Extensions of Mendelian Genetics

Dr. E. Hannig
BIOL3301_Sept. 2014

Ratio Review
3:1 Phenotypic Ratio, Monohybrid cross
WW x ww

Ww

F1 (100% express dominant phenotype)

self
WW
Ww
Ww
ww

F2 (3:1 phenotypic ratio)

F2: 2 phenotypes, 3 genotypes

o Self the F2 round seeds.1/3 true-breeding, 2/3 yield round and wrinkled in
3:1 ratio
o Self F2 wrinkle seeds.all are true-breeding for the recessive phenotype
Therefore, the 3:1 phenotypic ratio masks an underlying 1:2:1 genotypic ratio, where
the 2/4 represents the heterozygous genotype
That said, for some traits, the F2 may show a 1:2:1 phenotypic ratio if the heterozygotes
show a different phenotype from the homozygous dominant and homozygous recessive
phenotypes.

In this case, the R allele

is said to be incompletely
dominant.

9:3:3:1 ratio is characteristic of a dihybrid cross involving two independently-assorting

genes that determine discernable traits (e.g., seed color and seed shape, etc.)

RRYY x rryy

RrYy

9/16 round, yellow

3/16 round, green
3/16 wrinkled, yellow
1/16 wrinkled, green

P [R round and Y yellow are dominant]

F1

F2

The F2 generation (from selfing the F1s):

Gene Interaction Leads to Modified Dihybrid Ratios

What if, in a dihybrid cross, the two genes interact with each other in determining a
single phenotype (e.g., flower color or seed shape)??
http://www.nature.com/scitable/topicpage/epistasis-gene-interaction-and-phenotype-effects-460

Examples of Dihybrid (Digenic) Ratios

Ratio
Description
9:3:3:1

9:4:3

9:7

12:3:1

15:1

13:3

9:6:1

7:6:3

3:6:3:4

11:5

Name(s) of Relationship
(Used by Some Authors)
Complete dominance at both gene pairs; new Not named because the ratio
phenotypes result from interaction between looks like independent
dominant alleles, as well as from interaction assortment
between both homozygous recessives
Complete dominance at both gene pairs;
Recessive epistasis
however, when one gene is homozygous
recessive, it hides the phenotype of the other
gene
Complete dominance at both gene pairs;
Duplicate recessive epistasis
however, when either gene is homozygous
recessive, it hides the effect of the other gene
Complete dominance at both gene pairs;
Dominant epistasis
however, when one gene is dominant, it
hides the phenotype of the other gene
Complete dominance at both gene pairs;
Duplicate dominant epistasis
however, when either gene is dominant, it
hides the effects of the other gene
Complete dominance at both gene pairs;
Dominant and recessive
however, when either gene is dominant, it
epistasis
hides the effects of the other gene
Complete dominance at both gene pairs;
Duplicate interaction
however, when either gene is dominant, it
hides the effects of the other gene
Complete dominance at one gene pair and
No name
partial dominance at the other; when
homozygous recessive, the first gene is
epistatic to the second gene
Complete dominance at one gene pair and
No name
partial dominance at the other; when
homozygous recessive, either gene hides the
effects of the other gene; when both genes
are homozygous recessive, the second gene
hides the effects of the first
Complete dominance for both gene pairs
No name
only if both kinds of dominant alleles are
present; otherwise, the recessive phenotype
appears

Interacting Genes in the Same Pathway

Experiment:
Isolate mutants (screen/selection)

Is the mutation dominant or recessive? [here, we want recessive]

Does the mutant strain contain only one mutation relevant to the phenotype
screened/selected for? [here, the answer must be yes]

Construct strains true-breeding for the phenotype

Cross (mate) true-breeding mutants with each other [e.g., true-breeding mutant #1 x truebreeding mutant #2]

What is the phenotype of the progeny??

This is the standard way of doing complementation testing to determine if two mutants
harbor mutations in the same or in different genes.

Example I. Complementation (Complementary Gene Action)

o Complementary Gene Action yields a 9:7 modified dihybrid ratio
o If two true-breeding white-flowered plants (the mutant, recessive phenotype),
when crossed with each other, yield blue flowered plants (the wild-type, dominant
phenotype) in the F1, the mutations in each of the plant are said to complement
each otherthe implication here is that the mutations in the two whiteflowered plants lie in different genes.
o OTOH, if the cross of two true-breeding white-flowered plants yields whiteflowered F1s, the mutations fail to complement each other..the implication is
that the mutations in the two white-flowered plants lie within the same gene.

Lets call the w1 gene from above gene C, and the w2 gene above well call gene P in the
example below. They are different genes.
Thus, a CCpp (white) x ccPP (white) cross will yield CcPp dihybrid F1 progeny.
Because the mutants complement each other, they exhibit complementary gene action in
determining flower color.
That is, :

blue
Now lets self the F1 blue-flowered (due to anthocyanin production) plants.
In this case, the F1 genotype is CcPp, so the cross is CcPp x CcPp [you will recognize
this as a dihybrid cross; unlike the prior dihybrid crosses we discussed, this one
involves two genes that determine the SAME phenotype]
Analysis of the F2:
Genotype
Flower Color

Enzyme Activities

9 C_P_

Flowers colored;
anthocyanin produced

Functional enzymes from both genes

3 C_pp

Flowers white;
no anthocyanin produced

p enzyme non-functional

3 ccP_

Flowers white;
no anthocyanin produced

c enzyme non-functional

1 ccpp

Flowers white;
no anthocyanin produced

c and p enzymes non-functional

Phenotypically, this gives a 9:7 ratio (pigment : no pigment)this is an example of a

modified dihybrid ratio [modified from 9:3:3:1]

CP
Cp
Male
Gametes cP
cp

Female Gametes
CP
Cp
CCPP
CCPp
CCPp
CCpp
CcPP
CcPp
CcPp
Ccpp

cP
CcPP
CcPp
ccPP
ccPp

cp
CcPp
Ccpp
ccPp
ccpp

Modifications of the 9:3:3:1 dihybrid ratio is indicative of two genes

involved in determining a single phenotype!
Lets consider other examples..

Duplicate Genes
o Instead of two genes
acting sequentially in a
pathway, what if two
genes act at the same step
in a pathway such that
either alone is sufficient
to complete the pathway?
o Kernel color in wheat is a
good example [purple vs
non-purple]
here, either gene A or
gene B is sufficient
The cross: Purple x non-purple, both true-breeding
(P)
F1
F2
AABB (purple) x aabb (not purple) AaBb (purple) self ?????

AB
Ab
Male
Gametes aB
ab
9/16 A_B_
3/16 A_bb
3/16 aaB_
1/16 aabb

Female Gametes
AB
Ab
AABB
AABb
AABb
AAbb
AaBB
AaBb
AaBb
Aabb

aB
AaBB
AaBb
aaBB
aaBb

ab
AaBb
Aabb
aaBb
aabb

Purple kernels, both A and B functional

Purple kernels, A functional, B is not; either A or B alone is sufficient
Purple kernels, A non-functional, B functional; either A or B is sufficient.
Non-purple, neither A nor B functional.

The modified dihybrid ratio in the case of duplicate genes (functionally, if not
structurally) is 15:1.

Recessive epistasis: Generation of an F2 9:4:3 dihybrid ratio.

Epistasis (definition)
o Literally, stand upon;
o In the original sense, defined by Bateson, epistasis arises when the effects of
alleles at one locus are blocked by the presence of a specific allele at another
locus
o the ability of one mutation to override another in a double mutant..here, we are
usually dealing with 2 different mutant phenotypes in addition to wild type.
Mouse coat color primer
o Gene A and gene C are two unlinked genes involved in mouse coat color [other
loci also affect coat color].
o Two true-breeding colors with respect to the A and C genes: agouti (AACC) and
white (aacc)
o The agouti (normal) color begins as black pigmentation of coat hairs, followed
by yellow banding of the hair shafts.

Cross of true-breeding agouti and white mice:

Crossing truebreeding agouti and
white strains yields
all agouti F1
progeny.
Intercrossing F1
males and females
yields yet another
modified dihybrid
ratio, 9:3:4,
indicative of the
presence of 2
distinct genes
involved in the coat
color phenotype
Note the appearance
of a third phenotype
(black coat color)..specifically in a 3/16 ratioindicating that these mice are
either A-/cc or aa/C-.

The 4/16 white progeny indicate the genotype of of those mice (1/16 of
the total F2) is aacc.
9/16 A-C- [agouti]
3/16 A-cc [albino]
3/16 aaC- [black]
1/16 aacc [albino]
o The presence of the cc recessive genotype therefore blocks the
expression of the black coat color phenotype [aa].
o In genetic terms, cc is epistatic to aa, since the double mutant
expresses the c phenotype
o we can interpret this as the recessive c phenotype standing upon the
aa phenotype, and the C gene acting before the A gene in the pathway
leading to the agouti coat color as follows:
C

albino black agouti

Here, the c gene is referred to as the epistatic gene; the a gene is the
hypostatic gene in the c/a interaction.

Heres another gene involved in coat color, the E gene. ee mice show a
recessive yellow phenotype. An allele of the A gene, Ay, yields a dominant
yellow coat phenotype. The epistasis is complicated because the A gene and
the E gene act in an antagonistic manner (see below)

A agouti-signaling protein
C tyrosinase
E melanocortin-1 receptor (Mcr1)

The biochemistry of this pathway within the melanocyte has been elucidated. Activation
of MC1R (the E gene) turns on production of eumelanin (via the C gene product), as
opposed to the default production of pheomelanin. The agouti protein acts an antagonist
to MC1R, leading to periodic activation of the agouti protein (the A gene) and banding of
color on individual hairs. Disruption of other loci, such as the classic tyrosinase locus
(Tyr; previously known as albino..the C gene), destroys function of the entire pathway.
The specific interactions between the proteins in this pathway are representative of
functional epistasis.

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Other coat color genes in mice:

http://www.ncbi.nlm.nih.gov/books/NBK21249/
The B gene
This gene determines the color of
pigment. There are two major alleles,
B coding for black pigment and b for
brown. The allele B gives the normal
agouti color in combination with A
but gives solid black with a/a. The
genotype A/ b/b gives a streaked
brown color called cinnamon, and
a/a b/b gives solid brown. In horses,
the breeding of domestic lines seems
to have eliminated the A allele that determines the agouti phenotype, although certain
wild relatives of the horse do have this allele. The color we have called brown in mice is
called chestnut in horses, and this phenotype also is recessive to black.

The D gene
The D gene controls the intensity of pigment specified by the other coat color genes. The
genotypes D/D and D/d permit full expression of color in mice, but d/d dilutes the
color, making it look milky. The effect is due to an uneven distribution of pigment in the
hair shaft. Dilute agouti, dilute cinnamon, dilute brown, and dilute black coats all are
possible. A gene with such an effect is called a modifier gene. In horses, the D allele
shows incomplete dominance. Cases of dilution in the coats of house cats also are
commonly seen.

The S gene
The S gene controls the presence or absence of spots by controlling the migration of
clumps of melanocytes (pigment-producing cells) across the surface of the developing
embryo. The genotype S/ results in no spots, and s/s produces a spotting pattern called
piebald in both mice and horses. This pattern can be superimposed on any of the coat
colors discussed earlier, with the exception of albino, of course. Piebald mutations are
also known in humans.
Thus, normal coat appearance in wild mice
is produced by a complex set of interacting
genes determining pigment type, pigment
distribution in the individual hairs, pigment
distribution on the animals body, and the
presence or absence of pigment. Such
interactions are deduced from modified
ratios in dihybrid crosses. The figure
illustrates some of the pigment patterns in
mice. Interacting genes such as these
determine most characters in any organism.

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Coat color in Labrador retrievers

..yet another example of recessive epistasis

B is the dominant Black allele.

b the recessive brown allele.
E is the dominant Extension gene, in conjunction with B/b causes a dog to be black or
brown. ee results in cream color.

Suppression: Dominant
Example: Malvidin (an anthocyanin) production in
Primula

Requires the product of the K gene..but, the action of K

can be suppressed (negated, turned off, masked) by the presence of a non-allelic
suppressor, D, whos effect is dominant [i.e., K-D- strains fail to produce malvidin.
P

KKdd (malvidin) x kkDD (no malvidin)

F1
F2

KkDd (no malvidin) !!

9/16 K-D3/16 K-dd

3/16 kkD1/16 kkdd

(no malvidin)
(malvidin)
(no malvidin)
(no malvidin)

Thus, dominant suppression of the K gene by the D suppressor yields a 13:3

(mutant : wild-type) dihybrid ratio.
Ques: If the action of the suppressor was recessivewhat would be the phenotypes
of the F1 plants? the modified dihybrid ratio???
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Once you have answered the last question, you should realize that, while
modified dihybrid ratios indicate the involvement of two genes in
determining the same phenotype, they are more likely to rule out
certain types of gene interactions than they are at identifying a single,
specific mechanism.
Suppression: recessive
o A suppressor is an allele that reverses the effect of a mutation of
another gene, resulting in the normal (wild-type) phenotype.
Example: purple eye color in Drosophila
Experiment:
o Start with wild-type Drosophila (red eyes) and isolate (screen for) rare mutants
that show a purple eye phenotype.in this case, due to a single recessive
mutation in the pd gene.
o Construct true-breeding strains for the Pd- phenotype (pd/pd)
o Reversion analysis (whats that??) to isolate wild-type strains from the truebreeding pd/pd strains
o if reversion is due to an unlinked suppressor gene (su) that acts in a
recessive manner (therefore, the genotype would be pd/pd; su/su),
then

Note: alternatively, I could

cross the suppressor strain
(pd/pd su/su) with a wildtype strain (pd+/pd+; su+/su+)

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How do suppressors work?

Some possible explanations:
1. Nonsense suppressionthe pd allele contains a nonsense mutation
in the protein-coding sequence; su encodes a tRNA suppressor gene
that decodes (at a low rate) nonsense codons
2. The Pd protein normally forms an active complex with the Su protein;
however, the pd mutation encodes an altered Pd protein such that it no
longer interacts with Su..so no active complex is formed. The su
mutation alters the Su protein such that is restores the interaction Su
with the mutant Pd protein. alone!
Notice that, in this mechanism: only certain
mutations in su will suppress the pd mutation,
and the su mutation alone may have the same
phenotype as the pd mutation

3. Two pathways lead to the production of the correct eye color

pigmentone is constitutive, one regulated. The pd mutation knocks
out flow through the constitutive pathway; the su mutation, however,
alters the regulated pathway such that it now becomes constitutive.
4. A variation on mechanism #3 is that the su mutations bypasses the
pathway blocked by the pd mutation by channeling intermediates
beyond the block from related pathways.
5. Still another mechanism is that the pd mutation reduces the function
of the Pd protein to ~25%, which is insufficient to give red eyes. The
su mutation increases the expression (transcription) from the pd gene
such that, even though pd produces protein with 25% function, there
is now more of it.sufficient to give a red-eye phenotype
6. ..I could go on, but I think you get the point

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Interacting Genes in Different Pathways

o Here we have a situation where two genes are necessary for determining color;
however, in this case, the pathways are separate and both end products are
necessary for normal or wild-type color.

Color in corn snakes: normal (camouflage), black, orange, and albino are
true-breeding phenotypes.
(P) true-breeding orange x true-breeding black
(F1) all normal
..intercross F1 males and females

Top left: Normal (aka

camouflaged)
Top right: Anerythstic (unable to
make red/orange pigment)

Bottom left: Amelanistic (unable

to make black pigment)
Bottom right: Albino (unable to
make either pigment)
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Lethality and Pleiotrophy

Pleiotrophy = single allele having more than one phenotypic effect

Ay allele

dominant for yellow coat color

recessive lethal

QUES: How would I determine that all of my yellow mice are Ay/A
heterozygotes?
o In addition to a dominant yellow coat color, other phenotypes associated with
Ay/A mice include obesity, insulin-resistant type II diabetes, and increased
propensity to develop a variety of spontaneous and induced tumors.
o Molecularly, the Ay allele is the result of a deletion near the A locus that results in
overexpression of the agouti gene. Lethality is likely due to the deletion extending
into neighboring gene(s) and not to overexpression of agouti itself.

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The Manx cat

The tailless Manx is the result of a
genetic mutation that was then
intensified by the cats remote
location on the Isle of Man, off the
coast of Britain
o The Manx gene is a dominant
allele of the M gene (ML) that
interferes with spinal
development and shortens the
spine of the cat, however not
always to the same extent - creating various types of Manx

Synthetic Lethality

The search for synthetic lethals can be used to search for additional genes that affect the
pathway/mechanism you are studying. OTOH, it often yields mutations that alter a
(completely) different pathwaymutant 1 makes cells sick for one reason, mutation 2
also makes the cells sick, but for a different reason. Combining sick mutation 1 with sick
mutation 2 may make cells too weak to survive.

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Patterns of Dominance
Complete dominance
This is what we have been considering to date [example: RR (red) x rr (white) All red
F1s]
Possible explanations:
1. Allele R produces 20 units of an enzyme..lets say its required to make the amino
acid leucine
Recessive allele r produces 12 units of the enzyme
Dominant allele Rd produces 0 units of the enzyme
.but to give a wild-type Leu+ phenotype, an organism must produce 30 units of an
enzyme; anything less, the organism is Leu- and requires you add leucine to the media to
grow.
RR = 40 units of enzyme; Leu+
rr = 24 units of the enzyme; LeuRr = 32 units of the enzyme; Leu+
RRd = 20 units of the ezyme; Leu2. Consider transcriptional activator proteins. These typically contains 2 protein domains
within the same polypeptideone that binds DNA, the other that attracts RNA
polymerase to the gene so it can be transcribed.
- a deletion allele of the gene might be recessive, as only one copy of the gene is
necessary.
- how about a missense mutation in the gene that makes a protein that can bind DNA, but
lacks the transcriptional activation domain; this type of allele might be dominant, as it
can bind to DNA perfectly well and, in doing so, block access of the wild-type protein (in
a heterozygous strain) to the DNA. Another possible scenario is the poisoned complex
situation, where the active protein is a complex of multiple polypeptides (either the same
or different ones)..here, incorporation of a mutant/altered protein might prevent the
complex from functioning normally, potentially yielding an inactive complex.
3..and there a quite a few more possibilities

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Incomplete dominance:
o heterozygote phenotype is intermediate between a homozygous
dominant and homozygous recessive phenotype

Incomplete dominance can run the gamut between the rr and the RR
phenotypes, as shown below:

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Think of incomplete (partial) dominance as a scale. If A1 and A2 are two

alleles of the same gene:
o If A1 is completely dominant, then an A1 A2 heterozygote has the
same phenotype as an A1 A1 homozygote
o If A2 is completely dominant, then an A1 A2 heterozygote has the
same phenotype as an A2 A2 homozygote
o An A1 A2 phenotype that is roughly in the middle is sometimes
referred to as no dominance; however, for our purposes, unless you
have quantitative data that the phenotype is at the halfway point
between A1 and A2, well simply call this situation..and any
phenotype between A1 A1 and A2 A2 homozygotes partial
(incomplete) dominance

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Co-dominance
Blood types are an excellent example of codominance, where in the heterozygote
expresses both phenotypes (i.e., not some
intermediate phenotype)
The three common major blood group
alleles are IA, IB, and i

Possible combinations of major blood group alleles and their phenotypes:

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Bombay phenotype: the H gene

Now lets look at a cross in which we consider both gene sets together:
The cross: IAIB Hh x IAIB Hh [consider that these gene pairs assort
independently from each other] :

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Ratios look familiar? Maybe not.we havent seen a 3:6:3:4 ratio before,
but this is an excellent example of epistasis. Hmmm.I thought that was
9:3:4..well, it was in the example that we considered (mouse coat color
and the A and C genes). The difference lies in the fact that, in the present
situation, we are dealing with co-dominant alleles (IA and IB).whereas in
the case of the A and C genes..we were not!
In the above example:
1. Which is the epistatic allele?
2. Which is the hypostatic allele?
3. What is the predicted order of execution, assuming both genes operate
in the same linear pathway that leads to major blood group type?

Biochemical basis of
ABO blood group

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The sickle cell phenotype

The mutation (E6V) is a change in the -globin gene that changes amino
acid 6 from glutamic acid (an acidic amino acid) to valine (a hydrophobic
amino acid). The charge loss and its replacement by a hydrophobic amino
acid lead to a decrease in the solubility of hemoglobin and the resulting
symptoms.
Phenotype: anemia [HbA dominant]
HbAHbA not anemic
HbSHbS not anemic
HbAHbS anemic

Phenotype: RBC shape

[HbA incompletely
dominant]
HbAHbA normal
HbSHbS RBCs sickle
HbAHbS RBCs may sickle
under low pO2 (high
altitudes), dehydration, or
increased atmospheric
pressure (e.g., scuba diving),
but not all individuals with
SCT (sickle cell trait) are
affected to the same degree.

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Phenotype: production of specific hemoglobin (biochemical phenotype)

[HbA and HbS are co-dominant]
HbAHbA Hemoglobin A only
HbSHbS Hemoglobin S only
HbAHbS Hemoglobin A and Hemoglobin S [typically in ~ 60:40 ratio]

Take home: When indicating the dominance/recessiveness of alleles, it is

important to also indicate the phenotype to which you are referring!!

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Variable penetrance and variable expressivity 1

Variable expressivity of the Ay allele in mice:

Different alleles may show
variable penetrance and/or
variable expressivity. This
depends to a large degree on
the particular allele, but is
also influenced by non-allelic
modifying genes. Although
this can complicate genetic
analysis, it does open up new
research to identify the
modifying genes and
determine how they influence
expression of original gene.
Environment may also play a
role in some cases.

Unfortunately, these terms are often used interchangeably among non-geneticists, though each term has a
specific meaning.

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