Linkage, Recombination, and Crossing Over

Linkage, Recombination, and 

Crossing Over 

Genes that are on the same chromosome 

travel through meiosis together; however, 

alleles of chromosomally linked genes can 

be recombined by crossing over.

A Chromosome 

Map

Heterozygous 

for two traits 

Gametes: 

GR; 

Gr; 

gR; 

gr; 

GgRr 

Phenotypes: 

YeRo-YeWr-GrRo-GrWr 

9 - 3 - 3 - 1 

3

Linked Genes Do Not 

Assort Independently

Linkage Phases: 

Coupling and Repulsion


MAX 50% recombination

Multiple 

Crossovers

Crossing Over Occurs in 

Prophase of Meiosis I

Key Points 

• Linkage between genes is detected as a deviation 

from expectations based on Mendel’s Principle of 

Independent Assortment. 

• The frequency of recombination measures the 

intensity of linkage. In the absence of linkage, this 

frequency is 50 percent; for very tight linkage, it is 

close to zero.

Key Points 

• Recombination is caused by a physical exchange between 

paired homologous chromosomes early in prophase of the 

first meiotic division after chromosomes have duplicated. 

• At any one point along a chromosome, the process of 

exchange (crossing over) involves only two of the four 

chromatids in a meiotic tetrad. 

• Late in prophase I, crossovers become visible as 

chiasmata.

Chromosome Mapping 

Linked genes can be mapped on a 

chromosome by studying how often 

their alleles recombine.

Observable Outcomes of 


• Formation of chiasmata in late prophase. 

• Recombination between genes on opposites 

sides of the crossover point.

Genetic Map Distances 

• The distance between 

two points on the 

genetic map of a 

chromosome is the 

average number of 

crossovers between 

them.

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

Determining the Gene Order 

• There are 3 possible gene orders 

1. sc - ec - cv 

2. ec - sc - cv 

3. 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).

Calculation of Map Distances

Interference and the Coefficient 

of Coincidence 

• Assuming independence, the expected 

frequency of double crossovers is 0.091 × 

0.105 = 0.0095. 

• The observed frequency of double 

crossovers was 2/3248 = 0.0006. 

• A crossover in one region inhibited a 

crossover nearby.

Recombination Frequency and 

Genetic Map Distance

Recombination Frequency and 

Genetic Map Distance

Chiasma 

Frequency and 

Genetic Map 

Distance

Key Points 

• The genetic maps of chromosomes are based on 

the average number of crossovers that occur 

during meiosis. 

• Genetic map distances are estimated by 

calculating the frequency of recombination 

between genes in experimental crosses.

Key Points 

• Recombination frequencies less than 20 percent 

estimate map distance directly; however, 

recombination frequencies greater than 20 percent 

underestimate map distance because multiple 

crossover events do not always produce 

recombinant chromosomes. 

• An average of one chiasma during meiosis is 

equivalent to 50 centiMorgans of genetic map 

distance.

Genetic Distance 

and Physical Distance

Key Points 

• In Drosophila, genes can be localized on maps of the 

polytene chromosomes by combining recessive mutations 

with cytologically defined deletions and duplications. 

• A deletion will reveal the phenotype of a recessive 

mutation located between its endpoints, whereas a 

duplication will conceal the mutant phenotype. 

• Genetic and cytological maps are colinear; however, 

genetic distances are not proportional to cytological 

distances.

Linkage Analysis in Humans 

Pedigree analysis provides ways or 

localizing genes on human 

chromosomes.

Linkage Between the ABO and 

Nail-Patella Loci

Calculation of the Recombination 

Frequency 

• 4/13 offspring (31%) in 

this pedigree are 

recombinant. 

• Combining data from 

many pedigrees, the 

genetic distance between 

the ABO and NPS1 loci is 

10 cM. 

• Molecular markers can 

also be mapped.

Key Points 

• Linkage between human genes can be detected by 

analyzing pedigrees. 

• Pedigree analysis also provides estimates of 

recombination frequencies to map genes on human 

chromosomes.

• The coefficient of coincidence (c) is the 

ratio of observed double crossovers to 

expected double crossovers. 

c = 0.0006 / 0.0095 = 0.063 

• Interference (I) = 1 - c 

I = 1 - 0.063 = 0.937

Recombination and Evolution 

Recombination—or the lack of it— 

plays a key role in evolution.

Evolutionary Significance of 


• Meiotic recombination is a way of shuffling 

genetic variation to potentiate evolutionary 

change. 

• In sexually reproducing species, 

recombination can allow favorable alleles of 

different genes to come together in the same 

organism.

Inversions Suppress Recombination 

in Heterozygotes

Double Crossovers in Inversion 

Heterozygotes

The Human X and Y 

Chromosomes

Genetic Control of 


• The products of many genes are involved in 

recombination. 

• Crossing over does not occur in Drosophila 

males. 

• The amount of recombination varies among 

species.

Key Points 

• Recombination can bring favorable 

mutations together. 

• Chromosome rearrangements, especially 

inversions, can suppress recombination. 

• Recombination is under genetic control.

Chromosome 9 in Maize

Evidence that Crossing Over 

Causes Recombination

Linkage, Recombination, and Crossing Over

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