4
Gene Linkage and
Genetic Mapping
Mendel’s Laws: Chromosomes
Homologous pairs of chromosomes: contain
genes whose information is often nonidentical =alleles
• Different alleles of the same gene segregate
at meiosis I
• Alleles of different
genes assort
independently in
gametes
• Genes on the same
chromosome exhibit
linkage: inherited together
Gene Mapping
• Gene mapping determines the order of
genes and the relative distances between
them in map units
• 1 map unit=1 cM (centimorgan)
• Alleles of two different genes on the same
chromosome are cis
• Alleles of two different genes on different
homologues of the same chromosome are
trans
Gene Mapping
• Gene mapping
methods use
recombination frequencies between
alleles in order to determine the relative
distances between them
• Recombination frequencies between
genes are inversely proportional to their
distance apart
• Distance measurement: 1 map unit = 1
percent recombination
Gene Mapping
• Recombination between linked genes located
on the same chromosome involves
homologous crossing-over = allelic
exchange between
them
• Recombination changes
the allelic arrangement
on homologous
chromosomes =
recombinant
Gene Mapping
• Genes with recombination frequencies less
than 50 percent are on the same
chromosome (linked)
• Two genes that undergo independent
assortment have recombination frequency
greater than 50 percent
and are located on
nonhomologous
chromosomes or
far apart on the same
chromosome (unlinked)
Recombination
• Recombination between linked genes
occurs at the same frequency whether
alleles are in cis or trans configuration
• Recombination frequency is specific for a
particular pair of genes
• Recombination frequency increases with
increasing distances between genes
Genetic Mapping
• Map distance between two genes = one
half the average number of crossovers in
that region
• Map distance=recombination frequency
over short distances because all
crossovers result in recombinant gametes
• Genetic map = linkage map = chromosome
map
Genetic Mapping
• Linkage group = all known genes on a
chromosome
• Physical distance does not always
correlate with map distance; less
recombination occurs in heterochromatin
than euchromatin
• Locus=physical location of a gene on
chromosome
Gene Mapping: Crossing Over
• Crossing-over between genes on
homologous chromosomes changes the
linkage arrangement of alleles on a single
chromosome
• Two exchanges between the same
chromatids result in a
reciprocal exchange of
the alleles in the region
between the cross-over
points
Gene Mapping: Crossing Over
• Cross-overs which occur outside the region
between two genes will not alter their
arrangement
• Double cross-overs
restore the original allelic
arrangement
• Cross-overs involving
three pairs of alleles
specify gene order =
linear sequence of genes
Genetic vs. Physical Distance
• Map distances based on recombination
frequencies are not a direct measurement
of physical distance along a chromosome
• Recombination “hot spots” overestimate
physical length
• Low rates in heterochromatin and
centromeres underestimate actual
physical length
Gene Mapping
• Mapping function: the relation between
genetic map distance and the frequency of
recombination
• Chromosome interference: cross-overs in
one region decrease the probability of
second cross-over
• Coefficient of coincidence=observed
number of double recombinants divided
by the expected number
Gene Mapping: Human
Pedigrees
• Methods of recombinant DNA technology
are used to map human chromosomes
and locate genes
• Genes can then be cloned to determine
structure and function
• Human pedigrees and DNA mapping are
used to identify dominant and recessive
disease genes
Gene Maps: Restriction
Endonucleases
• Restriction endonucleases are used to map
genes as they produce a unique set of
fragments for a gene
• EcoR1 cuts ds DNA at the sequence = 5’GAATTC-3’ wherever it occurs
• There are >100
restriction
endonucleases in use,
and each recognizes
a specific sequence of
DNA bases
Gene Maps: Restriction
Enzymes
• Differences in DNA sequence generate
different recognition sequences and DNA
cleavage sites for specific restriction
enzymes
• Two different genes will produce different
fragment patterns when cut with the same
restriction enzyme due to differences
in DNA
sequence
Gene Maps: Restriction
Enzymes
• Polymorphism= relatively common genetic
difference in a population
• Changes in DNA sequence = mutation may
cause polymorphisms which alter the
recognition sequences
for restriction enzymes
= restriction fragment
length polymorphisms
(RFLPs)
Gene Maps: Restriction
Enzymes
• RFLPs can map human genes
• Genetic polymorphism resulting from a
tandemly repeated short DNA sequence =
simple tandem repeat polymorphism
(STRP)
• Most prevalent type of polymorphism is a
single base pair difference = simplenucleotide polymorphism (SNP)
• DNA chips can detect SNPs
Human Gene Mapping
• Human pedigrees can
be analyzed for the
inheritance pattern of different alleles of a
gene based on differences in STRPs and
SNPS
• Restriction enzyme cleavage of
polymorphic alleles differing RFLP
pattern produces different size fragments
by gel electrophoresis
Gene Mapping: Tetrad Analysis
• In Neurospora, meiotic cell division produces
four ascospores; each contains a single
product of meiosis
• Analysis of ascus tetrads
shows recombination of
unlinked genes
• Tetrad analysis shows
products of single and
double 2, 3 and 4 strand
cross-overs of linked
genes
Tetrad Analysis
• In tetrads when two pairs of
alleles are segregating, 3
possible patterns of
segregation:
-parental ditype (PD): two
parental genotypes
-nonparental ditype (NPD): only recombinant
combinations
-tetratype (TT): all four genotypes observed
Neurospora: Meiotic Segregation
• Products of meiotic segregation can be
identified by tetrad analysis
• Meiosis I segregation in the
absence of cross-overs
produces 2 patterns for a
pair of homologous chromosomes
• Meiosis II segregation after a
single cross-over produces
four possible patterns of
spores
Tetrad Analysis
• Unlinked genes produce parental and
nonparental ditype tetrads with equal
frequency
• Linked genes produce parental ditypes at
much higher frequency than nonparental
ditype
• Gene conversion = identical alleles
produced by heteroduplex mismatch
repair during recombination
Recombination: Holliday Model
Homologous recombination:
• single-strand break in homologues pairing
of broken strands occurs
• branch migration: single strands pair with
alternate homologue
• nicked strands exchange places and gaps
are sealed to form recombinant by
Holliday junction-resolving enzyme