Review: a) Classical gene independence, !

b) Classical non-independence due

to linkage on the same chromosome.!
!
Lecture 5: Non-classical Interactions : !
a) allelic interactions, !
b) interactions between genes!
!

Independent assortment of 2 genes on

different chromosomes.!
Recombinant gametes - metaphase
Meiosis1- random (independent)
homologue equatorial alignment!

Parental!

Inheritance!
F1 testcross!

Variation !

Genetics is the
study of
inheritance and
variation!

Expected proportions of !
F1 testcross progeny!

2!

Independent assortment of 2 genes on !

different chromosomes.!
Recombinant gametes - metaphase Meiosis1random (independent) tetrad (maternal / paternal)
equatorial alignment, sexual recombination!

R_ (0.75) * Y_ (0.75) = 9/16

R_ (0.75) * yy (0.25) = 3/16!
rr (0.25) * Y_ (0.75) = 3/16!
rr (0.25) * yy (0.25) = 1/16!

Dihybrid cross!

a) Punnett square!
b) Branching
combinations!
c) Multiplicative
rule!

3!

Independent assortment of 2 genes on

different chromosomes.!
Recombinant gametes - metaphase Meiosis1random homologue spindle alignment!

Recombination between 2 genes, one

chromosome.!
Recombinant gametes- prophase Meiosis1!
crossover frequency~ interlocus distance !
!

Inheritance!
Variation !
Test cross!

4!

% recombinants is
proportional to !
the distance between !
gene locations (locus, loci) !
on a chromosome!

Recombination between 2 genes, one

chromosome.!
Recombinant gametes prophasemetaphase Meiosis1!
crossover frequency~ interlocus distance !
!

G1!

For most animals & plants!

Very close< 1 cM - few X-overs, few
recombinants!
Close >1 cM < 20 cM, increasing %
recombinants accurate map distance !
Distant > 50 cM = independent assortment!

Average 2 crossover recombinant fraction=50%!

Mapping functions

(p=1/2 (1-e-2d)

d=crossover frequency

Multiple crossovers reduce large

map distance estimates (2 loci)
but interfere over short distances.!

6!

Interference = 1- coefficient of
coincidence measures the
difference between expected
double crossover and observed
double crossover.

1. Organize Data!
vbp

1779

VBP
vbp

1654
1779

Vbp

252

vBP

241

VbP

131

vBp

118

vbP

13

vbP

13

VBp

VBp

VBP

1654

A. Parentals!

B. Double recombinants!

!
C. Order ?!

V!

7!

P!

B!

2 . Calculate Map Distances!

VPB
vpb

1654
1779

vPB
Vpb

241
252

Region VP

= 241 + 252 + 13 + 9
515.000 /4197
0.123

VPb
vpB

131
118

Region PB

= 131 + 118 + 13 + 9
271.000 /4197
0.065

v Pb
VpB

13
9

Region VB

= 241+ 252 +131 + 118+ 2*(13+9)

786.000 /4197
0.187

4197

V! 12.3 m.u.!

P! 6.5 cM! B!

8!

F
f

A
a

Hl!
hl!

Parental F A Hl
45!
recombinant

recombinant

Parental f a hl

Mapping and recombination - the 5 step method

(1)Pair gametic types by complement & frequency
(2) ID parental chromosomes: F A Hl & f a hl (a) # highest ?
(b) complementary pairs ? (c) # similar ?
(3) Organize a table with the 2 or 3 mutant symbol heading the column tops,
corresponding parentals at the top, below each heading. Remember, you are
always organizing & comparing recombinants with parentals.
(4) If the problem involves 3 markers (loci), identify the double recombinant
chromosomes
F a Hl (a) # lowest ?
(c) complementary pairs ? f A Hl (c) # similar ?
Then you can ID the middle marker (pair that has flipped to parentals)
Then you have the gene order. Put the double -X -over pair at the bottom
(5) Table the single recombinant classes (middle):
(a) # similar ?
then estimate the required distances
(b) complementary pairs ?
2

Lecture 5: Gene interactions other than dominance cause

informative, non-classical phenotype ratios .

9!

Allele, Gene Interactions - modifying classical expectations !

One gene, 1 phenotype trait: variation in allele interactions!
!
1. Incomplete dominance!
2. Co-dominance!
3. Three or more alleles of a single gene!
4. Recessive lethal alleles!
Two genes, 1 phenotype trait: variation in gene interactions!
!
1 !Two genes that affect the same trait: duplicate genes!
2 Epistasis!
!

10!

Interactions between alleles of a

single gene: degrees of dominance:!
codominance, !
partial or incomplete dominance
(chapter 6.1)!

11

Incomplete dominance:

the phenotype of the heterozygote
is intermediate, its expression
somewhere between the two
homozygous genotypes.





Reserve the term codominance
for a categorical intermediate-

Codominant Phenotypes:!
!
All phenotypes indicate unique
phenotypes!

12

1. Co-dominance Inbreed F2 heterozygotes !

R r x R r!

RR
1 :

Rr
2
:

rr!
1!

r!

R!

R R!

R r!

r!

R r!

r r!

13

How do you recognize codominance ?

In a monohybrid cross:

(1) the F1 phenotype is intermediate

(2) in the F2 there are 3 phenotypes (1: 2: 1) rather than 2.



In a dihybrid cross where 1 gene has fully dominant allelic
interactions and the other is codominant:

0.75 A_

0.25 BB

0.5Bb

0.25bb

F 2!

0.25 BB

0.5Bb

0.25 aa

0.25bb

14

Genetic Interactions and Phenotypic Variation!

One gene, 1 phenotype trait: variation in allele

interactions!
!
1.
2.
3.
4.

Incomplete dominance!
Co-dominance!
Three or more alleles of a single gene!
Recessive lethal alleles!

Two genes, 1 phenotype trait: variation in gene

interactions!
!
1 !Two genes that affect the same trait: duplicate genes!
2 Epistasis!
!

15!

2. Co-dominance alleles are both fully expressed"

"
Example: Blood types A, B!

IA IA gives blood type A, A antigen on the red blood cell!

A!

A!

Antigen- any molecule detected by

antibodies - in this case a coating of
sugars !
A!

A!

IB IB gives blood type B, B antigen on the red blood cell!

B!

B!

B!

16!
B!

2. Co-dominance IA and IB alleles are both fully expressed"

"
Example: Blood types A, B!

IA IB gives blood type AB, !

!!
Both A antigen and B antigens are on the red blood cell!
A!
B! A!

B!

B!
A!
B!

A!

17!

2. Co-dominance IA and IB alleles are both expressed"

"
Example: Blood types A, B!

IA IB x IA IB mating may give three offspring types:!

!

IA IA

IA IB

A type

IB IB!

AB type

B type !

1
!

A!

1 !

A!
A!

B! A!

B!

B!

B!

B!

B!
A!

A!

A!
B!

A!

B!

18!

O is a loss of function allele, A, B are haplosufficient !

Multiple alleles one gene can have more than two
common alleles (polymorphism), where 1 allele is identified
by the absence of expression (null allele).!

IA i

ii
Type O

Type A

IA IB

IB i!

Type AB

Type B

A!

B! A!

B!

A!

A!

B!

B!

B!

A!
B!
A!

A!

B!
B!

A!

19!

3. One gene can have three (or more) alleles."

"
Blood type O, is produced by the i allele, !
The i allele is recessive to IA and IB !
Genotype: Blood type:
Genotype
ii
- type O !
i IA
type A !
i IB
- type B
IB IA
- type AB

native antibodies !
against foreign (non native) antigens !
!
Phenotype!
!
initiate !anti A or anti B!
!
initiate !anti B!
initiate anti A!
initiate !neither A nor B!

20!

Example: What are the expected genotype and phenotype

ratios from many matings of : i IA and i IB parents ?!

i!

I A!

Expected Ratios ?!

i!

ii!

i IA!

I B!

i IB

I B IA!

ii
- type O!
i IA type A!
i IB - type B!
IB IA - type AB!

21!

(A4). Lethal alleles: Expression of these alleles cause death, and

they may be dominant, partially dominant or recessive.!
Recessive lethal (1) a 2:1 ratio of progeny from a hetero cross!
(2) a trait that cannot be made to breed true!
Example: ML is a dominant allele!
(pp 229) causing the tailless character
in Manx cats. It is a recessive allele
for lethality!
Manx cats produce tailless offspring !
in a 2:1 ratio with tailed offspring.!
This is a modified 1:2:1 ratio, in which
the homozygous MLML individuals are
not observed because they die in utero.!
!
Tailless Manx cats are always
heterozygous. They cannot breed
true. !

22!

23!

!
Dominant lethal alleles exist, !
Why are they not segregating in high frequencies in most populations ?!
Why are they seen at all ? late onset lethal diseases e.g.
Huntingtons, Crones.!
!
Conditional lethal: environmental conditions trigger lethality-!
e.g. temperature sensitive lethals or conditional mutants!
!
Lethal alleles may also have partial dominance: !
e.g.:, a test cross yL x yy does not give a 1:1 ratio but repeatedly shows
70 / 30 or some ratio other than 50% each. This is called a sub-lethal
allele.!

24!

(A)Know the expected ratios for Monohybrid crosses

with different allele relations and expression in
diploids:!
(1)Full dominance!
(2)Partial or codominance!
(3)Lethal alleles: recessive, dominant, partially dominant,
conditional.!
(B) Multiple alleles affecting a character or phenotype
in different ways (1-3 above)!

Genetic Interactions and Phenotypic Variation!

25!

A) One gene, 1 phenotype trait : variation in allele interactions!

!
1. Incomplete dominance!
2. Co-dominance!
3. Three or more alleles of a single gene!
4. Lethal alleles!

B) A gene or allele may affect more than one character or

trait - pleiotropy pp 229!
!

C) 2 genes affect the classical Mendelian ratio: epistatic

interactions!
! !1 Two genes that affect the same trait (9:7) !
2 Two or more Duplicate Genes (15:1) !
3 Recessive epistasis (9:3:4) !
!4 Dominant epistasis (12:3:1) ! And others !

Classical epistasis occurs when the alleles of one gene

mask the effects of one or more alleles of another gene. !
!
How do you identify it ? !
!
Epistasis - reduces the classical dihybrid expected
number of phenotype categories (9:3:3:1), !
!
although it provides evidence for underlying meiotic
mechanism generating a 2 gene - 2 allele dihybrid F2
gamete assortment.!
!
!
26!

Gene duplications with functional drift - a

change in their expression.!
Intra chromosomal!
!
In recent years the degree of gene duplication
in eukaryotic organisms has been a
surprising discovery of genome research.!
!
Gene duplication is obvious from DNA
sequence analyses, however the duplicates
are not 100% identical.!
!
Whether duplicated genes have maintain their
original function or have evolved new
functions is not obvious. !
!
There are two duplication categories:!
(1) Intra-chromosomal (tandem duplications)!
27!
(2) Inter - chromosomal !

Capsella bursa pastorisShepards purse!

28!

29!

Duplicate dominant genes!

(without a cumulative effect)
Duplicate genes A1 and A2 !
controlling fruit shape!
in Shepard's Purse.!
!
Two independently segregating
genes A1A2, each with two
alleles (A,a) with the same
dominance /recessive
relationship.!
!
Only the individuals!
homozygous recessive for!
both genes have !
narrow fruit 1 / 16.!

(4) Chromosome Structure: Gene Duplications: Intergenic and tandem duplications have
functional and evolutionary significance. For example a duplication explains the difference in
color vision of new and old world primates. Note that green (G) and red (R) pigments are
polymorphic alleles in new world primates (NWMonkeys) but blue (B) is monomorphic.

30!

Recessive Epistasis 9: 3: 4!

31!

Example: c is a recessive allele of the C gene responsible !

for albinos.!
When homozygous it is epistatic to the B/b gene for black (B_) !
and brown hair, i.e. individuals who are cc will be white !
no matter the allele carried for the brown/black gene.!
!
B_C_ - have black hair!
bb C_ - brown hair!
BbCc x BbCc !
!
!
BBcc - are albino!
B_C_ - black
! 9!
bbcc - are albino !
bbC_ - brown
3!
B_cc - albino
3!
4!
bbcc - albino
1

 Dominant epistasis (12 : 3 : 1) Figure 6-21!

dd - light red!
D_ - dark red!
!
ww - pigment throughout!
W_ pigment restricted!
F1Self or inbreed D/d . W/w!
!
9 D_ W_ white spotted!
3 dd W_ white spotted!
3 D_ ww dark red!
1 dd ww light red!
!

33!

Many forms of
epistasis

34!