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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 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 of
50 percent (or more?) 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
Example: Trihybrid Mapping
• Counts from: LSG/lsg x lsg/lsg
L S G
286 Parental
• n=740
l
L
l
L
l
L
l
s
s
S
S
s
s
S
g
g
G
g
G
G
g
272
4
2
59
44
40
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Parental
r (L & SG)
r (L & SG)
r (G & SL)
r (G & SL)
r (S & GL)
r (S & GL)
&
• Distance L to S: (40+33+4+2)/740 * 100 = 11.2 cM
• Interference = 1-[f(doubles)/ f(single1) *f(single2)]
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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 near or in 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
Tetrad Analysis
• Meiotic spores held in asci
(ascospores)
• Allows recovery of all products of
meiosis
• Two types
• Unordered tetrads (yeast)
• Usually allows gene to gene map distances
• Under rare circumstances, gene to centromere
• Ordered tetrads (neurospora)
• Usually allows gene to centromere map distance
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Unordered Tetrads
• Four kinds of tetrads
• Parental ditype (AB, AB, ab, ab)
• Non-parental ditype (Ab, Ab, aB, aB)
• Tetra-type (AB, Ab, aB, ab)
• When genes tightly linked
• only parentals seen
• When genes unliked
• parentals and non-parentals equal
• tetratypes: gene-centromere X-over
• gene-centromere map possible (1 gene @ cen)
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Unlinked Genes in Tetrads
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Linked Genes in Tetrads
• Also three tetrad types seen
• parental ditypes: no X-overs (2 str doubles)
• non-parental ditypes: 4 str double X-overs
• tetratypes more complicated
• single X-overs
• 3 strand double X-overs
• Formula for Map distance:
• [(1/2 TT’s + 3 NPD’s)/total asci] * 100
• applies only to unordered tetrads
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Linkage and Tetrads
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Ordered Tetrads
• Neurospora Tetrads: two kinds
• First Division Segregation (FDS)
• occurs in absence of recombination
• two versions (rotationally equivalent)
• Second Division Segregation (SDS)
• occurs with gene-centromere X-overs
• four versions (rotationally equivalent)
• Gene-Centromere distance
• (1/2 SDS)/total asci * 100
• applies only to ordered tetrads
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Ordered Tetrads
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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