Chapter Seven: Linkage, Recombination, and Eukaryotic Gene

Mapping
COMPREHENSION QUESTIONS
*1. What does the term recombination mean? What are two causes of recombination?
Recombination means that meiosis generates gametes with different allelic
combinations than the original gametes the organism inherited. If the organism
was created by the fusion of an egg bearing AB and a sperm bearing ab,
recombination generates gametes that are Ab and aB. Recombination may be
caused by loci on different chromosomes that sort independently or by a physical
crossing over between two loci on the same chromosome, with breakage and
exchange of strands of homologous chromosomes paired in meiotic prophase I.
*2. In a testcross for two genes, what types of gametes are produced with (a comp!ete
!in"age, (b independent assortment, and (c incomp!ete !in"age?
(a) Complete linkage of two genes means that only nonrecombinant gametes will be
produced the recombination fre!uency is "ero.
(b) Independent assortment of two genes will result in #$% of the gametes being
recombinant and #$% being nonrecombinant, as would be observed for genes
on two different chromosomes. Independent assortment may also be observed
for genes on the same chromosome, if they are far enough apart that one or
more crossovers occur between them in every meiosis.
(c) Incomplete linkage means that greater than #$% of the gametes produced are
nonrecombinant and less than #$% of the gametes are recombinant the
recombination fre!uency is greater than $ and less than #$%.
#. What effect does crossing o$er ha$e on !in"age?
Crossing over generates recombination between genes located on the same
chromosome, and thus renders linkage incomplete.
%. Why is the fre&uency of recombinant gametes a!ways ha!f the fre&uency of crossing
o$er?
Crossing over occurs at the four&strand stage, when two homologous
chromosomes, each consisting of a pair of sister chromatids, are paired. 'ach
crossover involves (ust two of the four strands and generates two recombinant
strands. )he remaining two strands that were not involved in the crossover
generate two nonrecombinant strands. )herefore, the fre!uency of recombinant
gametes is always half the fre!uency of crossovers.
*'. What is the difference between genes in coup!ing configuration and genes in
repu!sion? What effect does the arrangement of !in"ed genes (whether they are in
coup!ing configuration or in repu!sion ha$e on the resu!ts of a cross?
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
*enes in coupling configuration have two wild&type alleles on the same
chromosome and the two mutant alleles on the homologous chromosome. *enes in
repulsion have a wild&type allele of one gene together with the mutant allele of the
second gene on the same chromosome, and vice versa on the homologous
chromosome. )he two arrangements have opposite effects on the results of a cross.
+or genes in coupling configuration, most of the progeny will be either wild&type
for both genes, or mutant for both genes, with relatively few that are wild&type for
one gene and mutant for the other. +or genes in repulsion, most of the progeny will
be mutant for only one gene and wild&type for the other, with relatively few
recombinants that are wild&type for both or mutant for both.
0. 1ow does one test to see if two genes are !in"ed?
,ne first obtains individuals that are hetero"ygous for both genes. )his may be
achieved by crossing an individual homo"ygous dominant for both genes to one
homo"ygous recessive for both genes, resulting in a hetero"ygote with genes in
coupling configuration. -lternatively, an individual that is homo"ygous recessive
for one gene may be crossed to an individual homo"ygous recessive for the second
gene, resulting in a hetero"ygote with genes in repulsion. )hen the hetero"ygote is
mated to a homo"ygous recessive tester and the progeny of each phenotypic class
are tallied. If the proportion of recombinant progeny is far less than #$%, the genes
are linked. If the results are not so clear&cut, then they may be tested by chi&s!uare,
first for e!ual segregation at each locus, then for independent assortment of the two
loci. .ignificant deviation from results expected for independent assortment
indicates linkage of the two genes.
2. What is the difference between a genetic map and a physica! map?
- genetic map gives the order of genes and relative distance between them based
on recombination fre!uencies observed in genetic crosses. - physical map locates
genes on the actual chromosome or /0- se!uence, and thus represents the
physical distance between genes.
*3. Why do ca!cu!ated recombination fre&uencies between pairs of !oci that are !ocated
re!ati$e!y far apart underestimate the true genetic distances between !oci?
)he further apart two loci are, the more likely it is to get double crossovers
between them. 1nless there are marker genes between the loci, such double
crossovers will be undetected because double crossovers give the same phenotypes
as nonrecombinants. )he calculated recombination fre!uency will underestimate
the true crossover fre!uency because the double crossover progeny are not counted
as recombinants.
4. -5p!ain how one can determine which of three !in"ed !oci is the midd!e !ocus from
the progeny of a three6point testcross.
/ouble crossovers always result in switching the middle gene with respect to the
two nonrecombinant chromosomes. 2ence, one can compare the two double
crossover phenotypes with the two nonrecombinant phenotypes and see which gene
is reversed. In the diagram on the facing page we see that the coupling relationship
30
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
of the middle gene is flipped in the double crossovers with respect to the genes on
either side. .o whichever gene on the double crossover can be altered to make the
double crossover resemble a nonrecombinant chromosome is the middle gene. If we
take either of the double crossover products ! / r or + m ,, changing the / gene
will make it resemble a nonrecombinant.
l m r l M r

L M R L m R
*17. What does the interference te!! us about the effect of one crosso$er on another?
- positive interference value results when the actual number of double crossovers
observed is less than the number of double crossovers expected from the single
crossover fre!uencies. )hus positive interference indicates that a crossover inhibits
or interferes with the occurrence of a second crossover nearby.
Conversely, a negative interference value, where more double crossovers occur
than expected, suggests that a crossover event can stimulate additional crossover
events in the same region of the chromosome.
11. +ist some of the methods for physica!!y mapping genes and e5p!ain how they are
used to position genes on chromosomes.
/eletion mapping3 Recessive mutations are mapped by crossing mutants with
strains containing various overlapping deletions that map to the same region as the
recessive mutation. If the hetero"ygote with the mutation on one chromosome and
the deletion on the homologous chromosome has a mutant phenotype, then the
mutation must be located on the same physical portion of the chromosome that is
deleted. If, on the other hand, the hetero"ygote has a wild&type phenotype (the
mutation and the deletion complement), then the mutation lies outside the deleted
region of the chromosome.
.omatic&cell hybridi"ation3 2uman and mouse cells are fused. )he resulting
hybrid cell randomly loses human chromosomes and retains only a few. - panel of
hybrids that retain different combinations of human chromosomes is tested for
expression of a human gene. - correlation between the expression of the gene and
the retention of a uni!ue human chromosome in those cell lines indicates that the
human gene must be located on that chromosome.
In&situ hybridi"ation3 /0- probes that are labeled with either a radioactive or
fluorescent tag are hybridi"ed to chromosome spreads. /etection of the labeled
hybridi"ed probe by autoradiography or fluorescence imaging reveals which
chromosome and where along that chromosome the homologous gene is located.
/0- se!uencing3 ,verlapping /0- se!uences are (oined using computer
programs to ultimately form chromosome&length se!uence assemblies, or contigs.
)he locations of genes along the /0- se!uence can be determined by searching for
matches to known gene or protein amino acid se!uences.
12. What is a !od score and how is it ca!cu!ated?
32
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
)he term lod means logarithm of odds. It is used to determine whether genes are
linked, usually in the context of pedigree analysis. ,ne first determines the
probability of obtaining the observed progeny given a specified degree of linkage.
)hat probability is divided by the probability of obtaining the observed progeny if
the genes are not linked and sort independently. )he log of the ratio of these
probabilities is the lod score. - lod score of 4 or greater, indicating that the
specified degree of linkage results in at least a 5$$$&fold greater likelihood of
yielding the observed outcome than if the genes are unlinked, indicates linkage.
APPLICATION QUESTIONS AND PROBLEMS
*1#. In the snai! Cepaea nemoralis, an autosoma! a!!e!e causing a banded she!! (6
6
is
recessi$e to the a!!e!e for unbanded she!! (6
,
. .enes at a different !ocus determine
the bac"ground co!or of the she!!8 here, ye!!ow (C
7
is recessi$e to brown (C
6w
. A
banded, ye!!ow snai! is crossed with a homo9ygous brown, unbanded snai!. :he ;
1

are then crossed with banded, ye!!ow snai!s (a testcross.
(a What wi!! be the resu!ts of the testcross if the !oci that contro! banding and co!or
are !in"ed with no crossing o$er?
8ith absolute linkage, there will be no recombinant progeny. )he +
5
inherited
banded and yellow alleles (B
B
(
<
together on one chromosome from the
banded yellow parent and unbanded and brown alleles (B
=
(
Bw
together on the
homologous chromosome from the unbanded brown parent. 8ithout
recombination, all the +
5
gametes will contain only these two allelic
combinations, in e!ual proportions. )herefore, the +
9
testcross progeny will be
: banded, yellow and : unbanded, brown.
(b What wi!! be the resu!ts of the testcross if the !oci assort independent!y?
8ith independent assortment, the progeny will be3
; banded, yellow
; banded, brown
; unbanded, yellow
; unbanded, brown
(c What wi!! be the resu!ts of the testcross if the !oci are !in"ed and 27 map units
apart?
)he recombination fre!uency is 9$%, so each of the two classes of recombinant
progeny must be 5$%. )he recombinants are banded, brown and unbanded,
yellow. )he two classes of nonrecombinants are <$% of the progeny, so each
must be =$%. )he nonrecombinants are banded, yellow and unbanded, brown.
In summary3
=$% banded, yellow
=$% unbanded, brown
5$% banded, brown
5$% unbanded, yellow
*1%. In si!"moths (6ombyx mori red eyes (re and white6banded wing (wb are encoded
by two mutant a!!e!es that are recessi$e to those that produce wi!d6type traits (re
>

and wb
>
8 these two genes are on the same chromosome. A moth homo9ygous for
33
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
red eyes and white6banded wings is crossed with a moth homo9ygous for the wi!d6
type traits. :he ;
1
ha$e norma! eyes and norma! wings. :he ;
1
are crossed with
moths that ha$e red eyes and white6banded wings in a testcross. :he progeny of this
testcross are*
wi!d6type eyes, wi!d6type wings %13
red eyes, wi!d6type wings 14
wi!d6type eyes, white6banded wings 10
red eyes, white6banded wings %20
(a What phenotypic proportions wou!d be e5pected if the genes for red eyes and
white6banded wings were !ocated on different chromosomes?
; wild&type eyes, wild&type wings
; red eyes, wild&type wings
; wild&type eyes, white&banded wings
; red eyes, white&banded wings
(b What is the genetic distance between the genes for red eyes and white6banded
wings?
)he +
5
hetero"ygote inherited a chromosome with alleles for red eyes and
white&banded wings (re wb from one parent and a chromosome with alleles for
wild&type eyes and wild&type wings (re
>
wb
>
from the other parent. )hese are
therefore the phenotypes of the nonrecombinant progeny, present in the highest
numbers. )he recombinants are the 5? with red eyes, wild&type wings and 5@
with wild&type eyes, white&banded wings.
R+ A recombinantsBtotal progeny C 5$$% A (5? > 5@)B<D? C 5$$% A =.$%
)he distance between the genes is = map units.
*1'. A geneticist disco$ers a new mutation in /rosophila melanogaster that causes the
f!ies to sha"e and &ui$er. )he ca!!s this mutation spastic (sps and determines that
spastic is due to an autosoma! recessi$e gene. )he wants to determine if the spastic
gene is !in"ed to the recessi$e gene for $estigia! wings (vg. )he crosses a f!y
homo9ygous for spastic and $estigia! traits with a f!y homo9ygous for the wi!d6type
traits and then uses the resu!ting ;
1
fema!es in a testcross. )he obtains the fo!!owing
f!ies from this testcross*
vg
>
sps
>
2#7
vg sps 22%
vg sps
>

42
vg
>
sps 44
tota! 0'7
Are the genes that cause $estigia! wings and the spastic mutation !in"ed? ?o a
series of chi6s&uare tests to determine if the genes ha$e assorted independent!y.
)o test for independent assortment, we first test for e!ual segregation at each
locus, then test whether the two loci sort independently.
)est for $g*
,bserved $g A 99= > ?D A 495
,bserved $g
>
A 94$ > ?? A 49?
'xpected $g or $g
>
@ : C @#$ A 49#



2

=
(
observed

expected

2

expected

@ (495 E 49#)
9
B49# > (49? 49#)
9
B49# A 5@B49# > 5@B49#
34
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
A $.$?<
8e have n A 5 degrees of freedom, where n is the number of phenotypic classes
A 9, so (ust 5 degree of freedom. +rom )able 4.=, we see that the F value is
between $.D and $.<. .o these results do not deviate significantly from the expected
535 segregation.
.imilarly, testing for sps, we observe 49D sps
>
and 494 sps and expect : C @#$
A 49# of each3

2
@ =B49# > =B49# A .$9#, again with 5 degree of freedom. )he F value is
between $.< and $.?, so these results do not deviate significantly from the expected
535 ratio.
+inally, we test for independent assortment, where we expect 5353535
phenotypic ratios, or 5@9.# of each.
,bserved 'xpected o E e (o E e)
9
(o E e)
9
Be
94$ 5@9.# @D.# =##@.9# 9<.$
99= 5@9.# @5.# 4D<9.9# 94.4
?D 5@9.# @#.# =9?$.9# 9@.=
?? 5@9.# @4.# =$49.9# 9=.<
8e have four phenotypic classes, giving us three degrees of freedom. )he chi&
s!uare value of 5$9.# is off the chart, so we re(ect independent assortment.
Instead, the genes are linked, and the R+ A (?D > ??)B@#$ 5$$% A 4$%,
giving us 4$ map units between them.
10. In cucumbers, heart6shaped !ea$es (hl are recessi$e to norma! !ea$es (2l and
ha$ing many fruit spines (ns is recessi$e to ha$ing few fruit spines (0s. :he genes
for !eaf shape and number of spines are !ocated on the same chromosome8 mapping
e5periments indicate that they are #2.0 map units apart. A cucumber p!ant ha$ing
heart6shaped !ea$es and many spines is crossed with a p!ant that is homo9ygous for
norma! !ea$es and few spines. :he ;
1
are crossed with p!ants that ha$e heart6shaped
!ea$es and many spines. What phenotypes and proportions are e5pected in the
progeny of this cross?
)he recombinants should total 49.@%, so each recombinant phenotype will be
5@.4% of the progeny. .ince the +
5
inherited a chromosome with heart&shaped
leaves and many spines (h! ns from one parent and a chromosome with normal
leaves and few spines (1! Bs from the other parent, these are the nonrecombinant
phenotypes, and together they total @D.=%, or 44.D% each. )he two recombinant
phenotypes are heart&shaped leaves with few spines (h! Bs and normal&shaped
leaves with many spines (1! ns.
2eart&shaped, many spines 44.D%
0ormal&shaped, few spines 44.D%
2eart&shaped, few spines 5@.4%
0ormal&shaped, many spines 5@.4%

*12. In tomatoes, ta!! (/ is dominant o$er dwarf (d, and smooth fruit (F is dominant
o$er pubescent (p fruit, which is co$ered with fine hairs. A farmer has two ta!! and
smooth tomato p!ants, which we wi!! ca!! p!ant A and p!ant B. :he farmer crosses
47
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
p!ants A and B with the same dwarf and pubescent p!ant and obtains the fo!!owing
numbers of progeny*
Crogeny of
C!ant A C!ant B
/d Fp 122 2
/d pp 0 32
dd Fp % 32
dd pp 12% %
(a What are the genotypes of p!ant A and p!ant B?
)he genotypes of both plants are ?dCp.
(b Are the !oci that determine height of the p!ant and pubescence !in"ed? If so,
what is the map distance between them?
7es. +rom the cross of plant -, the map distance is 5$B9#@ A 4.?% or 4.? m.u.
)he cross of plant 6 gives @B5D$ A 4.#% or 4.# m.u. If we pool the data from
the two crosses, we get 5@B=9@ A 4.<% or 4.< m.u.
(c -5p!ain why different proportions of progeny are produced when p!ant A and
p!ant B are crossed with the same dwarf pubescent p!ant.
)he two plants have different coupling configurations. In plant -, the dominant
alleles ? and C are coupled one chromosome is ? C and the other is d p. In
plant 6, they are in repulsion its chromosomes have ? p and d C.
13. A cross between indi$idua!s with genotypes a
>
a b
>
b D aa bb produces the fo!!owing
progeny*
a
>
a b
>
b 3#
a
>
a bb 21
aa b
>
b 14
aa bb 22
(a ?oes the e$idence indicate that the a and b !oci are !in"ed?
)he ratio of a
>
to a is 5$=B?@, and the ratio of b
>
to b is 5$9B?<, both close to
535 ratios. )he four phenotypic classes are not present in 5353535 ratios (no
need for chi&s!uare test), so they are linked.
(b What is the map distance between a and b?
)he recombinants are the two phenotypic classes with the fewest progeny3 R+
A (95 > 5?)B9$$ A =$B9$$ A $.9 A 9$% the two genes are 9$ m.u. apart.
(c Are the genes in the parent with genotype a
>
a b
>
b in coup!ing configuration or
in repu!sion? 1ow do you "now?
)hey are in coupling configuration because the nonrecombinants are a
>
b
>
and
ab.
14. In tomatoes, dwarf (d is recessi$e to ta!! (/ and opa&ue (!ight green !ea$es (op
is recessi$e to green !ea$es (,p. :he !oci that determine the height and !eaf co!or

41
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
are !in"ed and separated by a distance of 2 m.u. ;or each of the fo!!owing crosses,
determine the phenotypes and proportions of progeny produced.
(a
D Op
d op
D
d op
d op
)he recombinants in this cross would be ? op and d =p, and each would be
4.#% of the progeny to total D% recombinants. 'ach of the nonrecombinants
would be =@.#%, to total the remaining ?4%.
)all green =@.#%
/warf opa!ue =@.#%
)all opa!ue 4.#%
/warf green 4.#%
(b
D op
d Op
D
d op
d op
2ere with the genes in repulsion, the recombinants are ? =p and d op.
)all green 4.#%
/warf opa!ue 4.#%
)all opa!ue =@.#%
/warf green =@.#%
(c
D Op
d op
D
D Op
d op
)his is not a testcross, so we have to account for recombination in both
parents. )he most straightforward way is to do a Funnett s!uare, including the
types and proportions of gametes produced by meiosis in each parent. 6ecause
the genes are in coupling configuration in both parents, we can use the figures
from part (a).
42
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
? =p $.=@# ? op $.$4# d =p $.$4# d op $.=@#
? =p $.=@# )all, green
.95@
)all, green
.$5@
)all, green
.$5@
)all, green
.95@
? op $.$4# )all, green
.$5@
)all, opa!ue
.$$5
)all, green
.$$5
)all, opa!ue
.$5@
d =p $.$4# )all, green
.$5@
)all, green
.$$5
/warf, green
.$$5
/warf, green
.$5@
d op $.=@# )all, green
.95@
)all, opa!ue
.$5@
/warf, green
.$5@
/warf,
opa!ue
.95@
In summary, we get
)all green 4(.95@) > =(.$5@) > 9(.$$5) A .D5=
/warf opa!ue .95@
)all opa!ue 9(.$5@) > .$$5 A .$44
/warf green 9(.$5@) > .$$5 A .$44
(d
D op
d Op
D
D op
d Op
-gain, this is not a testcross, and recombination in both parents must be taken
into account. 6oth are in repulsion, so we use the proportions from part (b).
4#
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
? =p $.$4# ? op $.=@# d =p $.=@# d op $.$4#
? =p $.$4# )all, green
.$$5
)all, green
.$5@
)all, green
.$5@
)all, green
.$$5
? op $.=@# )all, green
.$5@
)all, opa!ue
.95@
)all, green
.95@
)all, opa!ue
.$5@
d =p $.=@# )all, green
.$5@
)all, green
.95@
/warf, green
.95@
/warf, green
.$5@
d op $.$4# )all, green
.$$5
)all, opa!ue
.$5@
/warf, green
.$5@
/warf,
opa!ue
.$$5
In summary, we get
)all, green 4(.$$5) > =(.$5@) > 9 (.95@) A .=??
/warf, opa!ue .$$5
)all, opa!ue 9(.$5@) > .95@ A .9=<
/warf, green 9(.$5@) > .95@ A .9=<
*27. In /rosophila melanogaster, ebony body (e and rough eyes (ro are encoded by
autosoma! recessi$e genes found on chromosome #8 they are separated by 27 map
units. :he gene that encodes for"ed brist!es (f is E6!in"ed recessi$e and assorts
independent!y of e and ro. .i$e the phenotypes of progeny and their e5pected
proportions when each of the fo!!owing genotypes is test6crossed.
(a
e
+
ro
+
e ro
f
+
f
8e can calculate the four phenotypic classes and their proportions for e and ro,
and then each of those classes will be split 535 for f, since f sorts
independently. )he recombination fre!uency between e and ro is 9$%, so each
4%
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
of the recombinants (e
>
ro and e ro
>
will be 5$%, and each of the
nonrecombinants (e
>
ro
>
and e ro will be =$%. 'ach of these will then be split
e!ually among f
>
and f.
e
>
ro
>
f
>
9$%
e
>
ro
>
f 9$%
e ro f
>
9$%
e ro f 9$%
e
>
ro f
>
#%
e
>
ro f #%
e ro
>
f
>
#%
e ro
>
f #%
(b
e
+
ro
e ro
+
f
f
8e can do the same calculations as in part (a), except the nonrecombinants are
e
>
ro and e ro
>
and the recombinants are e
>
ro
>
and e ro.
e
>
ro
>
f
>
#%
e
>
ro
>
f #%
e ro f
>
#%
e ro f #%
e
>
ro f
>
9$%
e
>
ro f 9$%
e ro
>
f
>
9$%
e ro
>
f 9$%
*21. A series of two6point crosses were carried out among se$en !oci (a, b, c, d, e, f, and
g, producing the fo!!owing recombination fre&uencies. /ap the se$en !oci,
showing their !in"age groups, the order of the !oci in each !in"age group, and
distances between the !oci of each !in"age group.
+oci ,ecombination fre&uency +oci ,ecombination fre&uency
a and b '7 c and d '7
a and c '7 c and e 20
a and d 12 c and f '7
a and e '7 c and g '7
a and f '7 d and e '7
a and g % d and f '7
b and c 17 d and g 3
b and d '7 e and f '7
b and e 13 e and g '7
b and f '7 f and g '7
b and g '7
#$% recombination indicates that the genes assort independently. Gess than #$%
recombination indicates linkage. .tarting with the most tightly linked genes a and g,
we look for other genes linked to these and find only gene d has less than #$%
4'
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
recombination with a and g. .o one linkage group consists of a, g, and d. 8e know
that gene g is between a and d because the a to d distance is 59.
.imilarly, we find a second linkage group of b, c, and e, with b in the middle.
*ene f is unlinked to either of these groups, on a third linkage group.
*22. Wa5y endosperm (wx, shrun"en endosperm (sh, and ye!!ow seed!ing (v are
encoded by three recessi$e genes in corn that are !in"ed on chromosome '. A corn
p!ant homo9ygous for a!! three recessi$e a!!e!es is crossed with a p!ant homo9ygous
for a!! the dominant a!!e!es. :he resu!ting ;
1
are then crossed with a p!ant
homo9ygous for the recessi$e genes in a three6point testcross. :he progeny of the
testcross are gi$en be!ow*
wx sh H 32
8x .h v 4%
8x .h H #%24
wx sh v #%23
8x sh H 1'1'
wx .h v 1'#1
wx .h H 242
8x sh v 237
tota! 17,2'0
(a ?etermine order of these genes on the chromosome.
)he nonrecombinants are W5 )h F and w5 sh $.
)he double crossovers are w5 sh F and W5 )h $.
Comparing the two, we see that they differ only at the $ locus, so $ must be the
middle gene.
(b (a!cu!ate the map distances between the genes.
W56F distanceIrecombinants are w5 F and W5 $*
R+ A (9?9>9<$><D>?=)B5$,D#@ A D#4B5$,D#@ A .$D A D% or D m.u.
)h6F distanceIrecombinants are sh F and )h $*
R+ A (5#5#>5#45><D>?=)B5$,D#@ A 499DB5$,D#@ A 4$ A 4$% or 4$ m.u.
)he W56)h distance is the sum of these two distances3 D > 4$ A 4D m.u.l.
(c ?etermine the coefficient of coincidence and the interference among these
genes.
'xpected dcos A R+5 C R+9 C Jtotal progeny A.$D(.4$)(5$,D#@) A 99@
C.o.C. A observed dcosBexpected dcos A (<D>?=)B99@ A $.<$
40
a d g
= <
b c e
5$ 5<
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
Interference A 5 E C.o.C A $.9$
2#. ;ine spines (s, smooth fruit (tu, and uniform fruit co!or (u are three recessi$e
traits in cucumbers whose genes are !in"ed on the same chromosome. A cucumber
p!ant hetero9ygous for a!! three traits is used in a testcross and the progeny at the
top of the fo!!owing page are produced from this testcross.
. 1 )u 2
s u )u 27
. u )u 21
s u tu %
. 1 tu 32
s 1 tu 21
s 1 )u 1#
. u tu 12
tota! 2#7
(a ?etermine the order of these genes on the chromosome.
0onrecombinants are s u :u and ) G tu.
/ouble crossovers are s u tu and ) G :u.
6ecause :u differs between the nonrecombinants and the double crossovers, :u
is the middle gene.
(b (a!cu!ate the map distances between the genes.
)6:u distance3 recombinants are ) :u and s tu.
R+ A (9 > = > 95 > 95)B94$ A =<B94$ A 95% or 95 m.u.
G6:u distance3 recombinants are u tu and G :u.
R+ A (9 > = > 54 > 5D)B94$ A 4@B94$ A 5@% or 5@ m.u.
(c ?etermine the coefficient of coincidence and the interference among these
genes.
'xpected dcos A (=<B94$)(4@B94$)(94$) A D.#
C.o.C. A observed dcosBexpected dcos A @BD.# A $.<
I A 5 E C.o.C. A $.9
(d +ist the genes found on each chromosome in the parents used in the testcross.
In the correct gene order for the hetero"ygous parent3 s :u u and ) tu G
+or the testcross parent3 s tu u and s tu u
*2%. In /rosophila melanogaster, b!ac" body (b is recessi$e to gray body (b
>
, purp!e
eyes (pr are recessi$e to red eyes (pr
>
, and $estigia! wings (vg are recessi$e to
norma! wings (vg
>
. :he !oci coding for these traits are !in"ed, with the map
distances*

0 1#
b
pr vg

:he interference among these genes is 7.'. A f!y with b!ac" body, purp!e eyes, and
$estigia! wings is crossed with a f!y homo9ygous for gray body, red eyes, and
42
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
norma! wings. :he fema!e progeny are then crossed with ma!es that ha$e b!ac"
body, purp!e eyes, and $estigia! wings. If 1777 progeny are produced from this
testcross, what wi!! be the phenotypes and proportions of the progeny?
-lthough we know what the recombination fre!uencies are between the pairs of
genes, these recombination fre!uencies result from both single crossover (sco) and
double crossover (dco) progenies. .o we must first calculate how many double
crossover progeny we should get.
8orking backward, given that interference A $.#, then the coefficient of
coincidence A 5 E interference A $.#.
8e now use the C.o.C. to calculate the actual dco progeny3
C.o.C. A $.# A actual dcosBtheoretical dcos A actual dcosB(.$@)(.54)(5$$$)
)he denominator calculates to D.<, so actual dcos A $.#(D.<) A 4.?
8e round 4.? to = double crossover progeny.
6ecause the parents were either homo"ygous recessive for all three loci or
homo"ygous dominant (wild type) for all three loci, the +
5
hetero"ygote fly has
chromosomes with b pr $g and b
>
pr
>
$g
>
. )hese are therefore the nonrecombinant
progeny phenotypes. )he double crossover progeny will be b pr
>
$g and b
>
pr $g
>
.
8e calculated above that there will be four double crossover progeny, so we should
expect two progeny flies of each double crossover phenotype.
0ext, we know that the recombination fre!uency between b and pr is @% or
$.$@. )his recombination fre!uency arises from the sum of the single crossovers
between b and pr and the double crossover progeny3
scos(b6pr > dcos A .$@(5,$$$) A @$. 6ut we already calculated that dcos A =, so
substituting in the above e!uation, we get3 scos(b6pr > = A @$ scos A #@. )he
single crossover phenotypes between b and pr are b pr
>
$g
>
and b
>
pr $g. )hese
total #@, or 9< each.
.imilarly, scos(pr6$g > dcos A .54(5$$$) A 54$ scos(pr6$g A 54$ E dcos A
54$ E = A 59@. )he single crossover phenotypes between pr and $g are b pr $g
>
and
b
>
pr
>
$g. )hese total 59@, or @4 each.
)he two remaining phenotypic classes are the nonrecombinants.
J nonrecombinants A 5$$$ E scos(b6pr E cos(pr6$g E dcos A 5$$$ E #@ E 59@ E =.
.o, J nonrecombinants A 5$$$ E 5<@ A <5=. )he nonrecombinant phenotypes are
b
>
pr
>
$g
>
and b pr $g8 we expect =$D of each, to total <5=.
In summary, the expected numbers of all eight phenotypic classes are3
b
>
pr
>
$g
>
=$D
b pr $g =$D
b
>
pr
>
$g @4
b pr $g
>
@4
b
>
pr $g 9<
b pr
>
$g
>
9<
b
>
pr $g
>
9
b pr
>
$g 9
*2'. :he !ocations of si5 de!etions ha$e been mapped to the /rosophila chromosome
shown on the fo!!owing page. ,ecessi$e mutations a, b, c, d, e, and f are "nown to be
!ocated in the same region as the de!etions, but the order of the mutations on the
43
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
chromosome is not "nown. When f!ies homo9ygous for the recessi$e mutations are
crossed with f!ies homo9ygous for the de!etions, the fo!!owing resu!ts are obtained,
where HmI represents a mutant phenotype and a p!us sign (> represents the wi!d
type. =n the basis of these data, determine the re!ati$e order of the se$en mutant
genes on the chromosome.
de!etion 1
de!etion 2
de!etion #
de!etion %
de!etion '
de!etion 0
chromosome
f? a f? c e d b
Kutations
/eletion a b c d e f
5 m > m > > m
9 m > > > > >
4 > m m m m >
= > > m m m >
# > > > m m >
@ > m > m > >
)he mutations are mapped to the intervals indicated on the figure above the table.
)he location of f is ambiguous it could be in either location shown above.
20. A pane! of ce!! !ines was created from mouse6human somatic6ce!! fusions. -ach !ine
was e5amined for the presence of human chromosomes and for the production of an
en9yme. :he fo!!owing resu!ts were obtained*
1uman chromosomes
(e!! !ine -n9yme 1 2 # % ' 0 2 3 4 17 12 22
A 6 > 6 6 6 > 6 6 6 6 6 > 6
B > > > 6 6 6 6 6 > 6 6 > >
( 6 > 6 6 6 > 6 6 6 6 6 6 >
? 6 6 6 6 > 6 6 6 6 6 6 6 6
- > > 6 6 6 6 6 6 > 6 > > 6
=n the basis of these resu!ts, which chromosome has the gene that codes for the
en9yme?
)he en"yme is produced only in cell lines 6 and '. ,f all the chromosomes, only
chromosome < is present in (ust these two cell lines and absent in all the other cell
44
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
lines that do not produce the en"yme. )herefore, the gene for the en"yme is most
likely on chromosome <.
*22. A pane! of ce!! !ines was created from mouse6human somatic6ce!! fusions. -ach !ine
was e5amined for the presence of human chromosomes and for the production of
three en9ymes. :he fo!!owing resu!ts were obtained*
-n9yme 1uman chromosomes
(e!! !ine 1 2 # % 3 4 12 1' 10 12 22 E
A > 6 > 6 6 > 6 > > 6 6 >
B > 6 6 6 6 > 6 6 > > 6 6
( 6 > > > 6 6 6 6 6 > 6 >
? 6 > > > > 6 6 6 > 6 6 >
=n the basis of these resu!ts, gi$e the chromosome !ocation of en9yme 1, en9yme 2,
and en9yme #.
'n"yme 5 is located on chromosome ?. Chromosome ? is the only chromosome that
is present in the cell lines that produce en"yme 5 and absent in the cell lines that do
not produce en"yme 5.
'n"yme 9 is located on chromosome =. Chromosome = is the only chromosome
that is present in cell lines that produce en"yme 9 (C L /) and absent in cell lines
that do not produce en"yme 9 (- L 6).
'n"yme 4 is located on the M chromosome. )he M chromosome is the only
chromosome present in the three cell lines that produce en"yme 4 and absent in the
cell line that does not produce en"yme 4.
CHALLENGE QUESTION
23. In ca!cu!ating map distances, we did not concern ourse!$es with whether doub!e
crosso$ers were two6stranded, three6stranded, or four6stranded8 yet, these different
types of doub!e crosso$ers produce different types of gametes. (an you e5p!ain
why we do not need to determine how many strands ta"e part in doub!e crosso$ers
in dip!oid organisms? (1int* ?raw out the types of gametes produced by the
different types of doub!e crosso$ers and see how they contribute to the
determination of map distances.
)he three&stranded double crossovers all generate two recombinant chromosomes
and two nonrecombinant chromosomes.
177
A B
a b
A B
A b
a B
a b
(hapter )e$en* +in"age, ,ecombination, and -u"aryotic .ene /apping
)he four&stranded double crossovers always generate four recombinant
chromosomes.
)he two&stranded double crossovers always generate four nonrecombinant
chromosomes.
.ince the four&stranded and two&stranded double crossovers are e!ually
probable, the net result of all types of double crossovers averaged together is #$%
recombinant and #$% nonrecombinant chromosomes.
171
A B
a b
A b
A b
a B
a B
A B
a b
A B
A B
a b
a b