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Genetic Linkage and Genetic
Maps
The Background
Index to this page
Independent Assortment
An example of linkage
Testcross
Chromosome Maps
What about humans?
Genetic vs. Physical Maps
Gregor Mendel analyzed the pattern of inheritance of seven pairs of
contrasting traits in the domestic pea plant. He did this by cross-breeding dihybrids; that is, plants that
were heterozygous for the alleles controlling two different traits.
Example
Producing dihybrids (F1)
He mated a variety that was pure-breeding (hence homozygous) for round (RR), yellow (YY) seeds
with one that was pure-breeding for wrinkled (rr), green (yy) seeds. All the offspring (F1) produced
from this mating were dihybrids; that is, heterozygous for each pair of alleles (RrYy). Furthermore,
all the seeds were round and yellow, showing that the genes for round and yellow are dominant.
Mating the dihybrids to produce an
F2 generation
Mendel then crossed these dihybrids. If it is
inevitable that round seeds must always be
yellow and wrinkled seeds must be green, then
he would have expected that this would
produce a typical monohybrid cross: 75%
round-yellow; 25% wrinkled-green. But, in
fact, his mating generated seeds that showed all
possible combinations of the color and texture
traits.
9/16 of the offspring were round-yellow
3/16 were round-green
3/16 were wrinkled-yellow, and
1/16 were wrinkled-green
Finding in every case that each of his seven traits was inherited independently of the others, he formed
his "second rule" the Rule of Independent Assortment:
The inheritance of one pair of factors (genes) is independent of the inheritance of the
other pair.
Today we know that this rule holds only if two conditions are met:
the genes are on separate chromosomes or
the genes are widely separated on the same chromosome.
Mendel was lucky in that every pair of genes he studied met one requirement or the other. The table
shows the chromosome assignments of the seven pairs of alleles that Mendel studied. Although all of
these genes showed independent assortment, several were, in fact, syntenic with three loci occurring
on chromosome 4 and two on chromosome 1. However, the distance separating the syntenic loci was
sufficiently great that the genes were inherited as though they were on separate chromosomes.
Trait
Seed form
Seed color
Pod color
Pod texture
Flower color
Flower location
Plant height
Phenotype
Alleles Chromosome
round-wrinkled R-r
7
yellow-green
I-i
green-yellow Gp-gp
smooth-wrinkled V-v
purple-white
axial-terminal
tall-dwarf
A-a
Fa-fa
Le-le
1
5
4
1
4
4
With the rebirth of genetics in the 20th century, it quickly became apparent that Mendel's second rule
does not apply to many matings of dihybrids. In many cases, two alleles inherited from one parent
show a strong tendency to stay together as do those from the other parent. This phenomenon is called
linkage.
An example of linkage
Start with two different strains of corn (maize).
one that is homozygous for two traits
yellow kernels (C,C) which are filled with endosperm causing the kernels to be
smooth (Sh,Sh).
a second that is homozygous for
colorless kernels (c,c) that are wrinkled because their endosperm is
shrunken (sh,sh)
When the pollen of the first strain is dusted on the silks of the second (or vice versa), the kernels
produced (F1) are all yellow and smooth. So the alleles for yellow color (C) and smoothness (Sh) are
dominant over those for colorlessness (c) and shrunken endosperm (sh).
To simplify the analysis, mate the
dihybrid with a homozygous
recessive strain (ccshsh). Such a
mating is called a test cross because
it exposes the genotype of all the
gametes of the strain being evaluated.
According to Mendel's second rule,
the genes determining color of the
endosperm should be inherited
independently of the genes
determining texture. The F1 should
thus produce gametes in
approximately equal numbers.
CSh, as inherited from one
parent.
csh, as inherited from the other parent
Csh, a recombinant
cSh, the other recombinant.
All the gametes produced by the doubly homozygous recessives would be csh.
If the inheritance of these genes observes Mendel's second rule; i.e., shows independent assortment,
union of these gametes should produce approximately equal numbers of the four phenotypes. But as
the chart shows, there is instead a strong tendency for the parental alleles to stay together. It occurs
because the two loci are relatively close together on the same chromosome. Only 3.0% of the gametes
contain a recombinant chromosome.
During prophase I of meiosis, pairs of duplicated homologous
chromosomes unite in synapsis and then nonsister chromatids exchange
segments during crossing over. It is crossing over that produces the
recombinant gametes. In this case, whenever a crossover occurs
between the locus for kernel color and that for kernel texture, the
original combination of alleles (CSh and csh) is broken up and a
chromosome containing Csh and one containing cSh will be produced.
Link to a discussion of the demonstration by Harriet Creighton and
Barbara McClintock that recombination of linked genes occurs during
crossing over.
Chromosome Maps
The percentage of recombinants formed by F1 individuals can range
from a fraction of 1% up to the 50% always seen with gene loci on
separate chromosomes (independent assortment). The higher the
percentage of recombinants for a pair of traits, the greater the distance
separating the two loci. In fact, the percent of recombinants is
arbitrarily chosen as the distance in centimorgans (cM), named for the
pioneering geneticist Thomas Hunt Morgan. In our case, the c and sh
loci are said to be 3.0 cM apart.
The procedure can be continued with another locus on the same
chromosome.
Example
Test crossing a corn plant that is dihybrid for the C,c alleles and the alleles for bronze color (Bz, bz)
produces 4.6% recombinants. So these two loci are 4.6 cM apart. However, is the bz locus on the
same side of c as sh or is it on the other side?
The answer can be found by test crossing the dihybrid Shsh, Bzbz. If the percentage of recombinants
is less than 4.6%, then bz must be on the same side of locus c as locus sh. If greater than 4.6%, it must
be on the other side.
In fact, the recombination frequency is
2.0%, telling us that the actual order of loci
is
c — sh — bz.
Mapping by linkage analysis is best done with loci that are relatively close together; that is, within a
few centimorgans of each other. Why? Because as the distance between two loci increases, the
probability of a second crossover occurring between them also increases.
View an example of multiple crossovers.
But a second crossover would undo the effect of the first and restore the parental combination of
alleles. These would show up as nonrecombinants. Thus as the distance between two loci increases,
the percentage of recombinants that forms understates the actual distance in centimorgans that
separates them.
And, in fact, that has happened in this example. Using a three-point cross reveals the existence of a
small number of double recombinants and tells us that the actual distance c—bz is indeed 5 cM as we
would expect by summing
c—sh = 3 cM
sh—bz = 2 cM
and not the 4.6 cM revealed by the dihybrid cross.
A three-point cross also tells us the gene order in a single cross rather than the three we needed here.
Read how.
There are other problems with preparing genetic maps of
chromosomes.
The probability of a crossover is not uniform along the entire
length of the chromosome.
Crossing over is inhibited in some regions (e.g., near
the centromere).
Some regions are "hot spots" for recombination (for
reasons that are not clear). Approximately 80% of
genetic recombination in humans is confined to just
one-quarter of our genome.
In humans, the frequency of recombination of loci on most
chromosomes is higher in females than in males. Therefore,
genetic maps of female chromosomes are longer than those
for males.
A genetic map of chromosome 9 (the one that carries the C, Sh, and
bz loci) of the corn plant (Zea mays) is shown on the right. If one
maps in small intervals from one end of a chromosome to the other,
the total number of centimorgans often exceeds 100 (as you can see
for chromosome 9). However, even for widely-separated loci, the
maximum frequency of recombinants that can form is 50%. And
this is also the frequency of recombinants that we see for genes
independently assorting on separate chromosomes. So we cannot
tell by simply counting recombinants whether a pair of gene loci is
located far apart on the same chromosome or are on different
chromosomes. As we saw above, several of Mendel's independently assorting traits are controlled by
genes on the same chromosome but located so far apart that they are inherited as if they were located
on different chromosomes.
Genes that are present on the same chromosome are called syntenic.
What about humans?
Obviously one cannot perform controlled matings of humans to map our chromosomes. However, it is
possible to estimate map positions by examining linkage in several generations of relatives.
For example, blood samples from several large Mormon families in Utah, where all the members of at
least three generations were alive to be sampled, have been collected and stored. These have already
been used to establish genetic linkage relationships and will be available in the years ahead to study
other human genes as they are identified.
Using restriction fragment polymorphisms (RFLPs) to map the location of disease-causing genes in
humans.
Genetic versus Physical Maps
Chromosome mapping by counting recombinant phenotypes produces a genetic map of the
chromosome. But all the genes on the chromosome are incorporated in a single molecule of DNA.
Genes are simply portions of the molecule (open reading frames or ORFs) encoding products that
create the observed trait (phenotype). The rapid progress in DNA sequencing has produced complete
genomes for hundreds of microbes and several eukaryotes.
Table showing some of the organisms for which the complete genome is known.
Having the complete sequence makes it possible to determine directly the order and spacing of the
genes. Maps drawn in this way are called physical maps.
What is the relationship between the genetic map and the physical map of a chromosome? As a very
rough rule of thumb, 1 cM on a chromosome encompasses 1 megabase (1 Mb = 106 bp) of DNA. But
for the reasons mentioned above, this relationship is only approximate. Although the genetic maps of
human females average 90% longer than the same maps in males, their chromosomes contain the
same number of base pairs. So their physical maps are identical.
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21 April 2014