Linkage, Crossing Over and
Chromosome Mapping in
Eukaryotes
Linked Genes Do Not Assort Independently
• Some of the first evidence for linkage came from the
experiments by Bateson and Punnett.
– Traits : Flower color and pollen length.
– Instead of 9:3:3:1, they observed a ratio of 24.3 :
1.1 : 1 : 7.1.
– Null hypothesis (flower color and pollen length
traits assort independently ) should be rejected.
• The genes for flower color and pollen length are
located on the same chromosome – they are linked.
Linked Genes Do Not Assort Independently
• When crossing over occurs between two genes and their
alleles are recombined, two other kinds of gametes are
produced, in addition to the nonrecombinant gametes.
• Linked genes move together!
– Nonrecombinant F1 gametes can not be Rl or rL. They
have to be RL (from one parent) or rl (from other parent).
• Frequency of recombination between these alleles depend
on the distance between them.
– The shorter the distance the more unlikely for
recombination.
Recombination Frequency
Testcrosses are helpful in determining the recombinant
frequency.
Since these genes are linked :
• If there is no recombination, all of the offsprings
show parental phenotypes.
• We see red-short and white-long only if there is
recombination.
So, we can estimate the frequency of recombinants as
(# of non-parental phenotypes)
(#total number of offspring)
Recombination Frequency
• For any two genes, the recombination frequency never
exceeds 50 %. AABB aabb
• This upper limit is obtained when genes are on different
chromosomes :
– 50 % recombination is, in fact, what we mean when we AaBb aabb
say that the genes assort independently.
• For example,
– Let’s assume that genes A and B are on different
chromosomes and that an AA BB individual is crossed to
an aa bb individual.
– From this cross the Aa Bb offspring are then testcrossed
to the double recessive parent.
Recombination Frequency
• For example,
– Let’s assume that genes A and B are on different AABB aabb
chromosomes and that an AA BB individual is crossed
to an aa bb individual. Dihybrid is then test-crossed.
– Because the A and B genes assort independently, the AaBb aabb
F2 will consist of two classes : (1) phenotypically like
the parents in the original cross (2) phenotypically
recombinant. 25 % AaBb
– Furthermore, each F2 class will occur with a frequency parental
of 25 percent. Thus, the total frequency of 25 % aabb
recombinant progeny from a testcross involving two
genes on different chromosomes will be50 %. 25 % aaBb
recombinant
• A frequency of recombination less than 50 percent
implies that the genes are linked on the same 25 % Aabb
chromosome.
Linkage Phases: Coupling and Repulsion
• Crosses involving linked genes are usually diagrammed to show the linkage phase—the way in which the alleles are
arranged in heterozygous individuals.
• The genotype of the heterozygous plants are written as R L/r l, where the slash (/) separates alleles inherited from
different parents.
RL/rl Rr Ll
Other homologous
We don’t know which
chromosome carry
allele is on which
One of the homologous only recessive alleles.
chromosome.
chromosomes carry only This type of symbolism
dominant alleles. doesn’t tell us anything
about the location of the
This symbolism tells us that these genes
genes.
are on the same chromosome.
Linkage Phases: Coupling and Repulsion
• Whenever the dominant alleles are all on one side of the slash, the genotype has the coupling linkage phase.
• When the dominant and recessive alleles are split on both sides of the slash, as in R l/r L, the genotype has the
repulsion linkage phase.
• These terms provide us with a way of distinguishing between the two kinds of double heterozygotes.
Crossing Over as the Physical Basis of Recombination
• An exchange between paired chromosomes during meiosis produces recombinant chromosomes at the end of
meiosis.
Consequences of
multiple exchanges
between chromosomes
and
exchange between
sister chromatids
during prophase I of
meiosis.
McClintock and Creighton
• In 1931, Harriet Creighton and Barbara McClintock obtained
evidence that genetic recombination was associated with a
material exchange between chromosomes. They studied
homologous chromosomes in maize that were morphologically
distinguishable.
• Barbara McClintock
– Genetic recombination by crossing-over
– First genetic map for maize.
– The role of the telomere and centromere.
– Discovered transposition.
– Nobel Prize in Physiology or Medicine was awarded to her
in 1983 for the discovery of genetic transposition.
– She is the only woman to receive an unshared Nobel Prize
in that category.
Chromosome 9 in maize
• Two forms of chromosome 9 were
available for analysis:
– one was normal,
– the other had cytological aberrations
at each end—a heterochromatic knob
at one end and a piece of a different
chromosome at the other.
Chromosome 9 in maize
• Two forms of chromosome 9 were
available for analysis:
– one was normal,
– the other had cytological aberrations
at each end—a heterochromatic knob
at one end and a piece of a different
chromosome at the other.
• These two forms of chromosome 9 were
also genetically marked to detect
recombination.
• One marker gene controlled kernel color
(C, colored; c, colorless), and the other
controlled kernel texture (Wx, starchy; wx,
waxy
Evidence that Crossing Over Causes Recombination
• Their findings strongly argued that recombination was caused by a physical exchange between paired
chromosomes.
Crossing over Exchange
Chromosome Mapping
Linked genes can be mapped on a
chromosome by studying how often
their alleles recombine.
Observable Outcomes of Crossing Over :
• Formation of chiasmata in late
prophase.
• Recombination between genes on
opposites sides of the crossover point.
Chromosome Mapping
observed
Parental Recombinant Parental Recombinant
phenotype phenotype phenotype phenotype
Recombination frequency from observed phenotypes = 22/100 = 0.22
→ Real r.f. is higher than observed r.f.
Recombination Mapping with a Two-Point Testcross
Recombination Mapping with a Two-Point Testcross
• The Recombination Frequency between
vg and b is 18%.
• This is equal to 18 map units, or 18
centiMorgans (cM) on the genetic map.
Recombination Mapping with a Three-Point Testcross
Recombination Mapping with a Three-Point Testcross
parental
recombinant
Determining the Gene Order
• There are 3 possible gene orders
– sc - ec - cv
– ec - sc - cv
– ec - cv - sc
• The two most common classes are the parentals.
• Among the recombinant classes, the 2 rare classes represent the double
crossovers.
• The gene that is “switched” in the double crossover classes compared to the
parental is the middle gene (in this case, ec).
Recombination Mapping with a Three-Point Testcross
parental
recombinant
Recombination Mapping
Single cross between
sc and ec
Double cross
It still has a cross between
sc and ec
Recombination Mapping
Single cross between
cv and ec
Double cross
It still has a cross between
cv and ec
Recombination Mapping with a Three-Point Testcross
Compared to the parental phenotypes, this could be either single or double cross.
BUT it the rare case. So, we know it should be double-cross.
We compare the double cross scenario with parentals → Echinus should be in the
middle.
Recombination Mapping
sc ec cv
9.1 cM 10.5 cM
cv ec sc
10.5 cM 9.1 cM
Recombination Frequency and Genetic Map Distance
Calculation of Map Distances
Genetic Distance and Physical Distance
