Ch02 Slides v03

GENETIC
AN I NTE G RATE D APPR OAC H
A N A LY S I S
Chapter 2
Transmission Genetics
Slides adapted from lectures by

Lectures by Kathleen
Kathleen Fitzpatrick
Fitzpatrick
Simon Fraser University
Mark F. Sanders
John L. Bowman
Copyright 2012 Pearson Education Inc.
Overview
Phenotypic ratios are produced in offspring as a result of
chromosome segregation.
In heterozygotes, alleles generally segregate equally into
meiotic products.
Expected progeny ratios can be predicted when genotypes
of parents are known.
Likely parental genotypes can be inferred from phenotypes
of progeny.
In many organisms, sex chromosomes determine sex.
Sex-linked genes can show different phenotypic ratios in
male and female progeny.
Single-gene traits can be studied in pedigrees.
Organelle genes are usually inherited maternally.
Genetics Analysis: An Integrated Approach
The historical question

The basic principal that like tends to beget like
had been known for millennia.
Artificial selection had been practiced for ages in
domestic plants and animals to produce desired
characteristics.
Breeders could not explain inheritance of traits,
such as why traits would sometimes disappear and
then reappear in subsequent generations.
What is inherited?
How is it inherited?
What is the role of chance?
2.1 Gregor Mendel (1822-1884) discovered the

basic principles of genetic transmission
Theories of inheritance prior to Mendel

N. Hartsoiker (1694) proposed that males contribute
most features because he could see a little person
(homunculus) in sperm. This model was not widely
accepted.
Since offspring were frequently intermediate to
parents, theories of blending inheritance were
popular. These called for the hereditary material to
be some sort of fluid or humor that could be
blended.
Progress was stymied by reliance upon false or
anecdotal information, and a lack of rigorous
scientific methods.
Mendels experiments
The garden pea was an ideal organism
vigorous growth
easy to cross or self-fertilize
large number of offspring
Mendel analyzed characters with discrete alternative forms

Purple vs. white flowers*
Yellow vs. green seeds
Round vs. wrinkled seeds
Inflated vs. constricted pods
Green vs. yellow pods
Axial vs. terminal flowers
Long vs. short stem length
Mendel began by establishing pure-breeding lines

Pure-Breeding Strains to Begin Experimental

Crosses
Mendel took 2 years prior to beginning his
experiments to establish pure-breeding (or
true-breeding) strains
These are strains that consistently produce the
same phenotype
Each experiment began with crosses between
two pure-breeding parental generation plants
(P generation) that produced offspring called F1
(first filial generation)
8
Further Experimental Crosses

Pure-breeding parental plants, when crossed,
produce F1 that all have the same phenotype
F1 offspring that are crossed to one another
produce the next generation of offspring, the
second filial generation (F2)
These can be crossed to produce the third filial
generation (F3) and so on, as needed
9
10
Mendel performed controlled crosses

Controlled mating
obtain desired genotype
deduce genotypes of parents
Selfing: individual with both reproductive

organs mates with itself
symbol is used to indicate a cross
a haploid mating: A a
a diploid mating: A/a A/a
A/ : represents either A or a
Review of some definitions:

Alleles - alternative forms of a gene
Homozygous both alleles of a diploid locus are
the same
Heterozygous two alleles of a diploid locus are
different
Yellow vs. green peas
Monohybrid crosses reveal units of

inheritance and Law of Segregation
Mendelian inference
P1(green) P2(yellow)
F1 (yellow)
parental generation (P0)

(intercrossing)
first filial generation
F2 (3 yellow : 1 green)
second filial generation
(selfing or intercrossing)
The disappearance of green in the F1 and its reappearance in

the F2 means that yellow is dominant to green. Also, the
production of both types in the F2 means that the F1 must
have been heterozygous.
Law of Equal
Segregation:
The Punnett
Square
Meiotic segregation
In meiosis, each of the four haploid products
receives one of each kind of chromosome
A/A homozygotes
A/a heterozygotes
all get A chromosomes

half get A chromosomes
half get a chromosomes
As a consequence of chromosome segregation,

alleles of heterozygotes segregate equally
Meiotic chromosomes
segregate equally
2002 byW.
H. Freeman
Company
Copyright
2012
Pearson and
Education
Inc.
Diploid crosses
Three possible diploid genotypes
A/A a/a A/a
Six possible diploid crosses
Cross
A/A A/A
a/a a/a
A/A a/a
A/a A/A
A/a a/a
A/a A/a
Genotypic ratio
A/A
a/a
A/a
1A/A:1A/a
1A/a:1a/a
1A/A:2A/a:1a/a
Phenotypic ratio
all A
all a
all A
all A
1A:1a
3A:1a
Mendels Results: Predictions

and Probability
Can we predict how many offspring will
be YY in a Yy x Yy cross?

and Probability
Can we predict how many offspring will
be YY in a Yy x Yy cross?
Chance of Y sperm uniting with a Y egg
chance of sperm with Y allele
chance of egg with Y allele
Chance of Y and Y uniting = x =

and Probability
Can we predict how many offspring will be
Yy in a cross of Yy x Yy pea plants?

and Probability
Can we predict how many offspring will be
Yy in a cross of Yy x Yy pea plants?
Two ways to get Yy offspring:
1. Y sperm unites with y egg
OR
2. y sperm unites with Y egg
probability of Yy =
Diploid crosses
Crosses between individuals heterozygous for the
same single gene are called monohybrid crosses
A heterozygote for unexpressed recessive allele is
sometimes called a carrier, particularly in humans
A cross between an unknown genotype (e.g., A/)
and the homozygous recessive genotype (a/a) to
attempt to infer the unknown is called a testcross
Testcross
Distinguishes between A/A and A/a genotypes
mated to a/a based on phenotypes of offspring
if all progeny have dominant phenotype, then unknown
is A/A
if at least one offspring has recessive phenotype, then
unknown is A/a
If:
genotypic outcome phenotypic outcome
A/A a/a
A/a
all A
A/a a/a
1A/a:1a/a
1A:1a
Rules of probability
Multiply probabilities of independent events to obtain
probability of joint occurrence
What is the probability that both A and B will occur?
Solution = determine probability of each and multiply
them together.
Add probabilities of mutually exclusive events to obtain
the probability of either one or another event occurrence
What is the probability of A or B occurring?
Solution = determine the probability of each and add
them together.
Mendels Second Law
Law of
Independent
Assortment
315
101
108
32
Why alleles at
different loci
assort
independently
Parental and
recombinant
combinations
Independent assortment
(sometimes called independent segregation)
Consequence of independent alignment of

chromosomes in meiotic bivalents for genes on
different (nonhomologous) chromosomes
A/A ; B/B a/a ; b/b
A/a ; B/b
OR
A;B
A;b
a;B
a;b
Alternatebivalents
bivalants
Alternate
Independent assortment
For genes on different (nonhomologous) pairs of
chromosomes, recombinant frequency is 50%
A/A ; B/B a/a ; b/b
A/A ; b/b a/a ; B/B
A/a ; B/b
A/a ; B/b
A;B
A;b
a;B
a;b
A;B
50%
A;b
recombinants
a;B
a;b
Dihybrid testcross
Determines genotype of dihybrid by crossing
to homozygous recessive tester
Parental A/A ; b/b a/a ; B/B
F1
testcross
tester gametes
a;b
progeny
proportions
progeny
phenotypes
A ; B
A/a ; B/b
AB
A ; b
A/a ; b/b
Ab
a ; B
a/a ; B/b
aB
a ; b
a/a ; b/b
ab
F1 gametes
1:1:1:1
ratio
A/a ; B/b a/a ; b/b
Dihybrid testcross
Best way to study recombination is in a
dihybrid testcross
only dihybrid produces recombinant genotypes
all homozygous recessive tester gametes alike
Typical 1:1:1:1 ratio a result of independent

assortment in dihybrid
Each genotype in progeny has distinct
phenotype
Observed by Mendel in testcrosses with two
pairs of traits
Dihybrid selfing
Equivalent to cross between two A/a ; B/b dihybrids
recombination occurs in both members of cross
recombination frequency is 50%
A;B
A;b
a;B
a;b
A;B
A/A ; B/B
A/A ; B/b
A/a ; B/B
A/a ; B/b
A;b
A/A ; B/b
A/A ; b/b
A/a ; B/b
A/a ; b/b
a;B
A/a ; B/B
A/a ; B/b
a/a ; B/B
a/a ; B/b
a;b
A/a ; B/b
A/a ; b/b
a/a ; B/b
a/a ; b/b
Ratio:
9 A/ ; B/
3 A/ ; b/b
3 a/a ; B/
1 a/a ; b/b
Dihybrid selfing: corn kernels

9 Purple+Smooth
3 Purple+wrinkled
3 yellow+Smooth
1 yellow+wrinkled
Mendels laws are probabilistic

Mendels laws do not predict the outcome for any
single offspring, but provide the bases for probabilistic
expectations.
They are used to predict the likelihood of the

different outcomes (i.e., genotypes and
phenotypes after a cross).
They are used to make inferences of how many
genes underlie a trait and the dominance
relationships.
Why are some alleles dominant

over others?
Shape seed trait

R/- (round) vs. rr (wrinkled)
Gene R
Function: Starch branching
enzyme 1
Half of the amount of enzyme is
enough to branch enough starch
to provide enough tension to
keep seed shape round
Mutation: Insertion of an 0.8 kb
transposable element
Autosomes and sex chromosomes

Sex chromosomes determine sex in most
animals and some plants
usually only one pair
one sex has two alike (e.g., XX)
one sex has two different types (e.g., XY)
Remaining chromosomes are called

autosomes
X chromosomes and autosomes contain
numerous genes
Y chromosomes typically have few genes
Autosomes and sex chromosomes
The duck-billed platypus has

weird sex chromosomes too
Human sex chromosomes

44A XX is female, homogametic (two X gametes)
44A XY is male, heterogametic (X and Y gametes)
Segregate equally into gametes at meiosis
Sperm
Gametes
Eggs
50% X
50% Y
50% X
XX
XY
50% X
XX
XY
Sex chromosomes differences
X-linked inheritance
Male inherits Y from father and X from mother
Female inherits one X from father and one X
from mother
In most mammals, including humans
Y chromosome has very few genes, but one
important gene is SRY (sex determining region of
the Y)
X chromosome has no corresponding loci on Y
Males express all recessive genes on X
chromosome (said to be hemizygous)
X-linked inheritance
Females: 3 possible X-linked genotypes
XAXA
XAXa
XaXa
Males: 2 possible X-linked genotypes

XAY
XaY
An XAXa XAY mating yields a 3A:1a phenotypic ratio, but the

recessive phenotype is restricted to 50% of male offspring.
Eggs
Gametes
50% XA
50% Xa
Sperm
50% XA
50% Y
XAXA
XAY
XAXa
XaY
Drosophila X-linked inheritance
Drosophila X-linked inheritance
Pedigree analysis
Pedigree analysis
Analysis of inheritance in families

Allows inferences concerning mode of inheritance (MOI),
unknown genotypes, and predictions concerning
phenotypes of future offspring
Usually too few offspring to observe meaningful departures
from Mendelian ratios
male
Pedigree
symbol
conventions
Learn them!
number of offspring
of indicated sexes
female
affected
sex unspecified
carriers of autosomal
recessive
mating
carrier of sex-linked
recessive
consanguineous mating
death
proband
miscarriage or stillbirth,
sex unspecified
dizygotic twins
monozygotic twins
I
1
II
1
convention for identifying individuals;

offspring listed in birth order; here, the 3rd
individual in generation II, or II-3, is affected
Single-locus MOIs
Autosomal recessive
e.g. PKU, Tay-Sachs, albinism
Autosomal dominant
e.g. Huntington disease
X-linked recessive
e.g. color-blindness, hemophilia
X-linked dominant
e.g. hypophosphatemia
Y-linked
e.g. hairy pinnae
Organellar
Autosomal dominant inheritance
Key characteristics:
Affected individuals have at least one affected parent
Two affected parents may produce unaffected children
No sex bias in affected status or allele transmission
53

Displays an unbroken or
vertical pattern of inheritance
in that every affected
individual has at least one
affected parent.
Achondroplasia
Autosomal is indicated by the lack of

clear sex-dependent transmission.

Displays an unbroken or
vertical pattern of inheritance
in that every affected
individual has at least one
affected parent.
Achondroplasia
Autosomal is indicated by the lack of

clear sex-dependent transmission.
Autosomal recessive inheritance
Key features:
Affected individuals often born to unaffected parents
If both parents are affected, all offspring will be affected
No sex bias in affected status or allele transmission
For rare traits, consanguinity is common
56

Albinism
Connie Chiu (photo: Thomas Paquet)
Consanguinity is typical for unaffected parents of individuals with

rare autosomal recessive traits.

Albinism
Connie Chiu (photo: Thomas Paquet)
X-linked recessive inheritance

More common in males
Affected individuals in a pedigree
will be related matrilineally
X-linked Hemophilia
X-linked recessive inheritance

More common in males
Affected individuals in a pedigree
will be related matrilineally
X-linked Hemophilia
X-linked dominant inheritance
Congenital
hypertrichosis
All daughters (but no sons) of affected males are affected

Offspring (either sex) of affected females may be either affected
or unaffected
X-linked dominant inheritance

All daughters (but no
sons) of affected males
are affected
Offspring (either sex)
of affected females may
be either affected or
unaffected
What is the mode of inheritance?
Conclusions:
mode of inheritance:
parents genotypes:
unaffected siblings probability of being carriers:
probability of next offspring being affected:
Conclusions:
mode of inheritance:
parents genotypes:
unaffected siblings probability of being carriers:
probability of next offspring being affected:
Conditional Probability
The conditional probability of an event A is the
probability that the event will occur given the
knowledge that an event B has already occurred.
P(A|B)=P(A and B)/P(B)
If your question is conditioned to a particular
subset of genotypes, you must account for that
when reporting the probability
In the cross of Yy x Yy pea plants, what is the
probability of an offspring being homozygous
dominant (YY) given that it is yellow?
P(YY|yellow)=P(YY and yellow)/P(yellow)
P(YY|yellow)=P(YY and yellow)/P(yellow)
= 0.25 / 0.75 = 1/3
Problem 1
What is the probability that the

offspring in question will have
the trait?
?
Chapter 5: Single-gene Inheritance
2002 by W. H. Freeman and Company
Problem 1

the trait?
?
The trait appears to be autosomal recessive and is assumed to

be rare.
Problem 1

the trait?
?

be rare.
What is the probability that the highlighted individual
expressing the dominant phenotype is a carrier of the
recessive allele?
Problem 1

the trait?
?

be rare.
What is the probability that the highlighted individual
expressing the dominant phenotype is a carrier of the
recessive allele?
P(Mm|M_)=P(Mm and M_)/P(M_)
P(Mm|M_)=0.50/0.75=2/3
Problem 1

the trait?
?

be rare. The probability that each grandmother is
heterozygous is 2/3; the probability that each parent of the
offspring is heterozygous is 2/3 x 1/2. If each is heterozygous,
the probability of an afflicted child is 1/4. Therefore, using the
product rule, the probability that the child will be afflicted is
2/3 x 1/2 x 2/3 x 1/2 x 1/4 = 1/36

Problem 2
This pedigree is for a mild and rare hereditary
disorder of the skin
Consider the parents
III-4 and III-5. What
was the probability of
having four
unaffected children
before they actually
had them?
Problem 2
having four
unaffected children
had them?
D+D D+D+
D+D+ D+D+ D+D+ D+D+
Problem 2
having four
unaffected children
had them?
D+D D+D+
Assuming autosomal
dominant...
D+D+ D+D+ D+D+ D+D+
p(4 unaffected children) = 1/2 x 1/2 x 1/2 x 1/2 = 0.063

Problem 3
What is the mode of inheritance of
this rare trait?
Problem 3
What is the mode of inheritance of
this rare trait?
Autosomal dominant
Problem 4
What is the probability of obtaining the genotype
A/-; B/-; C/-; D/- in the offspring of this cross?
P1 A/a ; B/b ; C/c ; D/d P2 a/a ; B/b ; C/c ; D/D
Independent assortment: multiple loci

Calculations can be made for any gene combination using
predicted outcomes at single loci and the product rule
P1 A/a ; B/b ; C/c ; D/d P2 a/a ; B/b ; C/c ; D/D

# gametes P1
# gametes P2
# genotypes in F1
# phenotypes in F1
2 x 2 x 2 x 2 = 16
1x2x2x1=4
2 x 3 x 3 x 2 = 36
2x2x2x1=8
Frequency of
x x x 1 = 9/32
A/ ; B/ ; C/ ; D/
Deducing genotypes from ratios

Genetic analysis works in two directions
predict genotypes in offspring
determine genotypes of parents in cross
Specific expectations, e.g., 1:1:1:1 and 9:3:3:1 can

be used to deduce genotypes
Testcross example:
Phenotype
A/ ; B/
A/ ; b/b
a/a ; B/
a/a ; b/b
# observed
310
295
305
290
The observed results are

close to 1:1:1:1, allowing the
deduction that the tested
genotype was a dihybrid.
Problem 5
Consider a hypothetical mating between two browneyed individuals heterozygous for the recessive
blue-eye allele (Bb). If the pair has five offspring,
what is the probability that two of them will have blue
eyes?
To answer this and similar questions, we will use the binomial

expansion equation:
(n)!
i ni
Pi
pq
i!(n i)!
n = total number of events (e.g. total # of offspring)
i = number of events in one category (e.g. # affected)
p = individual probability of event I (e.g. 0.25)
probability of the other category (= 1I = 0.75)
q = individual
(The symbol ! denotes factorial: 5! = 1x2x3x4x5 = 120)
This equation represents all of the possibilities for a given set

of unordered events.
Bd x Bd
3 B_: 1 bb
n = total number of events = 5
i = number of events in one category = 2 (blue eyes)
p = individual probability of event I = 0.25
q = individual probability of the other category = 0.75
Binomial expansion equation
(n)!
(5)!
i ni
2
52
Pi
pq
0.25 0.75 0.26
i!(n i)!
2!(5 2)!
Binomial Probability
Some questions involve predicting the likelihood of
a series of events (for which there are two
outcomes each time)
We use binomial probability calculations to
answer this type of question
It expands the binomial expression to reflect the
number of outcome combinations and the
probability of each
86
Construction of a Binomial Expansion

Formula
A binomial expansion contains two variables; p, the
frequency of one outcome, and q, the frequency of the
alternative outcome (p and q may or may not be equal,
depending on the type of outcome)
(p q) 1, since these are the only two outcomes
We expand the equation by the power of n, where
n the number of successive events: (p q)n
87
Binomial Expansion Formula Example

For families with three children, predict the proportions
with each possible combination of boys and girls
p probability of a boy ; q probability of
a girl
Binomial expansion: (p + q)3 p3 3p2q 3pq2 q3
p3 1/8 (3 boys); 3p2q 3/8 (2 boys, 1 girl); 3pq2 3/8
(1 boy, 2 girls); q3 1/8 (3 girls)
88
Application of Binomial Expansion to

Progeny Phenotypes
In a self-fertilized Gg pea plant, give the proportion of
yellow and green peas in pods with six peas each
p probability of yellow peas 3/4; q probability of
green peas
A shortcut to the binomial expansion is Pascals
triangle, which is easy to calculate
89
90
91
2.5 Chi-Square Analysis Tests the Fit Between

Observed and Expected Outcomes
Scientists must be able to make comparisons of
observed and expected results to objectively
determine whether results are consistent with
expectations
The chi-square test was developed to allow for these
objective comparisons
92
The Chi-Square Analysis

The 2 test (chi-square) is often used to quantify how
closely a set of experimental observations matches the
expected outcome
2 = (O E)2/E
O = observed values
E = expected values based on some predictive model
93
Interpreting the Chi-Square Analysis

The interpretation of the 2 values is done by means of
a probability (P) value
It is an estimate of the probability of obtaining results

that deviate as much or more from the expected
results by chance
94
Degrees of Freedom
The relationship between P value and 2 values for an
experiment depends upon the number of degrees of
freedom (df) i.e. the number of independent
variables
The df value is the number of mutually exclusive
outcome classes, n, minus 1;
The chi-square table includes values for different
degrees of freedom and the corresponding P values
95
96
Statistical Significance
A statistically significant result from 2 analysis is one
for which the P value is less than 0.05
When any experimental result has less than 5%

probability, the hypothesis of chance is rejected
P values above 5% indicate a nonsignificant deviation
between observed and expected results
This results in failure to reject the hypothesis of chance
97
Chi-Square Analysis of Mendels Data

Modern statistical methods allow us to test
Mendels experimental data for compatibility with
his laws
From statistical analysis of his data, we can
conclude that the results are consistent with the
predictions
98
Monohybrid Cross Example

For round vs. wrinkled seeds, Mendel observed 5475
round and 1850 wrinkled from his monohybrid cross
(Rr Rr), for a total of 7324 seeds
The expected values: (7324)(3/4) 5493 round (R-),
and (7324)(1/4) 1831 wrinkled (rr)
2 (5474 5493)2/5493 (1850 1831)2/1831
0.263
For df 1, the P value falls between 0.50 and 0.70,
well above the 0.05 cutoff value
99
100
2.6 Autosomal Inheritance and Molecular

Genetics Parallel the Predictions of
Mendels Hereditary Predictions
In the early 1900s biologists began to extend Mendels
findings to other organisms
They also began to identify exceptions to the
hereditary principles
Mendelian principles can be applied to transmission of
certain traits in humans
101
Molecular Genetics of Mendels Traits

A cornerstone of modern genetics is the integration of
the principles of transmission genetics with those of
molecular genetic analysis
Transmission of alleles is equated with transmission
of variable DNA sequences that act through mRNA to
produce proteins responsible for phenotypes
102
103
Central Conclusions from Molecular Studies

of Mendels Traits
1. Inheritance of alleles precisely parallels the pattern
of transmission of morphological variants
2. Morphologic variation results from differences in
structure and function of protein products of the
alleles
3. Molecular analysis led to identification of DNA
sequence differences between alleles, and their
consequences
4. Functional analysis of the protein products of each
allele led to understanding of its function in
producing the phenotype
104

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GENETIC

AN I NTE G RATE D APPR OAC H

Slides adapted from lectures by

Copyright 2012 Pearson Education Inc.

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

The historical question

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

2.1 Gregor Mendel (1822-1884) discovered the

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Theories of inheritance prior to Mendel

Copyright 2012 Pearson Education Inc.

Mendel analyzed characters with discrete alternative forms

Mendel began by establishing pure-breeding lines

Copyright 2012 Pearson Education Inc.

Pure-Breeding Strains to Begin Experimental

Copyright 2012 Pearson Education Inc.

Further Experimental Crosses

Copyright 2012 Pearson Education Inc.

Copyright 2012 Pearson Education Inc.

Mendel performed controlled crosses

Selfing: individual with both reproductive

Copyright 2012 Pearson Education Inc.

Review of some definitions:

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Yellow vs. green peas

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Monohybrid crosses reveal units of

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

parental generation (P0)

second filial generation

The disappearance of green in the F1 and its reappearance in

Copyright 2012 Pearson Education Inc.

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

all get A chromosomes

As a consequence of chromosome segregation,

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Genetics Analysis: An Integrated Approach

Mendels Results: Predictions

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Mendels Results: Predictions

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Mendels Results: Predictions

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Mendels Results: Predictions

Copyright 2012 Pearson Education Inc.

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

genotypic outcome phenotypic outcome

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Genetics Analysis: An Integrated Approach