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LINKAGE AND
CHROMOSOME MAPPNG
Prepared by -
RAKESH CHOUDHARY
M.Sc.(AGRI)
GENETICS AND PLANT BREEDING
WELCOME
Linkage and Chromosome
Mapping
Genetic linkage was first discovered by the British
geneticists William Bateson and Reginald Punnett shortly
after Mendel's laws were rediscovered. The understanding
of genetic linkage was expanded by the work of Thomas
Hunt Morgan. Morgan's observation that the amount of
crossing over between linked genes differs led to the idea
that crossover frequency might indicate the distance
separating genes on the chromosome.
Alfred Sturtevant, a student of Morgan's, first
developed genetic maps, also known as linkage maps.
Alfred H. Sturtevant discovered the linkage of genes and made the first genetic
map.
Terminology
• Linkage - The presence of two or more genes in the
same chromosome, which produces a tendency for
parental traits to be inherited together or travel together.
• Genes are units of heredity, whereas chromosomes are
units of transmission.
• Linkage may be complete, incomplete, or absent (not
detectable), depending upon the distance between
linked genes in a chromosome.
Linkage group.
A group of genes inherited together --because they are
in the same chromosome.
In any organism,there are as many linkage
groups as there are nonhomologous(haploid)
chromosomes.
Recombination- New combinations of linked genes
that result after crossing-over.
A
B
a
B
a
b
A
b
Parental
(old combination)
Recombinant (new combination,
nonparental)
COUPLING AND REPULSION PHASE
Genetic map.
A line diagram showing the (linear) order of
two or more linked genes and the distances between
them.
Map distance. % recombination between any two linked
genes x 100.
Map unit. 1 % recombination = 1 centi-Morgan (cM). This
is approximately one million bp. in duplex DNA.
Cytological map. A line diagram showing the actual physical
distances between linked genes.
Genetic and cytological maps have the same gene order
but different map distances.
a
a
b
b
c
c
d
Genetic map
d
Cytological map
Example. Genes "a" and "b" are in the same
chromosome: three possible scenarios (below).
Linkage
a
b
"a" and "b" are too close to each other.
a
<50
b
Complete linkage
In Complete linkage
"a" and "b" are separated to allow crossing-over
between them in up to 100% of meiocytes.
a
>50
b
Not detectable
"a" and "b" are too far apart to allow crossing-over
between them in all of % of meiocytes.
Linkage map
A linkage map is a genetic map of a
species or experimental population
that shows the position of its known
genes or genetic markers relative to
each other in terms of recombination
frequency, rather than as specific
physical distance along each
chromosome. Linkage mapping is
critical for identifying the location of
genes that cause genetic diseases.
How Linkage violates Mendel’s Second Law
A dihybrid testcross yields results that are not
consistent with the expected 1:1:1:1 ratio.
P
Tall, Round x Dwarf, Pear
(+ + / + +)
(dd / pp)
F1
Tall, Round
(+ d / + p)
Testcross
+d/+p x
Observed
Tall, round 81 (4)
Tall, pear 22 (1)
Dwarf, round 17 (1)
Dwarf, pear 79 (4)
199
If linkage
dd / pp
Expected
49.75 (1)
49.75 (1)
49.75 (1)
49.75 (1)
199
If independent
Drosophila, bw (brown eyes) and hv (heavy wing vein)
are closely linked and both wild types (red, thin) are
dominant
Cross homozygous bw hv+ with bw + hv homozygote
F1 is bw hv + /bw + hv (red with thin veins)
F2 has only 3 phenotypes (not four) at a 1:2:1 ratio
(brown, thin) : (red, thin) : (red, heavy)
Undetectable crossing-over or exchange
Detectable crossing-over or exchange
Why Recombination cannot exceed 50%?
because:
a)
Even if every meiocyte had a crossing-over
between
two linked genes, only 2 of 4 chromatids in a
bivalent
(tetrad) was involved in crossing-over. (2/4 = 50%)
Two-Point Crosses determine linkage,
and distance between two linked genes.
Cross parents differing with respect to the alleles of
two linked genes, testcross the F1, and analyze the
testcross progeny.
Map Distance = Total Recombinants
x 1oo
(% recomb.)
Total Recomb. + Parentals
Two-point crosses are good but not
adequate; they have disadvantages.
• Underestimate map distance when it is > 10 cM
(double crossovers cancel each other).
• Provide no information about relative positions of two
linked genes.
• Do not allow detection of double crossovers.
Cure: Three-point crosses.
Three point test cross involves three gene.
It helps to know the gene order or gene
sequence to overcome two point test cross
disadvantage.
In three point test cross two single crossing
over and double crossing over occurs
between different genes.
Single crossover frequencies give distance
between two loci but order can be more
difficult to determine based only upon this
type of data
Example of a double crossover using 3 marker
loci are shown in Figure 5-7
Frequency of a double crossover is expected
to the the product of the two individual
frequencies
Individual probabilities of 0.20 and 0.30
are going to both occur about 0.06
For 0.03 and 0.02 you get 0.0006 (lots of
flies to look over…)
LOD score method for estimating recombination frequency
The LOD score (logarithm (base 10) of odds), developed by Newton E. Morton,
is a statistical test often used for linkage analysis in human, animal, and plant
populations. The LOD score compares the likelihood of obtaining the test data if
the two loci are indeed linked, to the likelihood of observing the same data
purely by chance. Positive LOD scores favor the presence of linkage, whereas
negative LOD scores indicate that linkage is less likely. Computerized LOD score
analysis is a simple way to analyze complex family pedigrees in order to
determine the linkage between Mendelian traits (or between a trait and a
marker, or two markers).
NR denotes the number of non-recombinant offspring, and R denotes the
number of recombinant offspring. The reason 0.5 is used in the denominator is
that any alleles that are completely unlinked (e.g. alleles on separate
chromosomes) have a 50% chance of recombination, due to independent
assortment.
COEFFICIENT OF CO-INCIDENCE (CC) =
0 < CC > 1
INTERFERENCE =
1 - cc
OBSERVED NO. OF DOUBLE CROSSSOVER
EXPECTED FREQUENCY OF DOUBLE CROSS
OVER
Phenotypic recombination frequencies can be corrected to
approximate cross over frequencies with a equation.
It is curve between measured map distance against actual map
distance.
First mapping function-
1 -HALDANE FUNCTION- proposed by J.B.S HALDANE
X= 0.5log(1-2y)
2. KOSAMBI FUNCTION- proposed by D.D KOSAMBI
X= 0.25 log(1+2y)
(1-2y)
Here x = estimate of actual frquency of c.o.
y= phenotypic recombination frequency
1