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UNIVERSITY OF SOUTHERN MINDANAO

Gen 211a Lecture 12

PRINCIPLES OF GENETICS LINKAGE AND RECOMBINATION

GWEN IRIS D. EMPLEO

Subject Professor

Definition of Terms Definition of Terms

Linkage - condition in which 2 or more non-allelic genes
tend to be inherited together
- loci of the genes are on the same chromosome
- genes do not assort independently
- genes can be separated through crossing-over
Linkage group - group of genes that have their loci in
the same chromosome
- number of linkage groups = number of
chromosomes in a haploid cell
Complete linkage – genes on the same chromosome
are very close together so that they are always
transmitted together
Incomplete linkage – genes are on the same
chromosome
- genes are far from each other
- recombinant types are produced by crossing-over

Types of Linkage Types of Linkage

1. Complete linkage - two loci are so close that they 2. Incomplete linkage – due to crossing-over
are always inherited together Crossing over within a region is rare (so crossing-over
products are rare). Most of the time it will not occur, so
Dihybrid cross AABB x aabb AaBb parental types will be the most common gametes
produced
Test cross: AaBb x aabb

50% AB
50% ab
0% Ab
0% aB

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Gametes produced when genes assort Gametes produced when genes are linked
independently

Gametes produced when genes are linked Linkage Map

• A genetic map of a chromosome based on
recombination frequencies

• Distances between genes can be expressed as map

units; one map unit, or centimorgan, represents a 1%
recombination frequency

• Recombination frequency is determined by observing

the number of offspring showing recombinant
phenotypes

• Map units indicate relative distance and order, not

precise locations of genes

Determination of Linkage Testcross progeny

Phenotype Genotype Crossover type No.

The strength of linkage is expressed as linkage value. 1. Normal V G1 Va Parental 235

v g1 va
2. Virescent, glossy, variable sterile v g1 va Parental 270
Linkage value = Total number of crossover x 100 v g1 va
Total no. of population 3. Glossy, variable sterile V g1 va Single crossover region I 60
v g1 va
4. Virescent v G1 Va Single crossover region I 62
Linkage values involving three genes v g1 va

5. Variable sterile V G1 va Single crossover region II 40

Make a cross between an F1 and the recessive parent v g1 va
6. Virescent, glossy v g1 Va Single crossover region II 48
v g1 va
V G1 Va x v g1 va
v g1 va v g1 va 7. Glossy V g1 Va Double crossover 7
v g1 va
8. Virescent, variable sterile v G1 va Double crossover 4
v g1 va

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Computation of linkage values Interference and coefficient of coincidence

• The farther apart two genes are, the higher the • The strength of interference can be measured by the
probability that a crossover will occur between them, coefficient of coincidence (C.C.):
and therefore higher the recombination frequency
C.C. = actual DCO
Region I = 60 + 62 + 7 + 4 x 100 = 18.3% expected DCO
726
e.g. the coefficient of coincidence is:
Region II = 40 + 48 + 7 + 4 x 100 = 13.6 %
726 C.C. = 0.0152 = 0.61
0.0249
DCO = 7 + 4 x 100 = 1.52%
726

Interference and coincidence Interference and coincidence

• Crossing over does not occur uniformly along a
chromosome.
• Fewer crossovers occur in the area around the
centromere than in other areas of the chromosome
• This lack of independence is called interference
• Results in the observation of fewer double
crossover types than would be expected according
to true map distance.

• Making the loci appear closer together than they

actually are

• The formation of one chiasma typically makes it less

likely that a second chiasma will form in the immediate
vicinity of the first

Linkage Mapping is the Basis for Determining the proper gene order
Chromosome Mapping
A cross is made between homozygous wild-type
• Each gene has a particular, well-defined locus in the female Drosophila (a+a+b+b+c+c+) and triple-mutant males
(aabbcc) (the order here is arbitrary).
chromosome
The F1 (a+ab+bc+c) females are testcrossed back to
• Linkage values would indicate the definite serial order
the triple-mutant males and the F2 phenotypic ratios are
for the genes in a chromosome and would serve as as follows:
bases for mapping distance relations among linked
genes a+b c 18
• Chromosomes can be mapped effectively in terms of a b+c 112
crossover percentage obtained from genetic abc 308
experiments a+b+c 66
• 1% crossing-over is equivalent to 1 map unit or a b c+ 59
centiMorgan. a+b+c+ 321
a+b c+ 102
a b+c+ 15
1000

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Determining the proper gene order
1. The gene order can be determined by examination of
the relative frequencies of the F2 phenotypes.
a. Because linked loci tend to stay together, the
non-crossover (NCO) or parental phenotypes
should be most frequent (and equal in number).
In this case,
a+b+c+ (321) and abc (308)
b. Because simultaneous crossovers between the
outside and middle loci are unlikely, the double-
crossover (DCO) genotypes should be the least
frequent. We observe
Determining the proper gene order
c. Then, to determined the physical order of loci, compare
the parental and double crossover phenotypes. The
marker that appears to “switch places” is in the middle
[technically, this marker is said to be “out of phase”].
Here, the a+b+c+ NCO and ab+c+ DCO phenotypes
indicate that the a locus falls between the b and c loci.
The correct order of the loci is bac. [Note that this
order is equivalent to cab, and that the order of the
outside markers is arbitrary].

a+bc (18) and ab+c+ (15)

3. The percent recombination between two markers

2. The remaining two pairs of phenotypes correspond
indicates the map distance between them:
to single-crossovers (SCO) events in the region
between either b and a, or between a and c.
1% recombination = 1 map unit (m.u.).
a. b+ac (112) and ba+c+ (102) phenotypes indicate
To determine the map distance between a pair of loci,
crossovers between b and a.
count the number of SCO and DCO events, and use
b. b+a+c (66) and bac+ (59) phenotypes indicate
the following formula
crossovers between c and a.

Map distance = % recombination

SCO phenotypes + DCO phenotypes x 100

=
total progeny

Map distance = % recombination 4. We can now draw a map segment showing order
and distances among loci. Again, note that the orders
=SCO phenotypes + DCO phenotypes x 100 bac and cab are equivalent and that the left/right the
total progeny orientation of this map is arbitrary.

Map distance (ba) = 112 + 102 + 18 + 15 x 100 = 24.7% = 24.7 m.u.

b a c
1000
| 24.7 | 15.8 |
Map distance (ac) = 66 + 59 + 18 + 15 x 100 = 15.8% = 15.8 m.u.
1000 | 40.5 |

Map distance (bc) = 24.7 m.u. + 15.8 m.u. = 40.5 m.u.

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USING A GENE MAP USING A GENE MAP

• The gene map can be used as a table of
probabilities to predict the expected amount of
recombination between certain loci.
• In a test cross the male contributes only recessive
alleles.
• Recombination occurs in the formation of the
female gametes.
• Therefore, whatever alleles present in the female
gamete will be expressed in the phenotype of the
offspring.
• There is a certain probability that a crossover will
form between a and b loci (equivalent to the map
distance between a and b) and another
independent probability that a cross-over will occur
between b and c loci (equivalent to the map
distance between b and c).
• The probability of a double crossover is the
PRODUCT of these two independent probabilities.

Example 2: Given the map segment Expected SCO (cn-vg)

cn vg sm
| 9.5 | 24.5 | From the gene map 9.5% of the gametes would be expected
to have crossovers between cn and vg, however, this
In a testcross of cn+vg+sm+ // cn vg sm includes the 2.3% of double crossovers.

Expected DCO = (% recomb. cn-vg) (% recomb. vg-sm) Therefore, 9.5-2.3 = 7.2% of the female gametes should
= 0.095 x 0.245 = 2.3% have single crossovers:
Therefore , we expect to find 2.3% of the female gametes to 3.6% cn vg+ sm+ and 3.6% cn+ vg sm
be the results of double crossovers
1.15% cn+vg sm+
1.15% cn vg+ sm

Factors Affecting Recombination Frequencies

Expected SCO (vg-sm)
From the gene map 24.5% of the gametes would be
expected to have crossovers between vg and sm, this
includes the 2.3% of double crossovers.
Therefore 22.2% of the female gametes should have single
crossovers
11.1% cn+vg+sm and 11.1% cn vg sm+
1. Sex. In general, the heterogametic sex of a species has
lower crossover frequencies, e.g. Drosophila melanogaster
– crossing-over in males is completely supressed
2. Maternal Age. Crossing-over tends to decrease when the
maternal age increase.
3. Temperature. In Drosophila, crossing-over tends to
increase when the temperature is cooler or warmer than
22oC.
4. Cytoplasmic effect. Some female Drosophila had reduced
a recombination frequency that passes through their
daughters, indicating that the crossover factors are carried
in the cytoplasm.

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Factors Affecting Recombination Frequencies
5. Nutrition. Young Drosophila females on high calcium diet
showed deceased crossing-over. Larval starvation at
certain ages generally increased crossing-over.
6. Chemical effects. Crossing-over increased upon
injection of antibiotics, such as mitomycin C and
actinomycin D.
7. Radiation. When Drosophila exposed to X-ray irradiation,
crossing-over increases.
8. Genotype. Certain genes affected the preconditions for
exchange. e.g. chromosome pairing. Others acted after
pairing had been completed
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Factors Affecting Recombination Frequencies
9. Chromosome Structure. Crossing-over is reduced in the
heterozygotes of structural rearrangements of the
chromosome. Sturtevant (1926) observed that
aberrations in one pair of chromosomes increased the
frequency of crossing-over in other non-homologous
chromosomes.
10. Centromere. Genes located close to the centromere
tended to show reduced crossing-over, but the physical
distance between them was not changed.