In genetics, the coefficient of coincidence (c.o.c.) is a measure of interference in the formation of
chromosomal crossover
Chromosomal crossover, or crossing over, is the exchange of genetic material during sexual reproduction between two homologous chromosomes' non-sister chromatids that results in recombinant chromosomes. It is one of the final phases of geneti ...
s during
meiosis
Meiosis (; , since it is a reductional division) is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately resu ...
. It is generally the case that, if there is a crossover at one spot on a chromosome, this decreases the likelihood of a crossover in a nearby spot.
[ Griffiths AJF, Wessler SR, Lewontin RC, Carroll SB (2008) ''Introduction to Genetic Analysis''. New York: W. H. Freeman and Company.] This is called interference.
The coefficient of coincidence is typically calculated from recombination rates between three genes. If there are three genes in the order A B C, then we can determine how closely
linked they are by frequency of recombination. Knowing the recombination rate between A and B and the recombination rate between B and C, we would naively expect the double recombination rate to be the
product
Product may refer to:
Business
* Product (business), an item that serves as a solution to a specific consumer problem.
* Product (project management), a deliverable or set of deliverables that contribute to a business solution
Mathematics
* Produ ...
of these two rates.
The coefficient of coincidence is calculated by dividing the ''actual'' frequency of double recombinants by this expected frequency:
:c.o.c. = actual double recombinant frequency / expected double recombinant frequency
Interference is then defined as follows:
:interference = 1 − c.o.c.
This figure tells us how strongly a crossover in one of the DNA regions (AB or BC) interferes with the formation of a crossover in the other region.
Worked example
Drosophila
''Drosophila'' () is a genus of flies, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or (less frequently) pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many species ...
females of
genotype
The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the alleles or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a ...
''a
+a b
+b c
+c'' were crossed with males of genotype ''aa bb cc''. This led to 1000 progeny of the following
phenotype
In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological proper ...
s:
:a
+b
+c
+: 244 (parental genotype, shows no recombination)
:a
+b
+c: 81 (recombinant between B and C)
:a
+bc
+: 23 (double recombinant)
:a
+bc: 152 (recombinant between A and B)
:ab
+c
+: 148 (recombinant between A and B)
:ab
+c: 27 (double recombinant)
:abc
+: 89 (recombinant between B and C)
:abc: 236 (parental genotype, shows no recombination)
From these numbers it is clear that the b
+/b
locus
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** ''Locus Award' ...
lies between the a
+/a locus and the c
+/c locus.
There are 23 + 152 + 148 + 27 = 350 progeny showing recombination between genes A and B. And there are 81 + 23 + 27 + 89 = 220 progeny showing recombination between genes B and C. Thus the expected rate of double recombination is (350 / 1000) * (220 / 1000) = 0.077, or 77 per 1000.
However, there are actually only 23 + 27 = 50 double recombinants. The coefficient of coincidence is therefore 50 / 77 = 0.65.
Interference is 1 − 0.65 = 0.35.
High negative interference
When three genetic markers, a, b and c, are all nearby (e.g. within the same
gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
) the coefficient of coincidence (calculated as in the above example) is generally found to be significantly greater than 1. This implies that any individual
recombination event tends to be more closely associated with another nearby recombination event than would be expected by chance. This type of association is known as “negative interference”. When the coefficient of coincidence is substantially greater than 1, it is known as “high negative interference". High negative interference has been reported in
bacteriophage T4
Escherichia virus T4 is a species of bacteriophages that infect ''Escherichia coli'' bacteria. It is a double-stranded DNA virus in the subfamily '' Tevenvirinae'' from the family Myoviridae. T4 is capable of undergoing only a lytic lifecycle ...
(e.g. ) and in human imunodeficiency virus (
HIV
The human immunodeficiency viruses (HIV) are two species of ''Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the immune ...
) infections.
[Anderson JA, Teufel RJ 2nd, Yin PD, Hu WS. Correlated template-switching events during minus-strand DNA synthesis: a mechanism for high negative interference during retroviral recombination. J Virol. 1998 Feb;72(2):1186-94. PMID 9445017]
References
Genetics