unseen but logically deduced units (genes) called monohybrid crosses. He then harvested and counted
that determine when and how often these traits appear, and the peas of the resulting second filial (F2) generation,
analyzes the behavior of genes in simple mathematical progeny of the F1 generation. The progeny of one series of
terms to reveal previously unsuspected principles of hered- F1 self-fertilizations were 6022 yellow and 2001 green
ity. The paper would eventually become the cornerstone of F2 peas, an almost perfect ratio of 3 yellow : 1 green.
modern genetics. Let us examine its insights. F1 plants derived from the reciprocal of the original cross
produced a similar 3:1 ratio of yellow to green F2 progeny.
Figure 1.6 A monohybrid cross. Crosses of pure-breeding Genes: Discrete units of inheritance
parental plants produce F1 hybrids, all of which resemble one of the
parents. Self-pollination of F1 plants yields an F2 generation with a To account for his observations, Mendel proposed that for
3:1 ratio of individuals resembling the two original parental types. each trait, every plant carries two copies of a unit of in-
For simplicity, we do not show the plants that produce the peas or heritance, receiving one from its maternal parent and the
that grow from the planted peas.
other from the paternal parent. Today, we call these units of
Generation inheritance genes. The pea plants in Mendel’s collection
Parental (P) had two copies of a gene for seed color, two copies of an-
(pure-breeding) Yellow peas Green peas
( : sperm) ( : eggs) other for seed shape, two copies of a third for stem length,
and so forth.
Mendel further proposed that each gene comes in alter-
First filial (F1) native forms, and combinations of these alternative forms
All yellow determine the contrasting characteristics he was studying.
Self-fertilization
Today we call the alternative forms of a single gene alleles.
The gene for pea color, for example, has yellow and green
alleles; the gene for pea shape has round and wrinkled al-
leles. In Mendel’s monohybrid crosses, one allele of each
gene was dominant, the other recessive. In the P generation,
Second filial (F2) one parent carried two dominant alleles of the gene under
consideration; the other parent, two recessive alleles. The
F1 generation hybrids carried one dominant and one reces-
6022 yellow : 2001 green sive allele of the gene. Individuals having two different al-
3:1 leles of a single gene are monohybrids.
6 Chapter 1 Mendel’s Principles of Heredity
The law of segregation yellow and the egg green, the result will be a hybrid yellow
If a plant has two copies of every gene, how does it pass pea like the F1 monohybrids that resulted when pure-
only one copy of each to its progeny? And how do the off- breeding parents of opposite types mated. If the yellow-
spring then end up with two copies of these same genes, carrying sperm unites with a yellow-carrying egg, the
one from each parent? Mendel answered these questions in result will be a yellow pea that grows into a pure-breeding
terms of the two biological mechanisms behind reproduc- plant like those of the P generation that produced only
tion: gamete formation and the random union of gametes at yellow peas. And finally, if sperm carrying the allele for
fertilization. green peas f ertilizes a green-carrying egg, the progeny will
Gametes are the specialized cells—eggs within the be a pure-breeding green pea.
ovules of the female parent and sperm cells within the Mendel’s law of segregation encapsulates this gen-
pollen grains—that carry genes between generations. eral principle of heredity: The two alleles of each gene
Mendel imagined that during the formation of eggs and separate (segregate) during gamete formation, and then
sperm, the two copies of each gene in the parent separate unite at random, one from each parent, at fertilization.
(or segregate) so that each gamete receives only one allele Throughout this book, the term segregation refers to such
for each trait (Fig. 1.7a). Thus, each egg and each sperm equal segregation in which one allele, and only one allele,
receives only one allele for pea color (either yellow or of each gene goes to each gamete. Note that the law of
green). segregation makes a clear distinction between the somatic
At fertilization, a sperm with one or the other allele cells (body cells) of an organism, which have two copies
unites at random with an egg carrying one or the other al- of each gene, and the gametes, which bear only a single
lele, restoring the two copies of the gene for each trait in the copy of each gene.
fertilized egg, or zygote (Fig. 1.7b). If the sperm carries
The Punnett square
Figure 1.8 shows a simple way of visualizing the results of
the segregation and random union of alleles during gamete
Figure 1.7 The law of segregation. (a) The two identical
alleles of pure-breeding plants separate (segregate) during gamete
formation and fertilization. Mendel invented a system of
formation. As a result, each sperm or egg carries only one of each symbols that allowed him to analyze all of his crosses in the
pair of parental alleles. (b) Cross-fertilization between pure-breeding same way. He designated dominant alleles with a capital A,
parents with antagonistic characteristics results in F1 hybrid zygotes B, or C and recessive ones with a lowercase a, b, or c.
with two different alleles. For the seed color gene, a Yy hybrid Modern geneticists have adopted this convention for nam-
zygote will develop into a yellow pea.
ing genes in peas and many other organisms, but they often
(a) The two alleles for each trait separate during gamete
formation. choose a symbol with some reference to the trait in question—
Gametes
a Y for yellow or an R for round. Throughout this book, we
(sperm or eggs) present gene symbols in italics. In Fig. 1.8, we denote the
Y
Grows into plant Gamete
formation
YY yellow pea Y Figure 1.8 The Punnett square: Visual summary of a cross.
from a pure-breeding This Punnett square illustrates the combinations that can arise when
stock an F1 hybrid undergoes gamete formation and self-fertilization. The F2
y
generation has a 3:1 ratio of yellow to green peas.
Grows into plant Gamete
formation
yy green pea y P YY yy
from a pure-breeding
stock
Gametes Y y
(b) Two gametes, one from each parent, unite at random
at fertilization.
dominant yellow allele with a capital Y and the recessive the probability of a heads in the next toss. If you toss two
green allele with a lowercase y. The pure-breeding plants coins at the same time, the results are also independent
of the parental generation are either YY (yellow peas) or events. A heads for one coin neither increases nor decreases
yy (green peas). The YY parent can produce only Y gametes, the probability of a heads for the other coin. Thus, the prob-
the yy parent only y gametes. You can see in Fig. 1.8 why ability of a given combination is the product of their inde-
every cross between YY and yy produces exactly the same pendent probabilities. For example, the probability that
result—a Yy hybrid—no matter which parent (male or both coins will turn up heads is:
female) contributes which particular allele.
1/2 × 1/2 = 1/4
Next, to visualize what happens when the Yy hybrids
self-fertilize, we set up a Punnett square (named after the Similarly, the formation of egg and sperm are independent
British mathematician Reginald Punnett, who introduced it events; in a hybrid plant, the probability is 1/2 that a given
in 1906; Fig. 1.8). The square provides a simple and con- gamete will carry Y and 1/2 that it will carry y. Because
venient method for tracking the kinds of gametes produced, fertilization happens at random, the probability that a par-
as well as all the possible combinations that might occur at ticular combination of maternal and paternal alleles will
fertilization. As the Punnett square shows in the first col- occur simultaneously in the same zygote is the product of
umn and the first row, each hybrid produces two kinds of the independent probabilities of these alleles being pack-
gametes, Y and y, in a ratio of 1:1. Thus, half the sperm and aged in egg and sperm. Thus, to find the chance of a Y egg
half the eggs carry Y, while the other half of each gamete uniting with a Y sperm, you simply multiply 1/2 × 1/2
type carries y. to get 1/4. This is the same fraction of YY progeny seen in
Each box in the Punnett square in Fig. 1.8 containing the Punnett square of Fig. 1.8, which demonstrates that the
a colored pea represents one possible fertilization event. Punnett square is simply another way of depicting
At fertilization, 1/4 of the progeny will be YY, 1/4 Yy, the product rule. It is important to realize that each box
1/4 yY, and 1/4 yy. Because the gametic source of an al- in the Punnett square represents an equally likely outcome
lele (egg or sperm) for the traits Mendel studied had no of the cross only because each of the two types of sperm
influence on the allele’s effect, Yy and yY are equivalent. and eggs (Y and y) are produced at equal frequencies.
This means that 1/2 of the progeny are yellow Yy hy-
brids, 1/4 YY true-breeding yellows, and 1/4 true-
breeding yy greens. The diagram illustrates how the The sum rule
segregation of alleles during gamete formation and the While we can describe the moment of random fertilization
random union of egg and sperm at fertilization can as the simultaneous occurrence of two independent events,
produce the 3:1 ratio of yellow to green that Mendel ob- we can also say that two different fertilization events are
served in the F2 generation. mutually exclusive. For instance, if Y combines with Y, it
cannot also combine with y in the same zygote. A second
rule of probability, the sum rule, states that the probability
Mendel’s Results Reflect Basic of either of two mutually exclusive events occurring is the
sum of their individual probabilities. With mutually exclu-
Rules of Probability sive events:
Though you may not have realized it, the Punnett square Probability of event 1 or event 2 =
illustrates two simple rules of probability—the product
rule and the sum rule—that are central to the analysis of Probability of event 1 + probability of event 2
genetic crosses. These rules predict the likelihood that a To find the likelihood that an offspring of a Yy hybrid
particular combination of events will occur. self-fertilization will be a hybrid like the parents, you add
1/4 (the probability of maternal Y uniting with paternal y)
The product rule and 1/4 (the probability of the mutually exclusive event
The product rule states that the probability of two or more where paternal Y unites with maternal y) to get 1/2, again
independent events occurring together is the product of the the same result as in the Punnett square.
probabilities that each event will occur by itself. With inde- In another use of the sum rule, you could predict the
pendent events: ratio of yellow to green F2 progeny. The fraction of F2 peas
that will be yellow is the sum of 1/4 (the event producing
Probability of event 1 and event 2 = YY) plus 1/4 (the mutually exclusive event generating Yy)
Probability of event 1 × probability of event 2 plus 1/4 (the mutually exclusive event producing yY)
to get 3/4. The remaining 1/4 of the F2 progeny will be
Consecutive coin tosses are obviously independent green. So the yellow-to-green ratio is 3/4 to 1/4, or more
events; a heads in one toss neither increases nor decreases simply, 3:1.
8 Chapter 1 Mendel’s Principles of Heredity
YY
Self- Homozygous dominant Yellow
fertilization
F2 YY Yy Yy yy Dominant Recessive
allele allele
Yy Yellow
Self- Heterozygous
fertilization 3:1 3:1
F3 YY YY Yy Yy yy YY Yy Yy yy yy yy
Green
(All) (All) Homozygous recessive
1.2 Genetic Analysis According to Mendel 9
Figure 1.11 How a testcross reveals genotype. An Figure 1.12 A dihybrid cross produces parental types
individual of unknown genotype, but dominant phenotype, is crossed and recombinant types. In this dihybrid cross, pure-breeding
with a homozygous recessive individual. If the unknown genotype parents (P) produce a genetically uniform generation of F1 dihybrids.
is homozygous, all progeny will exhibit the dominant phenotype Self-fertilization or cross-fertilization of the F1 plants yields the
(Cross A). If the unknown genotype is heterozygous, half the progeny characteristic F2 phenotypic ratio of 9:3:3:1.
will exhibit the dominant trait, half the recessive trait (Cross B).
Cross A Cross B P
YY RR yy rr
P YY yy P Yy yy
Gametes YR yr
F1 F1
y y
F1 (all identical)
Y Yy Y Yy Yy Rr Yy Rr
YR Yr yR yr
Offspring all yellow Offspring 1:1 yellow to green
1/4 YR
crossed with an individual with the recessive phenotype, in YY RR YY Rr Yy RR Yy Rr
this case a yy plant grown from a green pea. As the Punnett 1/4 Yr
squares in Fig. 1.11 illustrate, if the dominant phenotype in YY Rr YY rr Yy Rr Yy rr
question derives from a homozygous YY genotype, all the
1/4 yR
offspring of the testcross will show the dominant yellow Yy RR Yy Rr yy RR yy Rr
phenotype. But if the dominant parent of unknown geno-
type is a heterozygous hybrid (Yy), half of the progeny are 1/4 yr
Yy Rr Yy rr yy Rr yy rr
expected to be yellow peas, and the other half green. In this
Each box:
way, the testcross establishes the genotype behind a domi- 1/4 × 1/4 = 1/16
nant phenotype. Type Genotype Phenotype Number Phenotypic
As we mentioned earlier, Mendel deliberately simpli- Ratio
fied the problem of heredity, focusing on traits that come in
Parental Y– R– yellow round 315 9/16
only two forms. He was able to replicate his basic monohy-
brid findings with corn, beans, and four-o’clocks (plants
with tubular, white or bright red flowers). As it turns out, Recombinant yy R– green round 108 3/16
his concept of the gene and his law of segregation can be
generalized to almost all sexually reproducing organisms. Recombinant Y– rr yellow wrinkled 101 3/16
fact, appear, providing evidence that some shuffling of the Figure 1.13 The law of independent assortment. In a
alleles of different genes had taken place. dihybrid cross, each pair of alleles assorts independently during
gamete formation. In the gametes, Y is equally likely to be found with
R or r (that is, Y R = Y r); the same is true for y (that is, y R = y r). As
a result, all four possible types of gametes (Y R, Y r, y R, and y r) are
The law of independent assortment produced in equal frequency.
From the observed ratios, Mendel inferred the biological Possible allele
Alleles in Gamete
mechanism of that shuffling—the independent assortment parental cell formation
combinations
of gene pairs during gamete formation. Because the genes in gametes
for pea color and for pea shape assort independently, the
allele for pea shape in a gamete carrying Y could with equal Y R 1/4
likelihood be either R or r. Thus, the presence of a particu-
lar allele of one gene, say, the dominant Y for pea color, Y r 1/4
Y
provides no information whatsoever about the allele of the y
second gene. Each dihybrid of the F1 generation can there- R
y R 1/4
fore make four kinds of gametes: Y R, Y r, y R, and y r. In a r
large number of gametes, the four kinds will appear in an
almost perfect ratio of 1:1:1:1, or put another way, roughly y r 1/4
1/4 of the eggs and 1/4 of the sperm will contain each of the
four possible combinations of alleles.
At fertilization then, in a mating of dihybrids, 4 differ-
ent kinds of eggs can each combine with any 1 of 4 differ- lleles segregate independently of each other (Fig. 1.13). The
a
ent kinds of sperm, producing a total of 16 possible independence of their segregation and the subsequent random
zygotes. Once again, a Punnett square is a convenient way union of gametes at fertilization determine the phenotypes
to visualize the process (Fig. 1.12). Using the same kind of observed. Using the product rule for assessing the probability
logic previously applied to the Punnett square for monohy- of independent events, you can see mathematically how the
brid crosses (review Fig. 1.8), each of the 16 boxes with 9:3:3:1 phenotypic ratio observed in a dihybrid cross derives
colored peas in the Punnett square for the dihybrid cross in from two separate 3:1 phenotypic ratios. If the two sets of
Fig. 1.12 represents an equally likely fertilization event. alleles assort independently, the yellow-to-green ratio in the
Again, each box is an equally likely outcome only because F2 generation will be 3/4 : 1/4, and likewise, the round-to-
each of the different gamete types is produced at equal wrinkled ratio will be 3/4 : 1/4. To find the probability that
frequency in each parent. Therefore, using the product two independent events such as yellow and round will occur
rule, the frequency of the progeny type in each box is simultaneously in the same plant, you multiply as follows:
1/4 × 1/4 = 1/16. Probability of yellow round = 3/4 × 3/4 = 9/16
If you look at the square in Fig. 1.12, you will see that
some of the 16 potential allelic combinations are identical. Probability of green round = 1/4 × 3/4 = 3/16
In fact, only nine different genotypes exist—YY RR, YY Rr, Probability of yellow wrinkled = 3/4 × 1/4 = 3/16
Yy RR, Yy Rr, yy RR, yy Rr, YY rr, Yy rr, and yy rr—because
the source of the alleles (egg or sperm) does not make any Probability of green wrinkled = 1/4 × 1/4 = 1/16
difference. If you look at the combinations of traits Thus, in a population of F2 plants, there will be a
determined by the nine genotypes, you will see only four 9:3:3:1 phenotypic ratio of yellow round to green round to
phenotypes—yellow round, green round, yellow wrinkled, yellow wrinkled to green wrinkled.
and green wrinkled—in a ratio of 9:3:3:1. If, however, you
look only at pea color or only at pea shape, you can see that
each trait is inherited in the 3:1 ratio predicted by Mendel’s Branched-line diagrams
law of segregation. In the Punnett square, 12 yellow are A convenient way to keep track of the probabilities of each
present for every 4 green F2 progeny, and 12 round are seen potential outcome in a genetic cross is to construct a
for every 4 wrinkled. In other words, the ratio of each dom- branched-line diagram (Fig. 1.14), which shows all the
inant characteristic (yellow or round) to its antagonistic possible genotypes or phenotypes for each gene in a
recessive characteristic (green or wrinkled) is 12:4, or 3:1. sequence of columns. In Fig. 1.14, the first column shows
This means the inheritance of the gene for pea color is un- the two possible pea color phenotypes; the second column
affected by the inheritance of the gene for pea shape, and demonstrates that each pea color can occur with either of
vice versa. two pea shapes. Again, the 9:3:3:1 ratio of phenotypes is
The preceding analysis became the basis of Mendel’s apparent. You will see later that branched-line diagrams
second general genetic principle, the law of independent are more convenient than Punnett squares for predicting the
assortment: During gamete formation, different pairs of outcomes of crosses involving more than two genes.
1.2 Genetic Analysis According to Mendel 11
Figure 1.14 Following crosses with branched-line Figure 1.15 Testcrosses with dihybrids. Testcrosses
diagrams. A series of columns tracks every gene in a cross, involving two pairs of independently assorting alleles yield different,
providing an organized overview of all possible outcomes. This predictable results depending on the tested individual’s genotype.
branched-line diagram of a dihybrid cross generates the same Cross A Cross B
phenotypic ratios as the Punnett square in Fig. 1.12, showing that
the two methods are equivalent. P YY RR yy rr P YY Rr yy rr
Gene 1 Gene 2 Phenotypes
F1 F1
3/4 round 9/16 yellow round yr yr
3/4 yellow
1/4 wrinkled 3/16 yellow wrinkled
YR YR
Yy Rr Yy Rr
3/4 round 3/16 green round
1/4 green
1/4 wrinkled 1/16 green wrinkled Yr
Yy rr
Cross C Cross D
Testcrosses with dihybrids P Yy RR yy rr P Yy Rr yy rr
An understanding of dihybrid crosses has many applica-
tions. Suppose, for example, that you work for a nursery F1 F1
yr yr
that has three pure-breeding strains: yellow wrinkled, green
round, and green wrinkled. Your assignment is to grow
pure-breeding plants guaranteed to produce yellow round YR YR
Yy Rr Yy Rr
peas. How would you proceed?
One answer is to cross two of your pure-breeding strains yR Yr
(YY rr × yy RR) to generate a dihybrid (Yy Rr). Then self- yy Rr Yy rr
cross the dihybrid and plant only the yellow round peas. yR
Only one out of nine of such progeny—those grown from yy Rr
peas with a YY RR genotype—will be appropriate for your
yr
uses. To find these plants, you could subject each yellow yy rr
round candidate to a testcross for genotype with a green
wrinkled (yy rr) plant, as illustrated in Fig. 1.15. If the test-
cross yields all yellow round offspring (testcross A), you
can sell your test plant, because you know it is homozygous You could set up a Punnett square to answer the question.
for both pea color and pea shape. If your testcross yields Because for each trait there are two different alleles, the
1/2 yellow round and 1/2 yellow wrinkled (testcross B), or number of different eggs or sperm is found by raising 2 to
1/2 yellow round and 1/2 green round (testcross C), you know the power of the number of differing traits (2n, where n is
that the candidate plant in question is genetically homozygous the number of traits). By this calculation, each hybrid par-
for one trait and heterozygous for the other and must there- ent in this cross with 4 traits would make 24 = 16 different
fore be discarded. Finally, if the testcross yields 1/4 yellow kinds of gametes. The Punnett square depicting such a
round, 1/4 yellow wrinkled, 1/4 green round, and 1/4 green cross would thus contain 256 boxes (16 × 16).
wrinkled (testcross D), you know that the plant is a hete- Setting up such a square may be fine if you live in a
rozygote for both the pea color and the pea shape genes. monastery with a bit of time on your hands, but not if
you’re taking a 1 hour exam. It would be much simpler to
analyze the problem by breaking down the multihybrid
Mendel’s Laws Predict Probabilities, cross into four independently assorting monohybrid
crosses. Remember that the genotypic ratios of each mono-
Not Specific Outcomes hybrid cross are 1 homozygote for the dominant allele, to
Mendelian analysis makes accurate predictions about the 2 heterozygotes, to 1 homozygote for the recessive allele =
offspring of complex multihybrid crosses: matings be- 1/4 : 2/4 : 1/4. Thus, you can find the probability of
tween the F1 progeny of pure-breeding parents that differ in AA bb Cc Dd by multiplying the probability of each inde-
three or more traits. Suppose you want to predict the occur- pendent event: AA (1/4 of the progeny produced by Aa × Aa);
rence of one specific genotype in a cross involving inde- bb (1/4); Cc (2/4); Dd (2/4):
pendently assorting alleles of several genes. For example, if
1/4 × 1/4 × 2/4 × 2/4 = 4/256 = 1/64
hybrids heterozygous for four genes are allowed to self-
fertilize—Aa Bb Cc Dd × Aa Bb Cc Dd—what proportion of The Punnett square approach would provide the same
their progeny will have the genotype AA bb Cc Dd? answer, but it would be far more tedious.
12 Chapter 1 Mendel’s Principles of Heredity
If instead of a specific genotype, you want to predict equal genetic contribution to the next generation. The
the probability of a certain phenotype, you can again use model of heredity that he formulated was so specific he
the product rule as long as you know the phenotypic ratios could test predictions based on it by observation and ex-
produced by each pair of alleles in the cross. For example, periment.
if in the multihybrid cross of Aa Bb Cc Dd × Aa Bb Cc Dd Mendel was so far ahead of his time that none of his
you want to know how many offspring will show the dom- contemporaries appreciated the importance of his research.
inant A characteristic (genotype AA or Aa = 1/4 + 2/4, or A key reason for the obscurity of Mendel’s work was that,
3/4), the recessive b characteristic (genotype bb = 1/4), the in the 1860s, no one had yet seen the structures within cells,
dominant C characteristic (genotype CC or Cc = 3/4), and the chromosomes, that actually carry the genes. That would
the dominant D characteristic (genotype DD or Dd = 3/4), happen only about 20 years later. If scientists had been able
you simply multiply: to see these structures, they might have more readily ac-
cepted Mendel’s ideas. As Chapter 3 will describe, the be-
3/4 × 1/4 × 3/4 × 3/4 = 27/256
havior of the chromosomes during a kind of cell division
In this way, the rules of probability make it possible to pre- called meiosis is the underlying basis of Mendel’s laws.
dict the outcome of complex crosses. Mendel’s work might have had an important influ-
You can see from these examples that particular prob- ence on early debates about evolution if it had been more
lems in genetics are amenable to particular modes of analy- widely appreciated. Charles Darwin (1809–1882), who
sis. As a rule of thumb, Punnett squares are excellent for was unfamiliar with Mendel’s work, was plagued in his
visualizing simple crosses involving a few genes, but they later years by criticism that his explanations for the per-
become unwieldy in the dissection of more complicated sistence of variation in organisms were insufficient.
matings. Direct calculations of probabilities, such as those in Darwin considered such variation a cornerstone of his
the two preceding problems, are useful when you want to theory of evolution, maintaining that natural selection
know the chances of one or a few outcomes of complex would favor particular variants in a given population in
crosses. If, however, you want to know all the outcomes of a a given environment. If the selected combinations of
multihybrid cross, a branched-line diagram is the best way to variant traits were passed on to subsequent generations,
go, because it will keep track of all the possibilities in an this transmission of variation would propel evolution.
organized fashion. He could not, however, say how that transmission might
Mendel realized that because of the effects of chance, occur. Had Darwin been aware of Mendel’s ideas, he
his laws would make the most accurate predictions only might not have been backed into such an uncomfortable
if he examined large numbers of pea plants. A simple corner.
coin toss experiment illustrates his reasoning. With each For 34 years, Mendel’s laws lay dormant—untested,
throw, the probability of the coin coming up heads is unconfirmed, and unapplied. Then in 1900, 16 years af-
equal to the likelihood it will come up tails. But if you ter Mendel’s death, Carl Correns, Hugo de Vries, and
toss a coin 10 times, you may get 30% (3) heads and 70% Erich von Tschermak independently rediscovered and ac-
(7) tails, or vice versa. If you toss it 100 times, you are knowledged his work (Fig. 1.16). The scientific commu-
more likely to get a result closer to the expected 50% nity had finally caught up with Mendel. Within a decade,
heads and 50% tails. The larger the number of trials, the investigators had coined many of the modern terms we
lower the probability that chance significantly skews the have been using: phenotype, genotype, homozygote, hete-
data. In Chapter 5, we discuss mathematical methods for rozygote, gene, and genetics, the label given to the twen-
assessing whether the chance variation observed in a tieth-century science of heredity. Mendel’s paper
sample of individuals is compatible with a genetic provided the new discipline’s foundation. His principles
hypothesis. and analytic techniques endure today, guiding geneticists
and evolutionary biologists in their studies of genetic
Mendel’s Genius Was Unappreciated variation.
Before 1900
Mendel’s insights into the workings of heredity were a Recessive Alleles Are Most Often
breakthrough of monumental proportions. By counting Nonfunctional, While Dominant
and analyzing data from hundreds of pea plant crosses, he
inferred the existence of genes—independent units that
Alleles Are Usually Functional
determine the observable patterns of inheritance for par- We now know that most genes specify the proteins that
ticular traits. His work explained the reappearance of hid- dictate the structure and function of cells. Recently,
den characteristics, disproved the idea of blended two genes were identified that are likely to correspond
inheritance, and showed that mother and father make an to Mendel’s genes for seed shape and seed color. The pea
1.2 Genetic Analysis According to Mendel 13
Figure 1.16 The science of genetics begins with the rediscovery of Mendel. Working independently at the beginning of the
twentieth century, Correns, de Vries, and von Tschermak each came to the same conclusions summarized in Mendel’s laws. (a): NML/Science
Source; (b): INTERFOTO/Alamy; (c): SPL/Science Source; (d): Ullstein Bild/Getty Images
(a) Gregor Mendel (b) Carl Correns (c) Hugo de Vries (d) Erich von Tschermak
shape gene specifies an enzyme known as Sbe1 shape. In contrast, the recessive allele r specifies no Sbe1
(for Starch-branching enzyme 1). Sbe1 catalyzes the enzyme. Sucrose builds up in homozygous recessive
conversion of amylose, an unbranched linear starch, to rr peas because less of it is converted into starch. The ex-
amylopectin, a starch composed of branching chains cess sucrose modifies the osmotic pressure, causing water
(Fig. 1.17a). The dominant R allele of the pea shape gene to enter the young seeds. As the rr seeds mature, they
determines a normal, functioning Sbe1 enzyme. In con- lose water, shrink, and wrinkle. The single dominant
trast, the recessive allele r specifies no Sbe1 enzyme. As a allele in Rr heterozygotes apparently specifies enough
result, RR homozygotes contain many branched starch of the normal Sbe1 enzyme to prevent wrinkling.
molecules, which allows the peas to maintain a rounded The pea color gene determines an enzyme called
Sgr (for Stay green). Sgr performs one step in the path-
Figure 1.17 Mendel’s pea shape and pea color genes. way leading to the breakdown of the green pigment
(a) The R allele of the pea shape gene specifies the enzyme Sbe1, chlorophyll, a process that occurs naturally in peas as
which converts unbranched starch (amylose) to branched starch they mature (Fig. 1.17b). The dominant Y allele speci-
(amylopectin). The r allele does not produce Sbe1. The buildup of fies Sgr, and the recessive y allele does not. Homozy-
unbranched starch in rr peas ultimately causes seed wrinkling. gous YY or heterozygous Yy peas are yellow because
(b) The Y allele of the pea color gene specifies the enzyme Sgr,
which helps break down chlorophyll, resulting in yellow peas. The
they each have enough Sgr to break down all the
y allele does not produce Sgr. Chlorophyll is not broken down in chlorophyll. Homozygous yy peas stay green because
yy peas, and they remain green. they lack the Sgr enzyme, and the chlorophyll
(a) Biochemical function of Mendel’s pea shape gene remains.
R : Sbe1 RR, Rr Two general principles emerge from these molecu-
r : No Sbe1 Sbe1 lar discoveries. First, a specific gene determines a spe-
cific protein (in each of these cases, an enzyme). The
activity of the protein may affect the phenotype of the
Amylose
Amylopectin pea plant in any number of ways, depending on the bio-
rr
chemical pathway in which it functions. Second, a pat-
(b) Biochemical function of Mendel’s pea color gene
Y : Sgr
tern can be seen in both of these examples: The dominant
y : No Sgr allele determines a normally functioning protein, while
YY, Yy O
Sgr the recessive allele does not specify a functional pro-
tein. You will see in Chapter 2 that this is the most com-
O
is, a mating between relatives; and a horizontal consistent with both possibilities. If the disease allele
line above a series of symbols ( ) indicates the is dominant, then the father and the affected son are
children of the same parents (a sibship) arranged and heterozygotes, while the mother and the unaffected son
numbered from left to right in order of their birth. Ro- are homozygotes for the recessive normal allele. If
man numerals to the left or right of the diagram indicate instead the disease allele is recessive, the father and af-
the generations. fected son are homozygotes for the recessive
To reach a conclusion about the mode of inheritance disease-causing allele, while the mother and the unaf-
of a family trait, human geneticists must use a pedigree fected son are heterozygotes.
that supplies sufficient information. For example, re- Several kinds of additional information could help
searchers could not determine whether the allele causing resolve this uncertainty. Human geneticists would par-
the disease depicted at the bottom of Fig. 1.18 is domi- ticularly want to know the frequency at which the trait in
nant or recessive to the normal (nondisease) allele solely question is found in the population from which the fam-
on the basis of the simple pedigree shown. The data are ily came. If the disease is rare in the population, then
the allele giving rise to the disease should also be rare,
and the most likely hypothesis would require that the
fewest genetically unrelated people carry the allele.
Figure 1.18 Symbols used in pedigree analysis. In the Only the father in Fig. 1.18 would need to have a domi-
simple pedigree at the bottom, I-1 is the father, I-2 is the mother, nant disease-causing allele, but both parents would need
and II-1 and II-2 are their sons. The father and the first son are both
to carry a recessive disease-causing allele (the father two
affected by the disease.
copies and the mother one). However, even the informa-
Male
tion that the condition is rare does not allow us to draw
Female Unaffected
the firm conclusion that it is inherited in a dominant
Sex unspecified fashion. The pedigree in the figure is so limited that we
Diseased Deceased cannot be sure the two parents are themselves unrelated.
5 3 14 Multiple progeny Consanguineous As we discuss later in more detail, related parents might
mating have both received the same rare recessive allele from
their common ancestor. This example illustrates why hu-
Mating line
Generation I man geneticists try to collect family histories that cover
Sibship line
1 2 Line of descent several generations.
Generation II We now look at more extensive pedigrees for the
1 2 Individual number within generation dominant trait of Huntington disease and for the recessive
16 Chapter 1 Mendel’s Principles of Heredity
condition of cystic fibrosis. The patterns by which these tion as a whole, a vertical pattern is strong evidence that
traits appear in the pedigrees provide important clues that a dominant allele causes the condition; the alternative
can indicate modes of inheritance and allow geneticists to would require that many unrelated people carry a rare
assign genotypes to family members. recessive allele. (A recessive trait that is extremely com-
mon might also show up in every generation; we exam-
ine this possibility in Problem 40 at the end of this
A Vertical Pattern of Inheritance Indicates chapter.)
In tracking a dominant allele through a pedigree, you
a Rare Dominant Trait can view every mating between an affected and an unaf-
Huntington disease is named for George Huntington, the fected partner as analogous to a testcross. If some of the
New York physician who first described its course. This offspring do not have Huntington disease, you know the
illness usually shows up in middle age and slowly de- parent showing the trait is a heterozygote. As an exercise,
stroys its victims both mentally and physically. Symp- you should check your own genotype assignments against
toms include intellectual deterioration, severe depression, those in the caption to Fig. 1.19.
and jerky, irregular movements, all caused by the pro- Notice also in the legend to Fig. 1.19 that human
gressive death of nerve cells. If one parent develops the geneticists use different symbols than Mendel’s for alleles
symptoms, his or her children have a 50% probability of of genes. In human genotypes, all alleles are written in
suffering from the disease, provided they live suffi- uppercase. If the allele specifies a normally functioning
ciently long. Because symptoms are not present at birth gene product, the allele symbol has a superscript +. Alleles
and manifest themselves only later in life, Huntington that specify no gene product or abnormal gene products
disease is known as a late-onset genetic trait. sometimes have no superscript at all, as in the Fig. 1.19
How would you proceed in assigning genotypes to legend, but in other cases they have a superscript other than
the individuals in the Huntington disease pedigree de- + that signifies a particular type of abnormal allele. (See
picted in Fig. 1.19? First, you would need to find out if the Appendix Guidelines for Gene Nomenclature for
the disease-producing allele is dominant or recessive to further discussion of genetic notation.)
the normal allele. Several clues suggest that Huntington The gene that causes Huntington disease has been
disease is transmitted by a dominant allele of a single identified and studied at the molecular level. In fact, in
gene. Everyone who develops the disease has at least one 1988 this was the first human disease gene identified molec-
parent who shows the trait, and in several generations, ularly using methods that will be described in Chapter 12.
approximately half of the offspring are affected. The The protein product of the Huntington disease gene, called
pattern of affected individuals is thus vertical: If you Huntingtin or Htt, is needed for the proper physiology of
trace back through the ancestors of any a ffected individ- nerve cells, but the protein’s precise role in these cells is
ual, you would see at least one affected person in each not yet understood. The dominant disease allele (HD) spec-
generation, giving a continuous line of family members ifies a defective Htt protein that over time damages nerve
with the disease. When a disease is rare in the popula- cells (Fig. 1.20).
III
1 2 3 4 5 6 7 8 9
IV
1 2 3 4 5 6
HD+ Normal Htt protein
14
V
1 2 3 HD Abnormal Htt protein
1.3 Mendelian Inheritance in Humans 17
The disease allele is dominant to the normal allele Figure 1.21 Cystic fibrosis: A recessive condition. In (a),
because the presence of the normal Htt protein in hete- the two affected individuals (VI-4 and VII-1) are CF CF; that is,
homozygotes for the recessive disease allele. Their unaffected
rozygotes does not prevent the abnormal protein from
parents must be carriers, so V-1, V-2, VI-1, and VI-2 must all be
damaging the cells. It is important to note that this expla- CF CF +. Individuals II-2, II-3, III-2, III-4, IV-2, and IV-4 are probably
nation for the Huntington disease allele is only one of also carriers. We cannot determine which of the founders (I-1 or I-2)
many different molecular mechanisms that may result in was a carrier, so we designate their genotypes as CF +–. Because
a disease allele that is dominant to the normal allele of a the CF allele is relatively rare, it is likely that II-1, II-4, III-1, III-3, IV-1,
and IV-3 are CF +CF + homozygotes. The genotype of the remaining
particular gene.
unaffected people (VI-3, VI-5, and VII-2) is uncertain (CF +–). (b and
No effective treatment yet exists for Huntington c) These two families demonstrate horizontal patterns of inheritance.
disease, and because of its late onset, there was until Without further information, the unaffected children in each
the 1980s no way for children of a Huntington parent to pedigree must be regarded as having a CF +– genotype.
know before middle age—usually until well after their (a) I
own childbearing years—whether they carried the 1 2
TABLE 1.2 How to Recognize Dominant In Fig. 1.21a, a mating between the unrelated carriers
and Recessive Traits in Pedigrees VI-1 and VI-2 produced a child with cystic fibrosis. How
likely is such a marriage between unrelated carriers for a
Dominant Traits
recessive genetic condition? The answer depends on the
1. Affected children always have at least one affected parent. gene in question and the particular population into which
2. Dominant traits show a vertical pattern of inheritance: The a person is born. As Table 1.1 shows, the incidence of
trait shows up in every generation. genetic diseases (and thus the frequency of their carriers)
3. Two affected parents can produce unaffected children, if varies markedly among populations. Such variation re-
both parents are heterozygotes. flects the distinct genetic histories of different groups.
Recessive Traits The area of genetics that analyzes differences among
groups of individuals is called population genetics, a sub-
1. Affected individuals can be the children of two unaffected
carriers, particularly as a result of consanguineous matings.
ject we cover in Chapter 24. Notice that in Fig. 1.21a,
several unrelated, unaffected people, such as II-1 and II-4,
2. All the children of two affected parents should be affected.
married into the family under consideration. Although it
3. Rare recessive traits show a horizontal pattern of is highly probable that these individuals are homozygotes
inheritance: The trait first appears in one or more members
of one generation and is not seen in earlier generations.
for the normal allele of the gene (CF+CF+), a small chance
(whose magnitude depends on the frequency of the dis-
4. Recessive traits may show a vertical pattern of inheritance
if the trait is extremely common in the population.
ease allele in the population) exists that any one of them
could be a carrier of a CF disease allele.
Genetic researchers identified the cystic fibrosis gene
caption. Note that for several individuals, such as the in 1989, soon after the Huntington disease gene was iden-
generation I individuals in part (a) of the figure, it is tified. The normal, dominant CF+ allele makes a protein
impossible to assign a full genotype. We know that one called cystic fibrosis transmembrane conductance regula-
of these people must be the carrier who supplied the tor (CFTR). CFTR protein forms a channel in the cell
original CF allele, but we do not know if it was the male membranes that controls the flow of chloride ions through
or the female. As with an ambiguous dominant pheno- lung cells. Recessive CF disease alleles either produce no
type in peas, the unknown second allele is indicated by CFTR or produce nonfunctional or less functional ver-
a dash (–). sions of the protein (Fig. 1.22). Because of osmosis, water
Figure 1.22 Why the cystic fibrosis disease allele is recessive. The CFTR protein regulates the passage of chloride ions (green
spheres) through the cell membrane. Homozygotes for a cystic fibrosis disease allele (CF CF) have the disease because recessive disease
alleles either specify no CFTR protein as shown, or encode abnormal CFTR proteins that do not function at all or function less well than the
normal protein (not shown). Disease alleles (CF) are recessive because CF CF+ heterozygotes produce sufficient CFTR from the normal (CF+)
allele for normal lung function.
CF + CF + or CF CF + CF CF
Mucus
Lipid bilayer of
cell membrane
Inside of the cell
Inside of the cell CFTR protein
Cl– ions
flows into lung cells without CFTR, while a thick, dehy- recently led to effective treatments for the disease in pa-
drated mucus builds up outside the cells. Thus, CF CF tients with particular mutant alleles. For example, in
homozygotes have no (or not enough) functional CFTR 2015 the U.S. Food and Drug Administration approved a
and exhibit cystic fibrosis. Physicians have tried to drug cocktail called Orkambi® that helps the particular
ameliorate the disease’s debilitating symptoms with gene defective form of CFTR specified by one of these alleles
therapy (insertion of a normal CF+ gene into lung cells of to function properly. Varied approaches to the treatment
patients), but so far without success. of cystic fibrosis and other inherited diseases will be dis-
Despite the failure to date of gene therapy, identifi- cussed later in the book.
cation of the gene responsible for cystic fibrosis has
S O LV E D P R O B L E M S
Solving Genetics Problems clearly between the upper- and lowercases of letters,
The best way to evaluate and increase your understanding such as C(c) or S(s).
of the material in the chapter is to apply your knowledge in c. Now, reassess the question and work toward the solu-
solving genetics problems. Genetics word problems are like tion using the information given. Make sure you
puzzles. Take them in slowly—don’t be overwhelmed by answer the question being asked!
the whole problem. Identify useful facts given in the prob- d. When you finish the problem, check to see that the
lem, and use the facts to deduce additional information. Use answer makes sense. You can often check solutions
genetic principles and logic to work toward the solutions. by working backward; that is, see if you can recon-
The more problems you do, the easier they become. struct the data from your answer.
Solving genetics problems requires much more than e. After you have completed a question and checked your
simply plugging numbers into formulas. Each problem is answer, spend a minute to think about which major
unique and requires thoughtful evaluation of the informa- concepts were involved in the solution. This step is
tion given and the question being asked. The following are crucial for improving your understanding of genetics.
general guidelines you can follow in approaching these
word problems: For each chapter, the logic involved in solving one or more
problems is described in detail.
a. Read through the problem once to get some sense of
the concepts involved.
b. Go back through the problem, noting all the geno- Solved Problem I
types and phenotypes supplied to you or otherwise In cats, white patches are caused by the dominant allele P,
implied. Represent the known information in a sym- while pp individuals are solid-colored. Short hair is caused by
bolic format—assign symbols for alleles; use these a dominant allele S, while ss cats have long hair. A long-haired
symbols to indicate genotypes; make a diagram of the cat with patches whose mother was solid-colored and short-
crosses. Be sure you do not assign different letters of haired mates with a short-haired, solid-colored cat whose
the alphabet to two alleles of the same gene, as this mother was long-haired and solid-colored. What kinds of
can cause confusion. Also, be careful to discriminate kittens can arise from this mating, and in what proportions?
20 Chapter 1 Mendel’s Principles of Heredity
What genotypes can you assign? Any cat showing a reces- Answer
sive phenotype must be homozygous for the recessive This problem requires an understanding of independent as-
allele. Therefore, the long-haired cats are ss; solid cats sortment in a dihybrid cross, as well as the ratios predicted
are pp. Cat 1 is long-haired, so it must be homozygous for from monohybrid crosses.
the recessive allele (ss). This cat has the dominant pheno- Designate the alleles:
type of patches and could be either PP or Pp, but because
the mother was pp and could only contribute a p allele in R = red, r = yellow
her gametes, Cat 1 must be Pp. Cat 1’s full genotype is Pp ss. P = purple stems, p = green stems
Similarly, Cat 2 is solid-colored, so it must be homozygous
for the recessive allele (pp). Because this cat is short- In genetics problems, the ratios of offspring can indicate
haired, it could have either the SS or Ss genotype. Its mother the genotype of parents. You will usually need to total the
was long-haired (ss) and could only contribute an s allele in number of progeny and approximate the ratio of offspring
her gamete, so Cat 2 must be heterozygous Ss. The full in each of the different classes. For this problem, in which
genotype is pp Ss. the inheritance of two traits is given, consider each trait
The cross is therefore between Pp ss (Cat 1) and pp Ss independently. For red fruit, there are 305 + 328 = 633
(Cat 2). To determine the types of kittens, first establish the red-fruited plants out of a total of 840 plants. This value
types of gametes that can be produced by each cat and then (633/840) is close to 3/4. About 1/4 of the plants have yel-
set up a Punnett square to determine the genotypes of the low fruit (110 + 97 = 207/840). From Mendel’s work,
offspring. Cat 1 (Pp ss) produces Ps and ps gametes in you know that a 3:1 phenotypic ratio results from crosses
equal proportions. Cat 2 (pp Ss) produces pS and ps gam- between plants that are heterozygous for one gene. There-
etes in equal proportions. Four types of kittens can result fore, the genotype for fruit color of each parent must have
from this mating with equal probability: Pp Ss (patches, been Rr.
short-haired), Pp ss (patches, long-haired), pp Ss (solid, For stem color, 305 + 110 or 415/840 plants had pur-
short-haired), and pp ss (solid, long-haired). ple stems. About half had purple stems, and the other half
(328 + 97) had green stems. A 1:1 phenotypic ratio occurs
Cat 1 when a heterozygote is mated to a homozygous recessive
Ps ps (as in a testcross). The parents’ genotypes must have been
Pp and pp for stem color.
pS Pp Ss pp Ss The complete genotype of the parent plants in this
cross was Rr Pp × Rr pp.
Cat 2
Solved Problem III
ps Pp ss pp ss
Tay–Sachs is a recessive lethal disease in which neurologi-
cal deterioration occurs early in life. This disease is rare in
The following table demonstrates that you could also work the population overall but is found at relatively high fre-
through this problem using the product rule of probability quency in Ashkenazi Jews from Eastern Europe. A woman
instead of a Punnett square. The principles are the same: whose maternal uncle had the disease is trying to deter-
Gametes produced in equal amounts by either parent are mine the probability that she and her husband could have
combined at random. an affected child. Her father does not come from a high-
risk population. Her husband’s sister died of the disease at
Cat 1 Cat 2 an early age.
gamete gamete Progeny
a. Draw the pedigree of the individuals described.
1/2 P s × 1/2 p S 1/4 Pp Ss patches, short-haired Include the genotypes where possible.
1/2 P s × 1/2 p s 1/4 Pp ss patches, long-haired
1/2 p s × 1/2 p S 1/4 pp Ss solid-colored, short-haired b. Determine the probability that the couple’s first child
1/2 p s × 1/2 p s 1/4 pp ss solid-colored, long-haired will be affected.
Problems 21
PROBLEMS
a. How do you know that only a single gene is respon- c. A man with a chin dimple and a nondimpled woman
sible for the color differences between these snakes? produce eight children, all having the chin dimple.
b. Which of these colors is controlled by a dominant Can you be certain of the man’s genotype? Why or
allele? why not? What genotype is most likely, and why?
c. A normal-colored female snake is involved in a 11. Some inbred strains of the weedy plant Arabidopsis
testcross. This cross produces 10 normal-colored thaliana flower early in the growing season, but other
and 11 albino offspring. What are the genotypes of strains flower at later times. Four different Arabdiposis
the parents and the offspring? plants (1–4) were crossed, and the resulting progeny
were tabulated as follows:
5. Two short-haired cats mate and produce six short-
haired and two long-haired kittens. What does this in- Mating Progeny
formation suggest about how hair length is inherited? 1×2 77 late : 81 early
6. Some humans exhibit piebald spotting: patches of skin 1×3 134 late
that lack pigmentation. The condition results from the 1×4 93 late : 32 early
inability of p igment-producing cells to migrate prop- 2×3 111 late
erly during development. Two adults with piebald spot- 2×4 65 late : 61 early
ting have one child who has this characteristic and a 3×4 126 late
second child with normal skin pigmentation.
a. Explain the genetic basis for the difference in flow-
a. Is piebald spotting dominant or recessive? What
ering time. How do you know that among this
information led you to this answer?
group of plants, the flowering time trait is influ-
b. What are the genotypes of the parents? enced by the action of a single gene? Which allele
7. Flies with short wings are homozygous for a recessive is dominant and which recessive?
allele of the wing-length gene. You have a fly that has b. Ascribe genotypes to the four plants.
normal wings (dominant phenotype). You need to c. What kinds of progeny would you expect if you al-
know if this fly with normal wings is pure-breeding lowed plants 1–4 to self-fertilize, and in what ratios?
or heterozygous for the wing-length trait. What cross
would you do to determine the genotype, and what re- 12. Among Native Americans, two types of earwax (ceru-
sults would you expect for each possible genotype? men) are seen: dry and sticky. A geneticist studied the
inheritance of this trait by observing the types of off-
8. A mutant cucumber plant has flowers that fail to open spring produced by different kinds of matings. He ob-
when mature. Crosses can be done with this plant by served the following numbers:
manually opening and pollinating the flowers with
pollen from another plant. When closed × open Offspring
crosses were done, all the F1 progeny were open. The Parents Number of mating pairs Sticky Dry
F2 plants were 145 open and 59 closed. A cross of Sticky × sticky 10 32 6
closed × F1 gave 81 open and 77 closed. How is the Sticky × dry 8 21 9
closed characteristic inherited? What evidence led Dry × dry 12 0 42
you to your conclusion?
9. In a particular population of mice, certain individuals dis- a. How is earwax type inherited?
play a phenotype called short tail, which is inherited as a b. Why are no 3:1 or 1:1 ratios present in the data
dominant characteristic. Some individuals display a reces- shown?
sive characteristic called dilute, which affects coat color.
Which of these phenotypes would be easier to eliminate 13. Imagine you have purchased a black stallion of un-
from the population by selective breeding? Why? known genotype. You mate him to a red mare, and
she delivers twin foals, one red and one black. Can
10. In humans, a dimple in the chin is a dominant charac- you tell from these results how color is inherited, as-
teristic controlled by a single gene. suming that alternative alleles of a single gene are in-
a. A man who does not have a chin dimple has volved? What crosses could you do to determine how
children with a woman with a chin dimple whose color is inherited?
mother lacked the dimple. What proportion of their 14. If you roll a die (singular of dice), what is the prob-
children would be expected to have a chin dimple? ability you will roll: (a) a 6? (b) an even number?
b. A man with a chin dimple and a woman who lacks (c) a number divisible by 3? (d) If you roll a pair of
the dimple produce a child who lacks a dimple. dice, what is the probability that you will roll two
What is the man’s genotype? 6s? (e) an even number on one and an odd number
Problems 23
on the other? (f) matching numbers? (g) two num- b. If the twins are identical, what is the probability
bers both over 4? that both will be girls and have galactosemia?
15. In a standard deck of playing cards, four suits exist For parts (c–g), assume that no twins exist among the
(red suits = hearts and diamonds, black suits = children.
spades and clubs). Each suit has 13 cards: Ace (A), c. If Susan and her husband have four children, what
2, 3, 4, 5, 6, 7, 8, 9, 10, and the face cards Jack (J), is the probability that none of the four will have
Queen (Q), and King (K). galactosemia?
a. In a single draw, what is the probability that you d. If the couple has four children, what is the probabil-
will draw a face card? A red card? A red face card? ity that at least one child will have galactosemia?
b. Now you draw 4 cards, one at a time. After each e. If the couple has four children, what is the proba-
draw, you return the card to the deck. What is the bility that the first two will have galactosemia and
chance that all four cards you pick are face cards? the second two will not?
c. Suppose instead you draw 4 cards without return- f. If the couple has three children, what is the proba-
ing any to the deck between draws. What is the bility that two of the children will have galactose-
chance that they are all face cards? mia and one will not, regardless of order?
16. How many genetically different eggs could be formed g. If the couple has four children with galactosemia,
by women with the following genotypes? what is the probability that their next child will
have galactosemia?
a. Aa bb CC DD
21. Albinism is a condition in which pigmentation is
b. AA Bb Cc dd
lacking. In humans, the result is white hair, nonpig-
c. Aa Bb cc Dd mented skin, and pink eyes. The trait in humans is
d. Aa Bb Cc Dd caused by recessive alleles. Two normal parents
17. What is the probability of producing a child that will have an albino child. What are the parents’ genotypes?
phenotypically resemble either one of the two parents What is the probability that the next child will be
in the following four crosses? How many phenotypi- albino?
cally different kinds of progeny could potentially 22. A cross between two pea plants, both of which grew
result from each of the four crosses? from yellow round seeds, gave the following numbers
a. Aa Bb Cc Dd × aa bb cc dd of seeds: 156 yellow round and 54 yellow wrinkled.
b. aa bb cc dd × AA BB CC DD What are the genotypes of the parent plants? (Yellow
and round are dominant traits.)
c. Aa Bb Cc Dd × Aa Bb Cc Dd
d. aa bb cc dd × aa bb cc dd 23. A third-grader decided to breed guinea pigs for her
school science project. She went to a pet store and
18. A mouse sperm of genotype a B C D E fertilizes an bought a male with smooth black fur and a female
egg of genotype a b c D e. What are all the possibili- with rough white fur. She wanted to study the inheri-
ties for the genotypes of (a) the zygote and (b) a tance of those features and was sorry to see that the
sperm or egg produced by the mouse that develops first litter of eight contained only rough black animals.
from this fertilization? To her disappointment, the second litter from those
19. Your friend is pregnant with triplets. She thinks it same parents contained seven rough black animals.
is equally likely she will be the mother of 3 sons, Soon the first litter had begun to produce F2 offspring,
3 daughters, 2 sons and 1 daughter, or 1 son and and they showed a variety of coat types. Before long,
2 daughters. Is she correct? Explain. (Assume that the child had 125 F2 guinea pigs. Eight of them had
each of the triplets is from a separate fertilization, and smooth white coats, 25 had smooth black coats, 23
that boys and girls are equally likely.) were rough and white, and 69 were rough and black.
a. How are the coat color and texture characteristics
20. Galactosemia is a recessive human disease that is inherited? What evidence supports your
treatable by restricting lactose and glucose in the diet. conclusions?
Susan Smithers and her husband are both heterozy-
gous for the galactosemia gene. b. What phenotypes and proportions of offspring
should the girl expect if she mates one of the
a. Susan is pregnant with twins. If she has smooth white F2 females to an F1 male?
fraternal (nonidentical) twins, what is the
probability both of the twins will be girls who 24. The self-fertilization of an F1 pea plant produced from
have galactosemia? a parent plant homozygous for yellow and wrinkled
24 Chapter 1 Mendel’s Principles of Heredity
seeds and a parent homozygous for green and round Eye shape: recessive allele for narrow eyes n;
seeds resulted in a pod containing seven F2 peas. dominant allele for normal (oval) eyes N.
(Yellow and round are dominant.) What is the probabil- For each of the four following crosses, give the
ity that all seven peas in the pod are yellow and round? genotypes of each of the parents.
25. The achoo syndrome (sneezing in response to bright
Male Female
light) and trembling chin (triggered by anxiety) are
Wings Eyes Wings Eyes Offspring
both dominant traits in humans.
1 tiny oval × tiny oval 78 tiny wings, oval eyes
a. What is the probability that the first child of parents 24 tiny wings, narrow eyes
who are heterozygous for both the achoo gene and 2 normal narrow × tiny oval 45 normal wings, oval eyes
the trembling chin gene will have achoo syndrome 40 normal wings, narrow eyes
but lack a trembling chin? 38 tiny wings, oval eyes
44 tiny wings, narrow eyes
b. What is the probability that the first child will have
3 normal narrow × normal oval 35 normal wings, oval eyes
neither achoo syndrome nor trembling chin?
29 normal wings, narrow eyes
26. A pea plant from a pure-breeding strain that is tall, 10 tiny wings, oval eyes
has green pods, and has purple flowers that are termi- 11 tiny wings, narrow eyes
nal is crossed to a plant from a pure-breeding strain 4 normal narrow × normal oval 62 normal wings, oval eyes
that is dwarf, has yellow pods, and has white flowers 19 tiny wings, oval eyes
that are axial. The F1 plants are all tall and have pur-
ple axial flowers as well as green pods. 30. Based on the information you discovered in the previ-
a. What phenotypes do you expect to see in the F2? ous problem, answer the following:
b. What phenotypes and ratios would you predict in a. A female fruit fly with genotype Tt nn is mated to
the progeny from crossing an F1 plant to the dwarf a male of genotype Tt Nn. What is the probability
parent? that any one of their offspring will have normal
characteristics for both traits?
27. The following table shows the results of different
matings between jimsonweed plants that had either b. What phenotypes would you expect among the off-
purple or white flowers and spiny or smooth pods. spring of this cross? If you obtained 200 progeny, how
Determine the dominant allele for each of the two many of each phenotypic class would you expect?
traits and indicate the genotypes of the parents for 31. Considering the yellow and green pea color pheno-
each of the crosses. types studied by Gregor Mendel:
a. What is the biochemical function of the protein
Parents Offspring that is specified by the gene responsible for the
Purple White Purple White pea color phenotype?
spiny spiny smooth smooth b. A null allele of a gene is an allele that does not
a. purple spiny × purple spiny 94 32 28 11 specify any of the biochemical function that the
b. purple spiny × purple smooth 40 0 38 0 gene normally provides. Of the two alleles Y and y,
c. purple spiny × white spiny 34 30 0 0 which is more likely to be a null allele?
d. purple spiny × white spiny 89 92 31 27 c. In terms of the underlying biochemistry, why is the
e. purple smooth × purple smooth 0 0 36 11 Y allele dominant to the y allele?
f. white spiny × white spiny 0 45 0 16
d. Why are peas that are yy homozygotes green?
e. The amount of the protein specified by a gene is
28. A pea plant heterozygous for plant height, pod roughly proportional to the number of functional
shape, and flower color was selfed. The progeny copies of the gene carried by a cell or individual.
consisted of 272 tall, inflated pods, purple flowers; What do the phenotypes of YY homozygotes, Yy
92 tall, inflated, white flowers; 88 tall, flat pods, heterozygotes, and yy homozygotes tell us about
purple; 93 dwarf, inflated, purple; 35 tall, flat, white; the amount of the Sgr enzyme (the product of
31 dwarf, inflated, white; 29 dwarf, flat, purple; the pea color gene) needed to produce a yellow
11 dwarf, flat, white. Which alleles are dominant color?
in this cross?
f. The Sgr enzyme is not needed for the survival of a
29. In the fruit fly Drosophila melanogaster, the follow- pea plant, but the genomes of organisms contain
ing genes and alleles are known: many so-called essential genes needed for an indi-
Wing size: recessive allele for tiny wings t; dominant vidual’s survival. For such genes, heterozygotes for
allele for normal wings T. the normal allele and the null allele survive, but
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