 Linkage, Recombination and Gene mapping

And related concepts in Population genetics

Recap
Linked genes sit Genes that are farther
close together on a Genes on away from each other are
chromosome, separate more likely to be
making them likely chromosomes separated during a
to be inherited are never linked process called homologous
together. recombination
Homologous chromosomes

 Homologous chromosomes
have the same genes arranged
in the same order, but they
have slightly different DNA
sequences. Different versions of
the same gene are called
alleles.

 Homologous chromosomes
often contain different alleles.
Alleles are important because
they account for the differences
in inherited characteristics from
one individual to another. For
example, different alleles of the
same genes can make our eyes
blue, green, or brown.
MORGAN’s EXPERIMENTS
 Both the white eye gene (w) and a gene for miniature wings (m)
are on the X chromosome.
 Morgan (1911) crossed a female white miniature (w m/w m)
with a wild-type male (w+ m+/ Y).
 In the F1, all males were white-eyed with miniature wings (w m/Y),
and all females were wild-type for eye color and wing size (w+ m+/w
m).
MORGAN’s EXPERIMENTS
 F1 interbreeding is the equivalent of a test cross for these X-linked
genes, since the male is hemizygous recessive, passing on recessive
alleles to daughters and no X-linked alleles at all to sons.
 What is the expected ratio of phenotypes in F2, if white and miniature
are on different chromosomes?
 In F2, the most frequent phenotypes for both sexes were the phenotypes of the
parents in the original cross (white eyes with miniature wings, and red eyes
with normal wings).
 Non-parental phenotypes (white eyes with normal wings or red eyes with
miniature wings) occurred in about 37% of the F2 flies. Well below the 50%
predicted for independent assortment, this indicates that non-parental flies
result from recombination of linked genes.
 Fig. 13.1 Morgan’s experimental crosses of white-eye and miniature-
wing variants of
Drosophila melanogaster

Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
MORGAN’S PROPOSAL
 During meiosis alleles  Parental phenotypes occur
of some genes assort most frequently, while
together because they recombinants less.
are near each other on  Terminology
the same  Chiasma: site of crossover
chromosome.  Crossing over: reciprocal
exchange of homologous
 Recombination occurs chromatid segments
when genes are  Crossing-over occurs at
prophase I in meiosis; each
exchanged between X event involves two of the
chromosomes of the four chromatids. Any
chromatids may be involved
F1 females in crossing over.
Linked genes and locus
 Genes located close together on the same
chromosome are called linked genes and belong
to the same linkage group.

 Linked genes travel together in meiosis,

eventually arriving at the same destination (the
same gamete).

 They are not expected to assort independently.

An example: Nonindependent assortment of flower color
and pollen shape in sweet peas (No 9:3:3:1)

These two are in excess.

 Two loci lie close together on the same chromosome

and therefore do not assort independently.

 Linkage and crossing over can be seen as processes that

have opposite effects: linkage keeps particular genes
together, and crossing over mixes them up.
Notation for Crosses with Linkage
 For linked genes, it’s necessary to write out the
specific alleles as they are arranged on each of
the homologous chromosomes.
Right notation:

Alleles A and a can never be on the same

Wrong notation:
chromosome.
Same order of the genes on both the sides
of the line are not maintained. This would
imply that alleles A and b are allelic (at the
same locus).
Complete Linkage Compared with Independent Assortment

(50 %)

(25 %)

(25 %)
(50 %)

(25 %)
(25 %)
Notations for earlier example

and

Non recombinant
gametes, or parental
gametes
Example to calculate
recombinant frequency
Calculation of Recombination
Frequency
 The percentage of recombinant progeny produced
in a cross is called the recombination frequency,
which is calculated as follows

 Thus, 12.2% of the progeny exhibit new combinations of

traits resulting from crossing over.

 The recombination frequency can also be expressed as a

decimal fraction (0.122).
Coupling (Cis) and Repulsion
(Trans)
 In crosses for linked genes, the arrangement of alleles
on the homologous chromosomes is critical in
determining the outcome of the cross.
 In Australian blowfly, Lucilia cuprina, one locus
determines the color of the thorax: a purple thorax (p)
is recessive to the normal green thorax (p+).
 A second locus determines the color of the puparium: a
black puparium (b) is recessive to the normal brown
puparium (b+).
 The loci for thorax color and puparium color are located
close together on the chromosome.
 Because these genes are linked, there are two possible
arrangements on the chromosomes of the heterozygous
progeny fly.
(Cis) (Trans)
Cis and trans coupling
 a problem
 The following testcross produces the progeny
shown: Aa Bb × aa bb → 10 Aa Bb, 40 Aa bb, 40
aa Bb, 10 aa bb.
 Were the genes in the Aa Bb parent in coupling
or in repulsion?
Problem-15 from B. Pierce
 In silkmoths (Bombyx mori), red eyes (re) and whitebanded wing (wb) are encoded
by two mutant alleles that are recessive to those that produce wild-type traits
(re+ and wb+); these two genes are on the same chromosome.
A moth homozygous for red eyes and white-banded wings is crossed with a moth
homozygous for the wild type traits. The F1 have normal eyes and normal wings.
The F1 are crossed with moths that have red eyes and white-banded wings in a
testcross. The progeny of this testcross are

1. wild-type eyes, wild-type wings 418

2. red eyes, wild-type wings 19
3. wild-type eyes, white-banded wings 16
4. red eyes, white-banded wings 426 testcross are:

 What phenotypic proportions would be expected if the genes for red eyes and
for white-banded wings were located on different chromosomes?
 What is the percent recombination between the genes for red eyes and those
for white-banded wings?
Chi-Square test for Linked genes
To illustrate this analysis, we will examine results from a
cross between German cockroaches, in which yellow body
(y) is recessive to brown body (y+) and curved wings (cv) are
recessive to straight wings (cv+). A testcross (y+y cv+cv × yy
cvcv) produced the progeny shown in Figure
What are testing ratios at each locus?

 Does each locus satisfy independent assortment?

 For example, At the first locus (for body color), the

cross between heterozygote and homozygote (yy + X
yy), does it satisfy null hypothesis?

 Similarly, what are the observed and expected ratios

for the second locus, which determines the type of
wing. At this locus, a heterozygote and homozygote
also were crossed (cv+cv X cvcv)
 DO THIS AS HW.
A example problem
 A geneticist discovers a new mutation in Drosophila melanogaster
that causes the flies to shake and quiver. She calls this mutation
spastic (sps) and determines that spastic is due to an autosomal
recessive gene. She wants to determine if the gene encoding spastic is
linked to the recessive gene for vestigial wings (vg). She crosses a fly
homozygous for spastic and vestigial traits with a fly homozygous for
the wild-type traits and then uses the resulting F1 females in a
testcross. She obtains the following flies from this testcross.
vg+ sps+ 230
Vg sps 224
vg sps+ 97
vg+ sps 99
Total 650

 Are the genes that cause vestigial wings and the spastic mutation
linked? Do a chi-square test of independence to determine whether
the genes have assorted independently
 Gene Mapping Using Two-Point Testcrosses
With autosomal recessive alleles, when a double heterozygote is testcrossed, four
phenotypic classes are expected. If the genes are linked, the two parental
phenotypes will be about equally frequent and more abundant than the two
recombinant phenotypes.

 For autosomal dominants, a double heterozygotes (A B/A+B+) is

testcrossed with a homozygous wildtype (recessive) individual
(A+B+/A+B+)

 For X-linked recessives, a female double heterozygote (a+ b+/a b) is

crossed with a hemizygous recessive male (a b/Y).

 For X-linked dominants, a female double heterozygote (A B/A+ B+)

is crossed with a male hemizygous for the wild-type (A+ B+).
 Phenotypes obtained in these crosses will depend on whether the
alleles are in cis or trans position.
GENETIC MAP
 Recombination frequency is used directly as an
estimate of map units.
 The measure is more accurate when alleles are close
together.
 Scoring large numbers of progeny increases accuracy.

 Thomas Hunt Morgan and his students developed the

idea that physical distances between genes on a
chromosome are related to the rates of recombination.
 GENERATING A LINKAGE MAP
 Genetic map is generated from estimating the
crossover rate in a particular segment of a the
chromosome. It may not exactly match the
physical map because crossover is not equally
probable at all sites on the chromosome.
 Recombination frequency is also used to predict
progeny in genetic crosses. For example, a 20%
crossover rate between two pairs of alleles in a
heterozygote (a+ b+/a b) will give 10% gametes of
each recombinant type (a+ b and a b+).
Gene Mapping with Recombination Frequencies

 (i) crossover events occur more or less at random up and

down the chromosome and (ii) that two genes that lie far
apart are more likely to undergo a crossover than are two
genes that lie close together.
 Recombination frequencies could provide a convenient
way to determine the order of genes along a chromosome
and would give estimates of the relative distances
between the genes
 Chromosome maps calculated by using the genetic
phenomenon of recombination are called genetic maps.
In contrast, chromosome maps calculated by using
physical distances along the chromosome (often
expressed as numbers of base pairs) are called physical
maps.
 LINKED or NON-LINKED?
 A recombination frequency of 50% means that
genes are unlinked. There are two ways in which
genes maybe unlinked:
 They may be on separate chromosomes.
 They may be far apart on the same chromosome.
Units – CentiMorgans (CM) or
map unit (m. u)
 Distances on genetic maps are measured in map units (abbreviated
m.u.).
 One map unit equals 1% recombination.
 Map units are also called centiMorgans (cM), in honor of Thomas Hunt
Morgan;
 100 centiMorgans equals 1 Morgan.
 Genetic distances measured with recombination rates are approximately
additive: if the distance from gene A to gene B is 5 m.u., the distance
from gene B to gene C is 10 m.u., and the distance from gene A to gene C
is 15 m.u., then gene B must be located between genes A and C.

Which is plausible?
Continued…
 If we obtained distances to an additional gene, then
we could position A and C relative to that gene.
 An additional gene D, examined through genetic
crosses, might yield the following recombination
frequencies:

 Based on the above information, show the right

genetic map.
 Keep in mind that 1 m.u = 1% recombination
Problems using recombinant
frequencies

 Two points should be emphasized about constructing

chromosome maps from recombination frequencies.
 First, recall that we cannot distinguish between genes
on different chromosomes and genes located far apart
on the same chromosome. If genes exhibit 50%
recombination, the most that can be said about them is
that they belong to different groups of linked genes
(different linkage groups), either on different
chromosomes or far apart on the same chromosome.
 Secondly, it does not reveal double crossovers that
might take place between the two genes
Constructing a Genetic Map with the Use of Two-
Point Test crosses
 A testcross between two genes is called a two-
point testcross or a two point cross for short.
 Suppose that we carried out a series of two-
point crosses for four genes, a, b, c, and d, and
obtained the following recombination
frequencies

 Construct the genetic map for the two point

cross.
 Genetic Variation
 Genetic recombination - source of most variation (in sexual organisms), via
new allele combinations.

 Mutation - ultimate source of variation, source of new alleles and genes.

Fitness
 = measure of the relative contribution of a given genotype to the
next generation

 Can measure for individual or population.

Fitness
= allele/genotype freq. in future generation allele/genotype
freq. in prev. generation

E. g., 1st gen. 25%AA : 50%Aa : 25%aa

[freq. A = 25% + .5(50%) = 50%]

2nd gen.: 36%AA : 48%Aa : 16%aa

[freq. A = 36% + .5(48%) = 60%]

Fitness of A allele is 60/50 = 1.2; a is 40/50 = 0.8

Fitness of AA genotype is 36/25 = 1.44 , etc.
 Hardy-Weinberg Equilibrium (1908)
 The frequency of a gene / allele does not change over time
(given certain conditions).
A,a = alleles of one gene, combine as AA, Aa, or aa
Generation 1: p = freq. A q = freq. a p + q = 1 (100%)

pA qa
=gene frequencies
pA
qa
p2AA
pqAa
pqAa
q2aa } in generation 1

p2AA + 2pqAa + q2aa = 1

 Hardy-Weinberg Equilibrium (1908)
 The frequency of a gene / allele does not change over time
(given certain conditions).

What will be the frequency of alleles in the second

generation?

p2AA + 2pqAa + q2aa = 1

} =gene frequencies
in generation 1
freq. A (generation 2) = (p2 + pq) / (p2 + 2pq + q2)
= p(p + q) / (p + q)2 = p / (p + q) = p

Therefore, freq. A = p; freq. a = q, same as in generation 1.

Hardy-Weinberg Equilibrium (assumptions)
 Maintained only if:
1) No new mutation
New mutations rare, but do occur
(1 new mutation in 10,000 - 1,000,000 genes per individual per
generation)

 2) No migration (no gene flow into or out of population)

But, can occur . . .

 3) Population size large

 Two things can disrupt:

 a) Population bottleneck (large pop. gets very small)
 b) Founder effect (one or a few individuals dispersed from a large
pop.)
 Hardy-Weinberg Equilibrium (assumption)

 4) Mating is random

 But, most animals mate selectively, e.g.,

 1) harem breeding (e. g., elephant seals);
 2) assortative mating (like mates with like)
 3) sexual selection

 5) All genotypes equally adaptive

(i.e., no selection)

 But, selection does occur . . .

 If any conditions of Hardy-Weinberg not
met:
 Genotype frequencies change

 Evolution occurs!

 Evolution = change in gene frequency

of a population over time.