Chapter 5

Linkage and
Chromosome Mapping in
Eukaryotes
Dr. Ayman El-Shibiny
aelshibiny@zewailcity.edu.eg
 Chapter 5 Contents

7.1 Genes Linked on the Same Chromosome Segregate Together

7.2 Crossing Over Serves as the Basis of Determining the Distance
between Genes during Mapping
7.3 Determining the Gene Sequence during Mapping Requires the
Analysis of Multiple Crossovers
7.4 As the Distance between Two Genes Increases, Mapping
Estimates Become More Inaccurate
7.5 Chromosome Mapping Is Now Possible Using DNA Markers and
Annotated Computer Databases
7.6 Other Aspects of Genetic Exchange
7.7 Did Mendel Encounter Linkage?
 Introduction

• Sutton (1903) stated that there are many more “unit

factors” than chromosomes
• Certain genes segregate as if they were linked and are
part of the same chromosome, thus being inherited as a
single unit (linked)
• During Meiosis I Prophase I, synapsed chromosomes
reciprocally exchange segments which reshuffles
(recombines) alleles between homologs
– The frequency of crossing over between any two loci
on a single chromosome is proportional to the
distance between them (interlocus distance)
• Allele: It is the alternative
form of a gene for a
character producing different
effects.
• Diploid organisms have one
copy of each gene (and,
therefore, one allele) on each
chromosome.
• A locus (plural loci) is the
specific location of a gene on
a chromosome.
• The ordered list of loci known
for a particular genome is
called a genetic map.
 MITOSIS MEIOSIS
Parent cell MEIOSIS I
Chiasma

Prophase Prophase I
Chromosome Chromosome
Duplicated Homologous
duplication duplication
chromosome 2n  6 chromosome pair

Metaphase Metaphase I

Anaphase Anaphase I
Telophase Daughter Telophase I
cells of Haploid
meiosis I n3

2n 2n MEIOSIS II
Daughter cells n n n n
of mitosis
Daughter cells of meiosis II
5.1 Genes Linked on the Same Chromosome
Segregate Together
 Complete Linkage and Crossing Over
• Complete linkage
– No crossing over between two genes
– Produces parental (non-crossover) gametes

• Crossing over
– Occurs between two nonsister chromatids
– Both parental and recombinant (crossover)
gametes are produced

© 2015 Pearson Education, Inc.

 Section 5.1

• Genes assort independently if they are on

different chromosomes but show linkage if they
are on the same chromosome
• Figure 7-1 contrasts the meiotic consequences of
(a) independent assortment, (b) linkage without
crossing over, and (c) linkage with crossing over
 Section 5.1

• With independent assortment of two pairs of

chromosomes, each containing one heterozygous
gene pair, no linkage is exhibited
• Four genetically different gametes, each
containing a different combination of alleles, are
formed in equal proportions
Figure 7-1
 Section 5.1

• In genes linked on the same chromosome, no

crossing over occurs and only two genetically
different gametes are produced. [Figure 7-1(b)]
– Complete linkage produces only parental or
noncrossover gametes in equal proportions
• Crossover between two linked genes involves
two nonsister chromatids and generates two
new allele combinations called recombinant or
crossover gametes [Figure 7-1(c)]
Figure 7-1
 Section 5.1

• When the loci of the two linked genes are far

apart, the number of recombinants approaches
and doesn’t exceed 50 percent
• Two parental types and two recombinant
gametes result when recombination
approaches 50 percent
Figure 7-1
 Linkage Ratio and Groups
• Linkage ratio
– Complete linkage between two genes due to close
proximity
– Unique F2 phenotypic ratio results
• Linkage group
– Genes on the same chromosome are part of a
linkage group
– Number of linkage groups should correspond to
haploid number of chromosomes

© 2015 Pearson Education, Inc.

Figure 7-2
 5.2 Crossing Over Serves as the Basis of
Determining the Distance between Genes
during Mapping
 Section 5.2

• The percentage of offspring resulting from

recombinant gametes is variable and depends on
the distance between the two genes on the
chromosome
 Section 5.2 Morgan, Sturtevant, and
Crossing Over
• Studies with Drosophila show that synapsed
chromosomes in meiosis wrap around each
other to create chiasmata, X-shaped
intersections, which are points of genetic
exchange
• Morgan suggested that such exchanges lead
to recombinant gametes (Figure 7-3)
Figure 7-3
 Section 5.2

• Linked genes exist in a linear order along the

chromosome, and the variable amount of
exchange occurs between any two genes during
gamete formation
• Two genes located relatively close to each other
along a chromosome are less likely to have a
chiasma form between them, and it is less likely
that crossing over will occur
 Section 5.2 Sturtevant and Mapping
• The recombination frequencies between linked
genes are additive, and the frequency of
exchange is an estimate of the relative distance
between two genes along the chromosome
• The data shown in previous figure present the
following recombination between each pair of
these three genes:
• 1- yellow- white 0.5%
• 2- white – miniature 34.5%
• 3- yellow – miniature 35.4%
• Yellow and white genes are apparently close to
each other because the recombination
frequency is low (0.5%)
• However both of these genes are much farther
apart from miniature genes because the white-
miniature (34.5%) and yellow-miniature
(35.4%) combinations show larger
recombination frequencies
• Because miniature shows more recombination
with yellow than with white (35.4% versus
34.5%), it follows that white is located
between the other 2 genes
• One map unit (mu) or centimorgans (cM) is
defined as 1 percent recombination between
two genes on a chromosome
 Section 5.2

• Figure 7-4 shows a chromosome map of three

genes on the X chromosome of Drosophila.
• Research has firmly established the chromosomal
theory that chromosomes contain genes in linear
order and are the equivalent of Mendel’s unit
factors
 Section 5.2 Single Crossover

• The farther apart two loci are along a

chromosome, the more likely a random
crossover will occur
• A single crossover (SCO) between two
nonsister chromatids alters the linkage
between two genes only if the crossover
occurs between those two genes (Figure 7-5)
Figure 7-5
 Single Crossovers

• Single exchange between two nonsister

chromatids in tetrad stage
– Two noncrossover (parental) gametes produced
– Two crossover (recombinant) gametes produced

© 2015 Pearson Education, Inc.

Figure 7-6
5.3 Determining the Gene Sequence
during Mapping Requires the
Analysis of Multiple Crossovers
 Multiple Exchanges

• Single crossover
– Used to determine distance between two linked
genes
• Double crossover
– Double exchanges of genetic material
– Used to determine distance between three linked
genes
– Genes must be heterozygous for two alleles

© 2015 Pearson Education, Inc.

 Section 5.3 Multiple Crossovers

• Double exchanges of genetic material result

from double crossovers (DCOs) and can be
used to determine the order of three genes
on the chromosome (Figure 7-7)
• To study double exchanges, three pairs of
genes must be investigated, each
heterozygous for two alleles
 Section 5.3
• The mathematical probability of two
independent events occurring simultaneously is
equal to the product of the individual
probabilities (product law)
• The expected frequency of double-crossover
gametes is much lower than that of either
single-crossover gamete class
• If four or five genes are being mapped, even
fewer triple and quadruple crossovers can be
expected
• Suppose that crossover gametes resulting
from single exchanges are recovered 20% of
the time (p= 0.20) between A and B, and 30%
of the time (p= 0.30) between B and C
• The probability of recovering a double
crossover gamete arising from 2 exchanges
(between A and B, and between B and C) is
predicted to be (0.20)(0.30)= 0.06 or 6%
Figure 7-7
 Three-Point Mapping in Drosophila
• To perform a successful mapping cross, three
criteria must be met:
– Parent must be heterozygous for all three
genes under consideration
– Phenotypic class must reflect genotype of
gametes of parents
– Sufficient number of offspring must be
produced for representative sample

© 2015 Pearson Education, Inc.

• In three-point mapping, the parent must be
heterozygous for all three genes under
consideration
• A three-point mapping cross is shown in
Figure 7-8
 Figure 7-8

(y) yellow body color,

(w) white eye color, and
(ec) echinus eye shape
 Section 5.3

• The noncrossover F2 phenotypes occur in the

greatest proportion of offspring
• The double-crossover phenotypes occur in the
smallest proportion
 Section 5.3

• Because the F2 phenotypes complement each

other (i.e., one is wild type and the other is
mutant for all three genes), they are called
reciprocal classes of phenotypes
 Section 5.3

• The distance between two genes in a three-point

cross is equal to the percentage of all detectable
exchanges occurring between them and includes
all single and double crossovers (Figure 7-8)
 Section 5.3 Determining the Gene
Sequence
• There is a straightforward method for
determining gene order from a three-point cross
• Figure 7-9 illustrates the steps applied to each of
the possible arrangements of the three genes
– First determine the arrangement of alleles on the
homologs of the heterozygote yielding the gametes
by locating the reciprocal noncrossover phenotypes.
Then test each of three possible orders to determine
which yields the observed double-crossover
phenotypes—the one that does so represents the
correct order
Figure 7-9

yellow body color, white eye color, and echinus eye shape
 Section 5.3 Solving an Autosomal
Mapping Problem
• An example of a three-point cross and mapping
of the three linked genes involved is shown in
Figures 7-10 and 7-11
• The experimental cross with corn still needs to
meet the three basic criteria as with Drosophila
– One parent must be heterozygous of all traits
studied
– The genotypes must be apparent from the
phenotype
– A sufficient sample size is needed
 Figure 7-10

The recessive mutant

genes bm (brown
midrib), v (virescent
seedling), and pr
(purple aleurone) are
linked on chromosome
5
Figure 7-11
5.4 As the Distance between Two Genes
Increases, Mapping Estimates Become
More Inaccurate
 Section 5.4

• The expected frequency of multiple exchanges

between two genes can be predicted from the
distance between them
• The farther apart two genes are, the greater the
probability that undetected crossovers will
occur
– The degree of inaccuracy increases as the distance
between them increases [Figure 7-12(b)]
– The most accurate maps are constructed from
closely linked genes
Figure 7-12
 Section 5.6 Sister Chromatid Exchanges
between Mitotic Chromosomes
• Sister chromatid exchanges (SCEs) occur
during mitosis but do not produce new allelic
combinations
 Section 5.6

• Sister chromatids involved in mitotic exchanges

are sometimes called harlequin chromosomes
because of their patchlike appearance when
stained and viewed under a microscope (Figure
7-14)
Figure 7-14
 Section 5.6
• The significance of SCEs is still uncertain, but it has
been observed that agents that induce
chromosome damage increase the frequency of
SCEs
– Viruses, X rays, UV light, chemical mutagens
5.7 Did Mendel Encounter Linkage?
 Section 5.7

• Mendel worked with three genes in chromosome

4, two genes in chromosome 1, and one gene
each in chromosomes 5 and 7.
• The genes, however, are so far apart that linkage
is not detected. Thus it is not astonishing that
Mendel did not run into the complications of
linkage and did not avoid it by choosing one
gene from each chromosome