Genetics From Genes To Genomes 5th Edition Hartwell Solutions Manual Download

Solution Manual for Genetics From Genes to Genomes
5th Edition by Hartwell Goldberg Fischer ISBN

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chapter
5
Linkage, Recombination, and the
Mapping of Genes on Chromosomes
Synopsis
In Chapter 5, we learn the consequences of the fact that hundreds or even thousands of genes can
be found on one chromosome. If two genes lie close together on a chromosome, their alleles
do not assort independently; instead, the genes are linked and parental classes of gametes will be
formed more frequently than recombinant classes. The Recombination Frequency (RF) increases
to a maximum of 50% as the distance between the two genes increases. The formation of
recombinant classes depends on the occurrence of physical crossovers between nonsister
chromatids that take place during prophase of the first meiotic division, after the chromosomes
have replicated and homologous chromosomes have paired with each other. The greater the
distance between the genes, the more likely the chance of a crossover and the greater the RF; the
50% limit to RF occurs when genes are sufficiently far apart that at least one crossover occurs
between them in every meiosis. By measuring RF, geneticists can map the location of genes
along the chromosomes.
In most organisms, RF can be tracked only by looking at individual progeny of a cross
involving at least one parent who is a heterozygote for the two genes in question. But in the
fungi S. cerevisiae and N. crassa, all the products of a meiosis remain together in a sac called an
ascus. As a result, researchers can infer more details about the locations and kinds of crossovers
that took place during the meiosis that produced that ascus.
Finally, Chapter 5 discusses what happens when recombination takes place during mitosis -
rather than meiosis. In contrast with meiotic recombination, which is a programmed event that
must occur at least once on every chromosome during every meiosis, mitotic recombination
reflects rare mistakes that occur (usually in response to DNA damage). Mitotic recombination
provides a valuable tool to researchers because it allows them to create mosaic organisms in
which different cells have different genotypes.
Key terms
syntenic genes – genes located on the same chromosome
parental types/classes – gametes whose 5-1alleles are in the same combinations as in the
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gametes that gave rise to previous generation; or progeny generated by parental
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gametes
recombinant types/classes – gametes whose alleles are in different combinations
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resulting from a meiosis in which a crossover took place between the two genes in
question.
linkage – when two genes are located close enough to each other on the same
chromosome so that a doubly heterozygous parent makes more parental type than
recombinant type gametes
recombination frequency (RF) – the proportion of the total number of gametes or
progeny that are recombinant types (recombinants/total)
map unit (mu)/centimorgan (cM) – a measure of genetic distance between linked
genes; 1 mu = 1 cM = 1% RF.
locus (singular)/loci (plural) – a specific location on a particular chromosome
interference – a phenomenon in which a crossover event on a chromosome prevents
or limits the occurrence of a second crossover event nearby on the same chromosome.
Interference is thought to take place as a way to help ensure that at least one crossover
occurs on each bivalent, so that homologous chromosomes segregate accurately
during the first meiotic division.
coefficient of coincidence (c.o.c.) – the ratio of the number of double crossovers
observed in a cross to the number of double crossovers expected if the two crossovers
were independent of each other. The interference = 1 – c.o.c. This makes sense because
the amount of interference reflects a decrease in the frequencies of double crossovers
(DCOs).
chi-square test – a statistical device used to measure the likelihood that a particular set
of observed experimental results could have been obtained as chance deviations
from the expectations from a particular hypothesis to be tested (the null
hypothesis)
significant result – experimental results that are highly unlikely to be explained by the
null hypothesis. A significant result allows you to reject the null hypothesis. An
insignificant result does not allow you to reject the null hypothesis. Note that
these definitions mean that the chi-square test can never prove a null hypothesis,
but can only reject the null hypothesis.
degrees of freedom (d.o.f) – In the chi-square test for the goodness of fit, the d.o.f. =
number of classes – 1. The d.o.f. is required for interpreting the chi-square test.
p value – the probability that the observed results could be obtained by chance deviations
from the expectations of the null hypothesis. If the p value is low (usually below 0.05
for genetic analysis), you can reject the null hypothesis.
ascus – in fungi, a sac that contains all four products of a single meiosis. These haploid
products are the ascospores (or simply spores). A tetrad is the collection of the 4
spores in one ascus. (In Neurospora, the ascus is an octad containing 8 spores due to
the occurrence of one round of mitosis after meiosis is complete.)
ordered versus unordered tetrad – In ordered tetrads (N. crassa), the geometry of the
spores in the ascus reflects the movement of chromatids during the two meiotic
divisions. In unordered tetrads (S. cerevisiae), the four ascospores are arranged at
random within the ascus.
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parental ditype (PD) – a tetrad in which all four spores are parental types (two spores
of each of the two parental types possible)
nonparental ditype (NPD) – a tetrad in which all four spores are recombinant types
(two spores of each of the reciprocal recombinant types)
tetratype (T) – a tetrad with four spores all of different genotypes (the two reciprocal
parental types and the two reciprocal recombinant types)
first-division segregation pattern (MI) and second-division segregation pattern
(MII) – arrangements of spores in ordered tetrads (octads in Neurospora). In an MI
pattern, if an imaginary line is drawn through the center of the ascus, all the spores
with one allele are on one side of the line and all those with the other allele are on
the other side of the line (4:4). In an MII pattern, pairs of spores with both alleles
are found on either side of the imaginary line at the ascus middle (2:2:2:2).
twin spots – adjacent patches of tissues that are phenotypically and genotypically
different from each other, and phenotypically and genotypically different from the
surrounding cells. Twin spots can result from mitotic crossing-over depending on
the arrangement of alleles and the sites of the mitotic crossovers.
mosaic – an organism harboring cells of different genotypes. For example, a fruit fly with
twin spots is a mosaic.
sector – in yeast, a region of a colony of cells in which the cells have a different phenotype
and genotype from the other cells in the same colony
Key Equations
• Recombination frequency (RF) = # recombinant progeny / total # progeny.
(Multiply × 100 to express the RF as %.)
• 1% RF = 1 mu or 1 cM.
• Coefficient of coincidence (c.o.c) = # DCOs observed / # DCOs expected. To
calculate the # DCOs expected, multiply the crossover frequency in interval 1 ×
crossover frequency in interval 2, and then multiply this value by the total number
of progeny.
• Interference = 1 – c.o.c.
• Χ2 = Σ [(# observed - # expected)2 / # expected].
(In other words, Χ2 is the sum over all classes of [(O-E)2 / E] calculated for each
class.)
• Degrees of freedom (d.o.f.) = # classes -1.
• In Χ2 analysis, the ultimate goal is to determine the probability p that the observed
results could have been obtained by chance if the null hypothesis is correct. To
determine p, you need to calculate Χ2 and d.o.f., and then you must consult a table
of critical values such as Table 5.2 on p. 147.
• See the equations in the box Three Easy Rules for Tetrad Analysis that follows.
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Three Easy Rules for Tetrad Analysis

To understand the derivation of the rules below, study Fig. 5.21 on p. 152 (two genes
on different chromosomes) and Fig. 5.23 on p. 153 (two linked genes). You should note
that the kind of tetrad analysis discussed in this chapter concerns the mapping of two
genes at a time; no three point cross analysis is involved.
Rule #1 - If the number of PD tetrads is about equal to the number of NPD tetrads, then
the genes are unlinked. Genes are unlinked if they are on nonhomologous chromosomes
or if the genes are far apart on the same chromosome. If the # PD tetrads >>> #
NPD tetrads, the genes are linked.
Rule #2 - Distance between linked genes is determined by calculating recombination
frequency using the equation:
RF = [(NPD + ½T)/ total # tetrads] × 100.
Rule #3 – If a crossover occurs between a gene and the centromere, the two alleles
separate from each other at the second meiotic division (MII segregation) instead of
during the first meiotic division (MI segregation). Centromere distance can be measured
in fungi with ordered asci such as Neurospora using the equation:
gene ↔ centromere distance = [(½ × # MII tetrads) / total # tetrads] × 100.
Problem
Solving
For many of the problems in this chapter, you will still need to start by answering the same
questions you dealt with in the first four chapters:
How many genes are involved in the cross?
For each of these genes, what is the dominance relationship between the alleles?
For each of these genes, is it X-linked or autosomal?
In the problems in this chapter, you now have to consider the additional possibility that genes may
be syntenic (on the same chromosome) and that they are genetically linked.
When thinking about genes that are linked, you must write the genotypes in a way that
represents the linkage. Remember that there is one allele per homolog, so aa becomes a / a. It is
usually advantageous to indicate the homologous chromosomes with horizontal, parallel lines so
that you can track which alleles of which genes were present on which chromosomes. Thus, a+
b+ c / a b c+ would be diagrammed as:
Although the two lines in the diagram above represent the two homologous chromosomes, you
should always keep in mind that recombination actually occurs at the four-strand stage, after
each chromosome has replicated into two sister chromatids. This fact plays an important role in
understanding why there is a 50% limit of the RF measured between two genes, and it also helps
you visualize what is occurring when you are analyzing tetrads in fungi.
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Tips for two-point crosses:

• The minimum requirement for detecting recombination is that one parent must be
heterozygous for 2 genes. The recombination events that can be detected are the ones
that occur between the 2 genes, giving recombinant gametes instead of parental
gametes.
• It is easiest to detect the parental versus recombinant gametes if you do a testcross.
• If the genes are assorting independently, in a test cross of aa+ bb+ × aa bb, the
expected phenotypic frequencies and classes of progeny are 1 a+– b+– : 1 aa bb : 1
a+– bb : 1 aa b+–. But the genes are genetically linked if you see more parental than
recombinant progeny.
• Recombination frequency (RF) = # recombinant progeny / total # progeny.
(Multiply × 100 to express the RF as %.) 1% RF = 1 mu or 1 cM.
• Genes on the X chromosome can be mapped without a testcross. Just use the
hemizygous male progeny as in Problem 5-6.
Tips for three-point crosses:

• In a three-point cross, a parent heterozygous for the three genes generates the
progeny. Therefore, all classes (parental, etc.) will occur as reciprocal pairs of progeny.
These reciprocal pairs will be both genetic reciprocals and numerically equivalent.
• Designate the different gametes or offspring as noncrossover (NCO; parental),
single crossover (SCO) or double crossover (DCO). The NCO classes are those
classes of progeny who have one of the intact, nonrecombinant homologs from the
parent. The NCO classes will be represented by the reciprocal pair with the greatest
numbers of offspring. There will be SCOs occurring between the gene on the left and
the gene in the middle (two reciprocal classes), and SCOs occurring between the
gene in the middle and the gene on the right (another two reciprocal classes). The
DCO classes will be represented by the reciprocal classes with the smallest numbers
of offspring (Fig. 5.12 on p. 138). Thus, in a three-point cross there will usually be 8
classes of progeny. However, sometimes one or both double crossover classes are
missing because they are rare.
• By examining the pattern of data seen in a problem, you can often start solving the
problem with a basic understanding of the linkage relationships of the genes. Some of
the more common patterns of data are:
- 3 unlinked genes give 8 classes of data that occur as 4 genetically reciprocal
pairs, but all classes are seen in a 1:1:1:1:1:1:1:1 ratio;
- 3 linked genes give 8 classes of data that occur as 4 reciprocal pairs
genetically and numerically unless one or both of the DCO classes are
missing, in which case you will see 6 classes as 3 reciprocal pairs or 7 classes
as 3 reciprocal pairs plus an additional unpaired class;
- 2 linked genes plus one unlinked gene will yield 8 classes of data. 4 of these
classes will be numerical equal to each other, while the other 4 classes will
also be numerically equal to each other. The group of 4 classes with larger
numbers will consist of the reciprocal parental classes for the linked genes
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together with either allele of the unlinked gene. The group of 4 classes with the
smaller numbers will be the reciprocal recombinant classes of the linked genes
together with either allele of the unlinked gene.
• Begin the process of mapping the genes by ordering the genes. To figure out which
gene is in the middle of a group of three genes, choose one of the double crossover
classes. Compare it to the most similar parental class of progeny where two of the
three genes will have the same combination of alleles. The gene that differs is the gene
in the middle. See Problem 5-22c for further explanation.
• The last step is to determine the distance between the genes on each end and the
gene in the middle. Use the formula RF = # recombinants between the 2 genes / total
# of progeny. Remember for each interval that the # recombinants is the number of
progeny in the reciprocal SCO classes representing crossovers in that interval, plus
the number of recombinants in the reciprocal DCO classes.
Tips for crosses involving 4 genes:

• A few problems in this chapter deal with crosses involving 4 genes. You should
realize that to provide you with easily solvable problems, the arrangements of the 4
genes were carefully chosen such that the data patterns immediately suggest rather
simple solutions. If you had 4 linked genes in a group, you would get 16 classes of
progeny in 8 reciprocal pairs, but this would be extremely difficult to analyze
because you would have to consider many types of double crossovers as well as
triple crossovers, in addition to the SCOs in each interval. You should thus be on
the lookout for the following patterns with simpler solutions:
- 4 unlinked genes give 16 classes of progeny in a 1:1:1:1:1:1:1:1:1:1:1:1:1:1:1:1
ratio;
- 3 linked genes and 1 gene assorting independently gives 16 classes of data
occurring as 8 reciprocal pairs genetically and 4 groups of 4 numerically.
- 4 linked genes that show only 8 classes of data indicate that two of these
genes are so tightly linked to each other that they never separate by
recombination. You can thus deal with this as a three-point cross.
Tips for tetrad analysis problems:

• Remember that the designations PD, NPD, and T refer to the set of four spores in
one ascus, NOT to individual spores.
• Although tetrad analysis may seem daunting, it is actually in many ways
straightforward, particularly if you follow the Three Easy Rules for Tetrad
Analysis presented above.
• Ordered tetrads such as those in Neurospora allow you to determine the distances
between genes and centromeres. (This is normally not possible in unordered tetrads,
except in one special and useful case described in Problem 5.46f in which one of the
genes is located right at the centromere.) To compute gene ↔ centromere distances,
you need to count the number of tetrads showing MI and MII segregation patterns.
To do this, draw an imaginary line through the middle of the ascus and assess for
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each gene whether all the spores in the ascus are the same allele (MI pattern) or
have different alleles (MII pattern).
Tips for mitotic recombination problems:
• For mitotic recombination in a heterozygous parental cell to produce daughter cells
homozygous for either allele, mitotic recombination must take place between the gene
and the centromere.
• Any mitotic recombination between a gene and the centromere will automatically
make homozygous any other gene that is even further from the centromere.
Vocabulary
1.
a. recombination 8. formation of new genetic combinations by exchange
of parts between homologs
b. linkage 4. when two loci recombine in less than 50% of gametes
c. chi-square test 1. a statistical method for testing the fit between
observed and expected results
d. chiasma 11. structure formed at the spot where crossing-over
occurs between homologs
e. tetratype 2. an ascus containing spores of four different genotypes
f. locus 5. the relative chromosomal location of a gene
g. coefficient of 6. the ratio of observed double crossovers to expected
coincidence double crossovers
h. interference 3. one crossover along a chromosome makes a second
nearby crossover less likely
i. parental ditype 10. an ascus containing only two nonrecombinant kinds
of spores
j. ascospores 12. fungal spores contained in a sac
k. first-division segregation 9. when the two alleles of a gene are segregated into
different cells at the first meiotic division
l. mosaic 7. individual composed of cells with different genotypes
Section 5.1
2. a. Diagram the cross. WT = wild type.
scabrous ♂ (scsc j+j+) × javelin ♀ (sc+sc+ jj) → F1WT ♀ (scsc+ j+j) ×
scabrous javelin ♂ (scsc jj) → 1/4 scabrous (P) : 1/4 javelin (P) : 1/4 WT (R) :
1/4 scabrous javelin (R).
This F1 female will make four different types of gametes in equal frequency – 1/4
sc+ j : 1/4 sc j+ : 1/4 sc+ j+ : 1/4 sc j. Because this is a testcross, the male parent
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will always provide the recessive alleles of the genes. Thus the phenotypes of the
progeny will be determined by the gamete they receive from the heterozygous F 1
female. (Recall that in Drosophila, meiotic recombination does not occur in the male
germ line, and so testcrosses are almost always set up like the one here.)
Of course these genes may be linked. In this case the cross would be
diagrammed as follows:
scabrous ♂ (sc j+ / sc j+) × javelin ♀ (sc+ j / sc+ j) → F1 WT ♀ (sc j+ / sc+ j)
× scabrous javelin ♂ (sc j / sc j) → scabrous (sc j+) (P) : javelin (s+ j) (P) : WT
(sc+ j+) (R) : scabrous javelin (sc j) (R).
Again, this F1 female will make 4 different types of gametes. There will be the two
Parental (P) types and two Recombinant (R) types - s + j (P) : sc j + (P) : sc +
j + (R) : sc j (R). The two Parental types must be of equal frequencies, and the two
Recombinant types must be equal to each other. The relative proportion of
Parentals to Recombinants will depend on the genetic distance (recombination
frequency = RF) between the genes on the chromosome. The recombination
frequency could be anything from 0 mu (the genes are very closely linked) to 50 mu
(the genes are far apart on the same chromosome). In the latter case P = R and the
proportions of the four types of gametes will also be 1 : 1 : 1 : 1.
b. In these results the Parentals (77 scabrous + 74 javelin) are equal frequency to the
Recombinants (76 wild type + 73 scabrous javelin). Thus the genes assort
independently.
c. F1 WT ♀ (sc sc+ j+j) × WT ♂ (sc+sc+ j+j+) → all wild-type (WT) progeny. The
F1 female will still make four types of gametes in equal frequency. However the
male parent in this cross can only contribute sc+ j+ gametes so all the progeny will
be phenotypically wild type. Thus you could not determine the frequency of
parental and recombinant gametes from the F1 female.
d. Diagram the cross.
javelin ♀ (sc+sc+ jj) ×scabrous javelin ♂ (scsc jj) → F1 javelin ♀ (scsc+ jj).
This F1 female will make sc+ j and sc j parental gametes. Her recombinant
gametes will be the same genotypes as her parental gametes thus making it
impossible to detect crossing-over. In order to detect crossing-over (or
independent assortment), the parent must be heterozygous for two genes or
markers. The crossovers detected will occur between the two genes.
3. a. Diagram this cross.
B1B2 D1D4 ♂ × B3B3 D2D3 ♀ → B1B3 D1D3 ♂ (John).
Thus John received a B1 D1 gamete from his father and a B3 D3 gamete from his
mother. John will produce parental gametes of these types: B 1 D 1 and B 3 D 3 .
b. The recombinant gametes produced by John will be B 1 D 3 and B 3 D 1 .
c. All 100 sperm have the parental genotypes. There are no recombinant sperm.
Therefore the B and D loci are linked and are 0 mu apart.
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4. a. The Punnett square that follows illustrates the outcomes expected for a dihybrid
cross where the F1 individuals are A B / a b. This Punnett square is adjusted so that
the width and height of the boxes reflect approximately the proportions of progeny
of each class you would expect to see in the F2 generation. The boxes with the F2
genotypes are not all equal in size because the 4 types of gametes are not produced
in equal amounts (as would be the case if the two genes were unlinked). Instead, there
are more Parental gametes (A B and a b) made by each parent than Recombinant
gametes (A b and a B). Because 80% of the gametes made by the F1 individuals are
Parental, and because the two Parental classes are equal to each other, 40% of
the gametes will be A B, 40% will be a b, 10% will be A b, and 10% will be a B. (The
two Recombinant classes are also equal to each other because they are the reciprocal
products of the same crossovers.) The color-coding in the Punnett square boxes
represents the phenotypic classes, and the numbers in the boxes represent the
proportions of the F2 in the given class. Among the F2s, 66% will be A– B–, 9%
will be aa B–, 9% will be A– bb, and 16% will be aa bb.
b. The Punnett square that follows shows the expected outcomes of a dihybrid cross if
the F1 generation is A b / a B and 80% of the gametes are the two Parental classes.
The color-coding of the boxes is the same as in part (a). Among the F2s, 51% will
be A– B–, 24% will be aa B–, 24% will be A– bb, and 1% will be aa bb.
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Section 5.2
5. a. The parental females are heterozygous for the X-linked dominant Greasy fur (Gs)
and Broadhead (Bhd) genes. They are crossed to homozygous recessive males. The
male progeny of this cross will show four phenotypes, which will fall into two
genetic reciprocal pairs. One pair will be Gs Bhd and wild type (Gs Bhd and Gs+ Bhd+)
while the other pair will be Gs and Bhd (Gs Bhd+ and Gs+ Bhd). If the genes are far
apart on the X chromosome, then they will assort independently and all four classes
will show equal frequency. If the genes are linked, then there will be a more frequent
reciprocal pair (the parental pair) and a less frequent pair (the recombinant pair). There
are 49 Gs Bhd+ and 48 Gs+ Bhd male progeny. Thus, this is the parental pair and the
genotype of the female is Gs Bhd+ / Gs+ Bhd. The cross can be diagrammed:
Gs Bhd + / Gs + Bhd ♀ × Gs + Bhd + / Y ♂ → 49 Gs Bhd + ♂ : 48 Gs +
Bhd ♂ : 2 Gs Bhd ♂ : 1 Gs + Bhd + ♂.
The distance between these two genes: RF = 2 + 1 / 100 = 0.03 = 3 mu.
b. The daughters in this cross must inherit the Gs+ Bhd+ X chromosome from their
fathers. This chromosome carries the recessive alleles of both genes, so this is a true
testcross. Thus the genotypes, phenotypes and frequencies of the female
progeny would be the same as their brothers.
6. The parents are from true-breeding stocks. Diagram the cross:
raspberry eye color ♂ × sable body color ♀ → F1 wild-type eye and body color
♀ × sable body color ♂ (if no mention is made of the eye color, then it is
assumed to be wild type) → F2 216 wild-type ♀ : 223 sable ♀ : 191 sable ♂ :
188 raspberry ♂ : 23 wild-type ♂ : 27 raspberry sable ♂
The phenotypes seem to be controlled by 2 genes, one for eye color and the other for
body color. The F1 female progeny show that the wild-type allele is dominant for body
color (s+ > s) and the wild-type allele is also dominant for eye color (r+ > r). Sable body
color is seen in the F1 males but not the F1 females, so the s gene is X-linked. In the F2
generation, the raspberry eye color is seen in the males but not in the females, so r is
also an X-linked gene. We can now assign genotypes to the true-breeding parents in this
cross:
r s + / Y (raspberry ♂ ) × r + s / r + s ♀ → F1 r s + / r + s ♀ (wild type) ×
r + s / Y (sable ♂) → [the heterozygous F1 female can make the following
gametes: (parentals) r s +, r + s and (recombinants) r s, r + s +; the F1 male
can make Y and r + s gametes] → F2 will be r s + / r + s (wild-type
females), r + s / r + s (sable females), r s / r + s (sable females), r + s + / r +
s (wild-type females), r + s / Y (sable males), r s + / Y (raspberry males), r
s / Y (raspberry sable males), r + s + / Y (wild-type males)
The F1 female is heterozygous for both genes and will therefore make parental and
recombinant gametes. The F1 male is not a true testcross parent, because he does not
carry the recessive alleles for both of the X-linked genes. However, this sort of cross
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can be used for mapping, because F2 sons receive only the Y chromosome from the F1
male and are hemizygous for the X chromosome from the F1 female. Thus the phenotypes
in the F2 males represent the array of parental and recombinant gametes generated by
the F1 female as well as the frequencies of these gametes. Using the F2 males, the RF
between sable and raspberry = 23 (wild-type males) + 27 (raspberry sable males)
/ 429 (total males) = 0.117 x 100 = 11.7 cM.
7. To determine the probability that a child will have a particular genotype, look at the
gametes that can be produced by the parents. In this example, A and B are 20 mu apart,
so in a doubly heterozygous individual 20% of the gametes will be recombinant and the
remaining 80% will be parental. The a b / a b homozygous man can produce only a b
gametes. The doubly heterozygous woman, with a genotype of A B / a b, can produce
40% A B, 40% a b, 10% A b and 10% a B gametes. (Total of recombinant classes =
20%.) The probability that a child receives the A b gamete from the female (and
is therefore A b / a b) = 10%.
8. a. Diagram the cross:
CC DD × cc dd → F1 C D / c d × cc dd → 997 Cc Dd, 999 cc dd, 1 Cc dd, 3
cc Dd.
Because the gamete from the homozygous recessive parent is always c d, we can ignore
one c and one d allele (the c d homolog) in each class of the F2 progeny. The remaining
homolog in each class of F2 is the one contributed by the doubly heterozygous F1, the
parent of interest when considering recombination. In the F2 the two classes of
individuals with the greatest numbers represent parental gametes (C D or c d from
the heterozygous F1 parent combining with the c d gamete from the homozygous
recessive parent). The other two types of progeny result from a recombinant gametes
(C d or c D combining with the c d gamete from the homozygous recessive parent).
The number of recombinants divided by the total number of offspring × 100 gives
the map distance: (1 + 3)/(997 + 999 + 1 + 3) =
4/2000 = 0.002 × 100 = 0.2% RF or 0.2 map units (mu) or 0.2 cM.
b. CC dd × cc DD → F1 C d / c D × c d / c d → ? As determined in part (a), c
and d are 0.2 cM apart. Thus the gametes produced by the heterozygous F1 will be
49.9% C d, 49.9% c D, 0.1% C D, 0.1% c d. After fertilization with c d gametes, there
would be 49.9% Cc dd, 49.9% cc Dd, 0.1% Cc Dd, 0.1% cc dd. Because this is a
testcross, the gametes from the doubly heterozygous F1 parent determine the
phenotypes of the progeny.
c. Because the RF is so low (0.2%), very few crossovers occur between genes C and D.
A single crossover in a single meiosis would produce 2 Recombinant progeny. With
an RF = 0.002, you would have 2 Recombinant progeny out of 1000 total progeny.
1000 progeny could be obtained in 1000/4 = 250 meioses. Thus, only 1 out of
every 250 meioses would have a crossover between genes C and D; in any one meiosis,
the chance of a crossover occurring between the genes would be 1/250 =
0.004 = 0.04%. Thus, in a typical meiosis, no crossovers would occur between
genes C and D.
d. In this case, you see equal frequencies of all progeny classes, so the number of
Recombinants equals the number of Parentals. In other words, the genes are
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syntenic but so far apart that they are genetically unlinked; the RF is ~50%. From
the discussion on p. 136 of the text, you should realize that when genes are
unlinked, every meiosis must have at least one recombination event occurring between
the two genes in question (in other words, when RF = 50%, no meiosis can be an
NCO). However, we cannot determine the average number of crossovers between
the two genes other to say that this number must be greater than 1. The reason is
that as the physical distance between syntenic but unlinked genes increases, the
number of double crossovers (DCOs) and triple or higher level crossovers increases
yet the RF still remains ~50%. Thus, in a typical meiosis, at least one crossover
occurs between genes C and D.
9. Designate the alleles of the genes: A = normal pigmentation and a = albino allele;
HbßA = normal globin and HbßS = sickle allele.
a. Because both traits are rare in the population, we assume that the parents are
homozygous for the wild-type allele of the gene dictating their normal traits (that is,
they are not carriers). Diagram the cross: a HbßA / a HbßA (father) × A HbßS / A
HbßS(mother) → a HbßA / A HbßS (son). Given that the genes are separated by 1
map unit, parental gametes = 99% and recombinant gametes = 1% of the gametes.
The son's gametes will consist of: 49.5% a Hb ßA , 49.5% A Hb ßS , 0.5% a
Hb ßS and 0.5% A Hb ßA .
b. In this family, the cross is A HbßA / A HbßA (father) × a HbßS / a HbßS
(mother) → a HbßS / A HbßA (daughter). The daughter's gametes will be:
49.5% a Hb ßS , 49.5% A Hb ßA , 0.5% a Hb ßA and 0.5% A Hb ßS .
c. The cross is: a HbßA / A HbßS (son) × a HbßS / A HbßA (daughter). The
probability of an a Hb ßS / a Hb ßS child (sickle cell and anemic) = 0.005
(probability of a Hb ßS from son) x 0.495 (probability of a Hb ßS from
daughter) = 0.0025.
10. a. Designate the alleles: H = Huntington allele, h = normal allele; B = brachydactyly, b
= normal fingers. John's father is bb Hh; his mother is Bb hh.
II
III
b. We know the John is Bb because he has brachydactyly. His complete genotype

could be Bb Hh or Bb hh.
In order to answer part (c) below, it would be helpful here to calculate the
probability that John is Hh rather than hh. This calculation is a bit tricky – it requires
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you to use conditional probability, something that you have done in previous problems
in the book, but those examples were simpler. For example, in Chapter 2 on p. 38,
to answer Solved Problem III you need to calculate the probability that the daughter
of two Tt parents is Tt. If you had no other information, the probability would be
1/2, as the progeny of a monohybrid cross appear in the ratio 1 TT : 2 Tt : 1 tt.
However, a condition exists in the problem: We are told that the daughter in question
does not have Tay-Sachs disease, which means that she is not tt. This fact means
that the “1 tt ” can be eliminated from the set of her possible genotypes, leaving
1 TT : 2 Tt and thus a 2/3 chance that she is Tt.
Now back to John. If we had no information about John, the probability that
John is Hh because he inherited H from his Hh father would be 1/2. However, we
do have some information about John - he is 50 and has no symptoms of Huntington
disease; this fact - or condition – as well as the information that 2/3 of people who
inherit H have symptoms of the disease by age 50 - has to be used to calculate the
chance that John inherited the H allele from his father. The easiest way to think about
this conditional probability is the following:
John’s father or anyone else who is Hh could have two classes of children: those
who inherit the H allele (Hh), and those who inherit the h allele (hh). As we said
previously, with no other knowledge, the ratio of John’s progeny would be 1 Hh : 1
hh. However, we know that John is 50 and has no symptoms. All of the hh progeny
will have no symptoms at 50, and also 1/3 of the Hh progeny will have no symptoms.
These facts change the genotypic ratio, because we are considering the symptom-free
people only; for symptom-free people, the ratio is 1/3 Hh : 1 hh. Another way to
express the same ratio is 1/3 Hh : 3/3 hh, or 1 Hh : 3 hh. Thus, the chance that John
is Bb Hh is 1/4.
c. In order for the child to express both diseases, the child must be Bb Hh, and so
John must be Bb Hh. We just calculated in part (b) that the probability John is Bb
Hh is 1/4. The chance that the child is Bb Hh is 1/4 (the chance that John has the H
allele) × 1/2 (the chance that the child inherits H from John) × 1/2 (the chance
that the child inherits B from John) = 1/16. The chance that a Bb Hh child will
express brachydactyly is 90%, and the chance such a child will have Huntington
disease by age 50 is 2/3. Therefore, the probability that John and his wife’s
child will express both diseases is 1/16 × 0.90 × 2/3 = 0.0375 = 3.75%.
d. If the two loci are linked, the alleles on each of John's homologs will be either B h /
b H or B h / b h. The B H gamete could only be produced if John is B h / b H and
recombination occurs. The probability of that specific recombinant gamete = 10%
(the other 10% of the recombinant gametes are b h). As shown in part (b), the
probability that John's genotype is B h / b H = 1/4. The probability that John's
child will have both Huntington and brachydactyly = 1/4 (probability that
John is B h / b H) × 1/10 (probability of child inheriting B H recombinant
gamete from John) × 9/10 (probability of expressing brachydactyly) × 2/3
(probability of expressing Huntington's by age 50) = 0.015 = 1.5%.
11. Diagram the cross:
CC bb (brown rabbits) × cc BB (albinos) → F1 Cc Bb × cc bb → 34 black : 66
brown : 100 albino.
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a. If the genes are unlinked, the F1 will produce C B, c b, C b and c B gametes in equal
proportions. A mating to animals that produce only c b gametes will produce four
genotypic classes of offspring: 1/4 Cc Bb (black) : 1/4 cc Bb (albino) : 1/4 Cc bb
(brown) : 1/4 cc BB (albino); that is, a ratio of 1/4 black : 1/2 albino : 1/4 brown.
b. If gene C and gene B are linked, then the genotype of the F1 class is C b / c B and
you would expect the parental type C b and c B gametes to predominate; c b and C B
are the recombinant gametes present at lower levels. The parental gametes are
represented in the F2 by the Cc bb (brown) and cc Bb (albino) classes. Since we
cannot distinguish between the albinos resulting from fertilization of recombinant
gametes (c b), and those resulting from parental gametes (c B), we have to use the
proportion of the C B recombinant class and assume that the other class of
recombinants (c b) is present in equal frequency. Because crossing-over is a
reciprocal exchange, this assumption is reasonable. There were 34 black progeny;
assuming that 34 of the 100 albino progeny were the result of recombinant gametes,
the genes are (34 + 34) recombinant / 200 total progeny = 34% RF = 34 cM
apart.
blue smooth × yellow wrinkled → 1447 blue smooth, 169 blue wrinkled, 186
yellow smooth, 1510 yellow wrinkled.
a. To determine if genes are linked, first predict the results of the cross if the genes are
unlinked. In this case, a plant with blue, smooth kernels (A– W–) is crossed to a plant
with yellow, wrinkled kernels (aa ww). As there are four classes of progeny, the parent
with blue, smooth kernels must be heterozygous for both genes (Aa Ww). From this
cross, we would predict equal numbers of all four phenotypes in the progeny
if the genes were unlinked. Since the numbers are very skewed, with the
smaller classes representing recombinant offspring, the genes are linked. RF
= (169 + 186) / (1447 + 169 + 186 + 1510) = 355/3312 = 10.7% = 10.7 cM.
b. The genotype of the blue smooth parent was Aa Ww. The arrangement of alleles in
the parent is determined by looking at the phenotypes of the largest classes of progeny
(the parental reciprocal pair). Since blue, smooth and yellow wrinkled are found in
the highest proportion, A W must be on one homolog and a w on the other = A
W / a w.
c. The genotype of the blue, wrinkled progeny is A w /a w. This genotype can produce
A w or a w gametes in equal proportions. Recombination cannot be detected here,
because this genotype is heterozygous for only one gene. Recombination between
these homologs yields the same two combinations of alleles (A w and a w) as the
parental, so each type of gamete is expected 50% of the time. The yellow smooth
progeny plant has a genotype of a W / a w. Again since recombination cannot be
detected, the frequency of each type is 50%. Thus the cross is A w / a w (blue
wrinkled) × a W / a w (yellow smooth). Four types of offspring are expected in
equal proportions: 1/4 A w / a W (blue smooth) : 1/4 A w / a w (blue
wrinkled) : 1/4 a w / a W (yellow smooth) : 1/4 a w / a w (yellow wrinkled).
13. a. AA BB × aa bb → F1 A B / a b (A B on one homolog and a b on the other
homolog). The F1 progeny will produce parental type gametes A B and a b and the
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recombinant types A b and a B. The genes are 40 cM apart, so the recombinants

will make up 40% of the gametes (20% A b and 20% a B). The remaining
60% of the gametes are parental: 30% A B and 30% a b. Set up a Punnett
square to calculate the frequency of the 4 phenotypes in the F2 progeny. In the
Punnett square the phenotypes associated with the genotypes in each box are
indicated with the same colors as was used previously in Problem 4 above. The F2
phenotypic ratio is: 0.59 A– B– : 0.16 A– bb : 0.16 aa B– : 0.09 aa bb.
b. If the original cross was AA bb × aa BB, the allele combinations in the F1 would be
A b / a B. Parental gametes in this case are 30% A b and 30% a B and the
recombinant gametes are 20% A B and 20% a b. Set up a Punnett square, as in part
(a). The F2 phenotypic ratio is: 0.54 A– B– : 0.21 A– bb : 0.21 aa B– : 0.04 aa
bb.
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14. Notice that you are asked for the number of different kinds of phenotypes, not the number
of individuals with each of the different phenotypes.
a. 2 (A- and aa);
b. 3 (AA, Aa, and aa);
c. 3 (AA, Aa, and aa);
d. 4 (A– B–, A– bb, aa B–, and aa bb);
e. 4 [A– B–, A– bb, aa B–, and aa bb; because the genes are linked, the frequency of
the four classes will be different than that seen in part (d)];
f. Nine phenotypes in total. There are three phenotypes possible for each gene. The
total number of combinations of phenotypes is (3)2 = 9 [(AA, Aa, and aa) × (BB,
Bb, and bb)].
g. Normally there are four phenotypic classes, as in parts (d) and (e): (A– B–, A– bb,
aa B–, and aa bb). In this case, there is recessive epistasis, so two of the classes (for
example, A– bb and aa bb) have the same phenotype, giving 3 phenotypic
classes.
h. Two genes means four phenotypic classes (A– B–, aa B–, A– bb and aa bb).
Because gene function is redundant, the first three classes are all phenotypically
equivalent in that they have function, and only the aa bb class will have a different
phenotype, being without function. Thus there are only 2 phenotypic classes.
i. There is 100% linkage between the two genes. The number of phenotypic classes
will depend on the arrangement of alleles in the parents. If the parents are A B /
a b × A B / a b, the progeny will be 3/4 A– B– : 1/4 aa bb and there will be
two phenotypic classes. If the parents are A b / a B × A b / a B, the
progeny will be 1/4 AA bb : 1/2 Aa Bb : 1/4 aa BB and there will be three
phenotypic classes in the offspring.
15. V1, V2, and V3 are codominant alleles of the DNA variant marker locus, while D and
d are alleles of the disease gene. The marker and the disease locus are linked. Diagram
the cross:
V1 D / V2 d (father) × V3 d / V3 d (mother) → V2 ? / V3 d.
The fetus must get a V3 d homolog from the mother. The fetus also received the V2 allele
of the marker. The father could have given a V2 d (nonrecombinant) or a V2 D
(recombinant) gamete.
a. If the D locus and the V1 allele of the marker are 0 mu apart (there is no recombination
between them; they appear to be the same gene), the probability that the child,
who received the V 2 allele of the marker, has the D allele = 0.
Parts (b)-(d) require thinking in terms of conditional probability – similar to Problem 10
above. In this case, the condition is the fact that you already know that the child received
the V2 marker allele. This fact alters the otherwise simple expectations based on
recombination frequency and equal segregation of alleles into gametes.
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b. If the distance between the disease locus and marker is 1 mu, 1% of the father's
gametes are recombinant between D and the marker locus, and 99% of his gametes
are parentals. Half of the recombinant gametes will be V2 D, and the other half will
be V1 d; half of the parental gametes will be V1 D, and the other half will be V2 d .
If we consider 200 of his gametes, there will be 1 V2 D : 1 V1 d : 99 V1 D : 99 V2
d. As we already know that the child inherited V2, and the ratio of gametes with the
V2 allele is 1 V2 D : 99 V2 d, you can see that the chance that the fetus has the
D allele is 1/100 = 1%. Parts (b) – (d) are solved using the same logic.
c. 5%.
d. 10%.
e. 50%.
16. a. You would know that this figure represents meiosis I in a mouse primary
spermatocyte (as opposed to a human primary spermatocyte) because you can see
that there are 20 bivalents, each bivalent being represented by one red line
showing the synaptonemal complex [with the exception of the X-Y pair, see part
(d) below.] In humans, there would be 23 bivalents because there are 23 pairs
of chromosomes.
b. Because of a printing error, it is very hard to discern the blue color in this
micrograph, so you may not be able to answer this problem based on what you
see. (Our apologies.) If you could see the blue color, it would be located at
one end of each red string of synaptonemal complex. (At the end of this answer
is a similar photograph properly showing the blue staining.) This fact indicates that
all mouse chromosomes are acrocentric because the centromere staining in blue is
at one chromosomal end. Interestingly, you know from various karyotypes you have
already seen in this book that many human chromosomes are metacentric. Thus,
similar preparations from human primary spermatocytes would show in some cases
blue staining in the middle of a red strand. The location of the centromeres is thus
another criterion by which you could be sure you are looking at mouse rather than
human primary spermatocytes.
c. In mice, n = 20 so 2n = 40. The figure legend indicates that these are primary
spermatocytes in mid-prophase of meiosis I (which makes sense because this is the
time at which the synaptonemal complexes are present). At this stage of meiosis, the
chromosomes have already replicated and each chromosome is made of two sister
chromatids. Thus, the cell contains 2 × 2n chromatids, or 80 chromatids.
d. The X-Y bivalent is indicated by the white arrow in Fig. 5.7a on p. 134. The
reason you know this to be the case is that the two chromosomes are associated at
only one end. The problem tells you that there is only one PAR on the mouse X
and Y chromosomes, so this is where they associate. If you look hard at the point of
association (just at the arrowhead), you can see a small green spot, indicating that a
recombination event (represented by a recombination nodule) is occurring between
the PARs on the X and the Y. This recombination event is absolutely required for
proper disjunction of the X and Y chromosomes during meiosis I [see part (e) below].
(Note: If you could see the centromeres in blue, you would find that they are
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located at the ends of the X and the Y chromosome that do not contain the PARs;
see the additional figure at the end of this answer.)
In case you are curious, the reason the red color extends along the length of the
X and Y chromosomes, even though pairing occurs only at the PARs, is that the
synaptonemal complex includes some proteins that extend along the chromosome
length (these form so-called lateral elements) as well as proteins that are found only at
the sites of pairing (forming so-called central elements). The protein stained in red is
part of the lateral elements. A figure summarizing the structure of the X-Y bivalent
is shown below. The colors are as in Fig. 5.7a, including the blue centromeres if they
were visible at the ends of these two acrocentric chromosomes.
e. In order for the X and Y chromosomes to segregate faithfully so that each

sperm contains either an X or a Y but not both, the X and Y need to pair with
each other. The X and the Y also need to stay together so that they can migrate
to the metaphase plate during meiosis I before they separate at anaphase of
meiosis I. The pseudoautosomal regions of the X and the Y have nearly
identical DNA sequences. This allows the X and Y chromosomes to pair with
each other. Crossing-over within the pseudoautosomal regions holds the
X-Y pair together until anaphase of meiosis I.
Special note: The photograph that follows shows a different mouse primary spermatocyte
prepared in the same way, but in this case the blue centromere staining demonstrating that
mouse chromosomes are all acrocentric is clearly visible. The arrow points to the PAR
region of the X-Y bivalent (note again the green recombination nodule in the PAR region);
the longer, somewhat more brightly red staining strand in this bivalent is the X.
© Dr. Paula Cohen & Dr. Kim

Holloway, The Cohen Lab, Center
for Reproductive Genomics,
Cornell University
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17. The figure that follows shows clearly that the cohesin complexes located distal
to the chiasmata (that is, further away from the centromere than the site of
recombination) are the critical cohesin complexes for maintaining the
homologous chromosomes together in a bivalent. The two centromeres are being
pulled towards the opposite spindle poles. The left panel of the figure below shows what
would occur if only the cohesin complexes distal to the chiasmata remained (and none
proximal to the chiasmata existed). The cohesin complexes distal to the centromere are
sufficient to prevent the homologous chromosomes from separating. As seen at the
center and right, the cohesin complexes proximal to the chiasmata have no such function;
in the absence of the distal complexes, there is nothing to prevent the homologous
chromosomes from being separated and being pulled to opposite spindle poles (right).
Careful observation of the drawing will also illustrate some additional points of
interest. (i) Note that these are acrocentric mouse chromosomes, so the centromeres are
found at one chromosome end. The centromeres (dark green and light green ovals) are
made of many cohesin complexes that are not shown. The spindle fibers exerting
poleward forces (black arrows) are connected to the kinetochores (not shown), which are
found at the centromeres but which involve proteins other than the cohesin complexes.
(ii) At anaphase of meiosis I, the cohesin complexes along the arms (both proximal and
distal to the chiasmata) dissolve, allowing the homologous chromosomes to be pulled to
opposite spindle poles. (iii) Note that the cohesin complexes are rings inside of which
are the two sister chromatids. In other words, the rings include two light green
chromatids or two dark green chromatids, but never a light green and a dark green
chromatid. The reason for this is straightforward: The cohesin rings are made immediately
after chromosomes replicate into sister chromatids, before the homologous
chromosomes pair with each other.
Section 5.3
wild type ♀ × reduced cinnabar ♂ → F1 ♀ × F1 ♂ → 292 wild type, 9 cinnabar, 7
reduced, 92 reduced cinnabar.
Two genes are involved in this cross, but the frequencies of the phenotypes in the second
generation offspring do not look like frequencies expected for a cross between double
heterozygotes for two independently assorting genes (9:3:3:1). The genes must
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be linked. Designate the alleles: cn+ = wild type, cn = cinnabar; rd+ = wild type, rd =
reduced. The cross is:
cn+ rd+ / cn+ rd+ ♀ × cn rd / cn rd ♂ → F1 cn+ rd+ / cn rd.
Recombination occurs in Drosophila females but not in males. Thus males can
produce only the parental cn + rd + or cn rd gametes. The females produce both
the parental gametes and the recombinant gametes cn + rd and cn rd + . These
gametes can combine as shown in the Punnett square that follows. The phenotypes in the
boxes are indicated with various colors. You do not need to fill in the numbers in the
Punnett square to solve this problem, but they are added as a check of the final answer
described below the table.
The reduced flies and the cinnabar flies are recombinant classes. However, there
should be an equal number of recombinant types that have a wild-type phenotype
because they got a cn+ rd+ gamete from the male parent. If we assume that these
recombinants are present in the same proportions, then RF = 2 × (7+9)/400 = 9%.
The genes are separated by 8 cM.
19. a. There are four equally frequent phenotypic classes in the progeny; these must
include a reciprocal pair of parentals and a reciprocal pair of recombinants. The
parental reciprocal pair could either be [(wild-type wings, wild-type eyes) and
(dumpy wings, brown eyes)] or [(wild-type wings, brown eyes) and (dumpy wings,
wild-type eyes)]. The first possibility means the genotype of the heterozygous
female was dp+ bw+ / dp bw while the second pair means the genotype of the
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female was dp bw+ / dp+ bw. In either case the recombination frequency is 50%
(178 + 181 / 716 or 185 + 172 / 716) so the two genes are assorting
independently.
b. In this cross the heterozygous parent is the male and there is no recombination in
Drosophila males. If dumpy and brown were on separate chromosomes then they must
assort independently and there would be four classes of progeny as in part (a). We can
tell that the two genes are on the same chromosome because the lack of
recombination in the male parent then explains why only two (parental) classes of
progeny are seen. The genotype of the heterozygous male must have been dp +
bw + / dp bw.
c. If the genes are far enough apart on the same chromosome they will assort
independently in the first cross. This is because (1) recombination occurs at the
four strand stage of meiosis; and (2) in every meiosis, at least one crossover
will occur between the two genes. Independent assortment does not occur in the
second cross because there is no recombination in Drosophila males. In Drosophila,
therefore, it is a simple matter to decide if genes are syntenic (located on the
same chromosome), even if the alleles of these genes assort independently. A
cross between a male heterozygous for the two genes of interest and a recessive female
will clearly distinguish between genes on separate chromosomes and syntenic genes.
In the case of genes on separate chromosomes there will be four equally frequent
classes of progeny. In the case of genes on the same chromosome (even genes that
are very far apart on the same chromosome) there will only be two classes of
progeny – the parental classes.
d. The dp ↔ bw distance cannot be measured in any two-point cross. The measured
recombination frequency can be no higher than 50% when looking at data involving
a single pair of genes. Large genetic distances can be measured accurately only
by summing up the values obtained for smaller distances separating other
genes in between those at the ends.
20. a. A testcross is the best way to find the map distance between two genes. One parent
must be heterozygous for both genes and the other parent must homozygous
recessive. Thus the cross would be Bb Cc × bb cc. Because these genes are syntenic
the heterozygous parent may be either B C / b c or B c / b C.
b. There are two possible orders for these genes, shown in the following figure:
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c. Because the map positions of A and D are so close, the relative order of A and D
is not clear. Another uncertainty is the location of gene E. This gene must be
on this chromosome because we are told all of these genes are syntenic. However
the E gene is genetically unlinked to any of the other genes (A, B, C and D).
d. To figure out the actual order of the genes you must do a three-point cross with
either B A D or A D C and order the genes by finding the double crossover
class, comparing this to the parental class and ascertaining the order of the genes. This
procedure is described in the Tips for Three-Point Crosses in the Problem
Solving section at the beginning of the chapter. Also see Problem 5-22c for a
further explanation of this method of determining the gene order.
The location of the E gene can be determined by finding new genes that
are genetically linked to the left of C and to the right of B in the maps seen in part
(b). This extension of the linkage group will eventually allow the placement of
gene E when it shows genetic linkage to one of these new genes.
21. The shortest distances are the most accurate. Therefore begin assembling a map using
the genes that are closest together. MAT-LEU2 are 16 cM apart and MAT-THR4 are
20 cM apart. This gives two possible maps: MAT - (16 cM) - LEU2/THR4 or LEU2 -
(16 cM) - MAT - (20 cM) - THR4. Because THR4 is 35 cM from LEU2 the second
map must be the correct one. Note that the two smaller distances do not sum to the
longer distance because these recombination frequencies are based on two-point
crosses. The HIS4 gene is 23 cM from LEU2. This initially leads to two possible maps: HIS4
- (23 cM) - LEU2 - MAT - THR4 or LEU2 - (23 cM) - HIS4/MAT - THR4. The first map
is the most likely because HIS4 is 37 cM from MAT instead of being very close to MAT.
So the order of the genes is HIS4 - LEU2 - MAT - THR4 (or the inverse).
22. In foxgloves, wild-type flower color is red and the mutant color is white; the mutation
peloria causes the flowers at the apex of the stem to be very large; normal foxgloves are
very tall, and dwarf affects the plant height. When you describe the phenotype of an
individual you usually only refer to the non-wild type traits. The cross is:
white flowered × dwarf peloria → F1 white flowered × dwarf peloria → 172 dwarf
peloria, 162 white, 56 dwarf peloria white, 48 wild type, 51 dwarf white, 43 peloria, 6
dwarf, 5 peloria white.
a. Because there is only 1 phenotype of F1 plant, the parents must have been homozygous
for all three genes. The phenotype of the F1 heterozygote indicates the dominant
alleles: white flowers , tall stems, and normal-sized flowers.
b. Designate the alleles for the 3 genes: W = white, w = red; P = normal-sized flowers,
p = peloria; T = tall, t = dwarf. The cross is: WW PP TT (white flowered) ×
ww dd pp (dwarf peloria).
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c. Note that all 3 of these genes are genetically linked. There are only 2 classes of
parental progeny as defined both phenotypically and numerically. In order to draw a
map of these genes, organize the testcross data (see the Table that follows), figure out
which of the 3 genes is in the middle and calculate the recombination
frequencies in regions 1 and 2. By definition, the parentals are the class with the
same phenotype as the original parents of the cross, and the DCO class is the least
frequent reciprocal pair of progeny. At this point, arbitrarily one of the remaining 2
reciprocal pairs of progeny is SCO 1 and the last remaining pair is SCO 2.
Classes
of Genotype Numbers
gametes
Parental WPT 162
(P) wpt 172
Wpt 56
SCO 1 wPT 48
WPt 51
SCO 2 wpT 43
wPt 6
DCO WpT 5
Compare the DCO class with the parental class. Remember that a DCO comes
from a meiosis with a simultaneous crossover in regions 1 and 2. As a result, the allele
of the gene in the middle switches with respect to the alleles of the genes on the ends.
In this data set, take one of the DCO classes (for example W p T) and compare it
to the most similar parental gamete (W P T). Two alleles out of three are in
common; the one that differs (p in this case) is the gene in the middle. Thus, the order
is W P T (or T P W).
Once you know the order of the 3 genes, you must calculate the 2 shortest
distances - from the end to the center (W↔P) and from the center to the other end
(P↔T). The total number of progeny in this testcross = 543. RF W↔P = (56 + 48
+ 6 + 5)/543 = 115/543 = 21.2 cM; RF P↔T = (51 + 43 + 6 + 5)/543 = 19.3 cM.
The map is:
d. Interference (I) = 1 - coefficient of coincidence (coc)

coc = frequency of observed DCO / frequency of expected DCO
The expected percentage of double crossovers is the product of the RF in each
interval: (0.193) × (0.212) = 0.0409. The observed DCO frequency = 11/543 =
0.0203; coc = 0.0203/0.0409 = 0.496; I = 1 - 0.496 = 0.504.
23. Although this problem considers three different genes, each cross only considers two at
a time. You are thus asked to construct a map of the three genes based on 3 two-point
crosses. Note the unusual usage of a comma to separate the genes in the genotypes written
for the parents of each cross. This is meant to show that we don't know if any
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of the genes are on the same chromosome. If the two genes in each cross are assorting
independently then the four phenotypic classes in the testcross progeny must occur in
equal frequencies. This is clearly not the case in any of the three crosses. Therefore the
mb, e and k genes are all linked. The genotypes of the parents in the first cross may be
correctly written as mb+ e+ / mb+ e+ × mb e / mb e.
In the first cross, the mb+ e+ and mb e classes are the parentals. This is based both
on the known genotypes of the true breeding parental generation and on the fact that this
reciprocal pair is the most frequent. The recombinants are the mb+ e and the mb e+ flies,
so the RF = 11 + 15 / 250 = 0.104 = 10.4 mu. In the second cross the recombinant
reciprocal pair is k+ e+ and k e, so the recombination frequency is 11 + 7
/ 312 = 0.058 = 5.8 mu. The k mb+ and k+ mb classes are the recombinant reciprocal
pair for the third cross. In this case the RF = 11 + 15 / 422 = 0.062 = 6.2 mu. The mb
and e genes in the first cross are the furthest apart, so the k gene must be in between them.
Thus the map of these data is:
Note that the distance calculated between e and mb in cross one (10.4 mu) does
NOT equal the sum of the two shorter distances (12.0 mu). The distance calculated
from cross one is less accurate because it is based on single crossovers between e and mb
and does not include any of the double crossovers that occurred in the e↔k and
k ↔mb regions simultaneously. Thus, the best map of these genes is:

pink petals, black anthers, long stems × pink petals, black anthers, long stems → the
progeny listed in the table.
a. Looking at flower color alone, the cross is pink × pink → (78 + 26 + 44 + 15)
red : (39 + 13 + 204 + 68) pink : (5 + 2 + 117 + 39) white = 163 red : 324 pink :
163 white. The appearance of two new phenotypes (red and white) suggests that
flower color shows incomplete dominance. This idea is confirmed by the 1:2:1
monohybrid ratio seen in the self-cross progeny. The pink flowered plants are
Pp, red are PP and white are pp.
b. The expected ratio of red: pink : white would be 1:2:1. Calculating for the 650
plants, this equals 162.5 red, 325 pink, and 162.5 white.
c. The monohybrid ratio of the black and tan anthers = (78+26+39+13+5+2) tan :
(44 + 15 + 204 + 68 + 117 + 39) black = 163 tan : 487 black = ~ 1 tan : 3 black.
Therefore black (B) is dominant to tan (b). The monohybrid ratio for the stem
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length = 487 long stems : 163 short stems. = ~ 3 long : 1 short, so long (L) is
dominant to short (l).
d. Designate the alleles: PP = red, Pp = pink, p = white; B = black, b = tan, L = long, l
= short. Because all 3 monohybrid phenotypic ratios are characteristic of
heterozygous crosses, the genotype of the original plant is Pp Bb L l.
e. If the stem length and anther color genes assort independently, the 9:3:3:1
phenotypic ratio should be seen in the progeny. Totaling all the progeny in each of
the classes: 365 long black : 122 short black : 122 long tan : 41 short tan. The observed
dihybrid ratio is close to a 9:3:3:1 ratio, so the genes for anther color (B) and stem
length (L) are unlinked.
The expected monohybrid ratio for flower color is 1 red : 2 pink :1 white, while
that for stem length is 3 long :1 short. If the two genes are unlinked, the expected
dihybrid ratio can be calculated using the product rule to give 3/8 long pink : 3/16
long red : 3/16 long white : 1/8 short pink : 1/16 short red : 1/16 short white, or a
6 L– Pp : 3 L– PP : 3 L– pp : 2 ll Pp : 1 ll PP : 1 ll pp ratio. The observed numbers
are: 243 long pink : 122 long red : 122 long white : 81 short pink : 41 short red : 41
short white. This observed ratio is close to the predicted ratio, so the genes for petal
color (P) and stem length (L) are unlinked.
The same analysis is done for flower color and anther color. The expected
dihybrid ratio here is also 6:3:3:2:1:1. The observed numbers are: 272 black pink : 59
black red : 156 black white : 52 tan pink : 104 tan red : 7 tan white. Because these
numbers do not fit a 6:3:3:2:1:1 ratio, we can conclude that flower color (P) and
anther color (B) are linked genes.
f. It is clear that the original snapdragon was heterozygous for Pp and Bb. However
the genotype of this heterozygous plant could have been either P B / p b or P b /
p B. If it is the former and the genes are closely linked, then the pp bb phenotype will
be very frequent (almost 1/4 of the progeny because it is nonrecombinant). Instead
the pp bb class is very infrequent, accounting for only about 1% (7/650) of the progeny.
Thus, the parental genotype must have been P b / p B. In this case, the
infrequent pp bb class received a p b recombinant gamete from each parent.
The frequency of the pp bb genotype = (frequency of the p b recombinant
gamete)2. The recombination frequency (RF) between the P gene and the B
gene = frequency of P B + p b gametes = 2(√(#pp bb/# total progeny) =
2(√(7/650)) = ~20 map units.
25. a. See Problem 5-29 for a detailed explanation of the methodology. Diagram the cross:
a+ b+ c+ / a b c ♀ × a b c / a b c ♂ → ?.
Recombination occurs in Drosophila females, so the female parent will make the
following classes of gametes. Because this is a testcross, these gametes will
determine the phenotypes of the progeny. The Table that follows indicates the
kinds of gametes that the female parent will produce and their frequencies.
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# of
Classes Frequenc
Frequency of progeny
of Genotype Numbers y of each
reciprocal freq x
gametes class 1,000
pair
1 - (0.18 +
Parental a+ b+ c+ 1 - all else
0.36 360
0.08 + 0.02)
(P) a b c 0.36 360
= 0.72
a+ b c RF in region 1 SCO 1 = 0.2 0.09 90
SCO 1
a b+ c+ = SCO 1 + - 0.02 = 0.18 0.09 90
a+ b+ c DCO
RF in region 2 SCO 2 = 0.1 0.04 40
SCO 2
a b c+ = SCO 2 + - 0.02 = 0.08 0.04 40
a+ b c+ DCO
(RF in region 1) x (0.2) x (0.1) = 0.01 10
DCO
a b+ c (RF in region 2) 0.02 0.01 10
b. Diagram the cross: a+ b+ c+ / a b c ♂ × a b c / a b c ♀ → ?. Here, the

heterozygous parent is the male. Recombination does not occur in male Drosophila.
Thus, the heterozygous parent will generate only 2 types of gametes, the parental
types. If you score 1,000 progeny of this cross, you will find 500 a + b + c + and
500 a b c progeny.
26. First re-write the data as genotypes grouping the genetic reciprocal pairs.
Classes of
Genotype Numbers
gametes
th h st 432
Parental (P) + + + 429
th h + 37
Recombinant + + st 33
th + st 35
Recombinant + h+ 34
The th h st and wild-type (+ + +) classes are defined as parental because they are the
most frequent reciprocal pair.
a. Each class of the parental reciprocal pair corresponds to one homolog of the
heterozygous Drosophila female that was testcrossed to the homozygous recessive
male. Thus the genotype of this female is th h st / th + h + st +.
b. This is a testcross with three linked genes, but there are only 6 classes of data (3
reciprocal pairs) instead of 8 classes. The missing reciprocal pair is th + + and + h st.
This pair must be the least frequent DCO class. Comparing the th + + DCO class
to the + + + parental class (the most similar) shows that th is the gene that differs,
so th must be the gene in the middle. The h ↔th distance is 35 + 34 / 1000 = 0.069
= 6.9 mu. The th ↔st distance is 37 + 33 / 1000 = 0.07 = 7 mu. The best map is:
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c. I = 1 – coefficient of coincidence; coefficient of coincidence = observed DCO /

expected DCO. Thus coefficient of coincidence = 0 / (0.069)(0.07) = 0 and I = 1 –
0 = 1. The interference is complete.
27. a. wild type ♀ × scute echinus crossveinless black ♂ → 16 classes of data
Among the 16 classes there are wild type for all traits and scute, echinus, crossveinless,
and black. This tells you that the parental female was heterozygous for all 4 traits.
The fact the parental female is wild type also tells you that the wild- type alleles of all
4 genes are dominant. Remember that if you do a testcross with a female that is
heterozygous for 3 linked genes, the data shows a very specific pattern. Because
each type of meiosis (no recombination, DCO, etc.) gives a pair of gametes, you will
see 8 classes of data that will occur in 4 pairs, both genetically and numerically. Thus,
if you begin a cross with a female that is heterozygous for 4 linked genes, you
should see 16 classes of progeny in a pattern of 8 genetic and numeric pairs. Although
we have 16 classes of data, they do not occur in numeric pairs - instead we see numeric
groups of 4. If one (or more) of the genes instead assorts independently of the others,
then in a testcross you must see numeric groups of 4. For example, the most frequent
classes will be parental, and there will be a
1:1:1:1 ratio of the 4 parental types.
Which gene is assorting independently relative to the other 3 genes? To answer
this question, list the genotypes of the gametes that came from the heterozygous
parent in the largest group of 4. This group should include the parental classes for the
3 linked genes; there are 4 genotypes here to account for the independent assortment
of the unlinked gene. Then choose one of the 4 genes, and remove the allele of that
gene from all 4 groups. When you do this with the gene that is assorting
independently of the rest, you will find there are only 2 reciprocal classes of data
left, which are the parental classes for the linked genes. If you choose one of the linked
genes to remove, you will still have 4 different phenotypic classes left.
Try removing the b gene first, as shown in the third column of the Table that
follows. You see that when the b allele is removed, only 2 classes are left: s e c and
+ + +. But when this analysis is repeated removing the allele of the s gene there are
still 4 different phenotypes left (see the right column of the Table).
remove remove
Genotype Numbers
b s
b s e c 653 s e c b e c
+ s e c 670 s ec + e c
+ + + + 675 + + + + + +
B + + + 655 + + + b + +
The b gene is therefore assorting independently of the other 3 genes. When the b gene
is removed from all 16 classes of data, you can see that the data reduces to 8 classes
that form 4 genetic and numeric reciprocal pairs, just as in any three-point cross [see
answer to part (b) below]. Thus, the genotype of the parental female is:
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b. Write the classes out as reciprocal pairs.

Classes of
Genotype Numbers
gametes
+ + + 1323
Parental (P) s e c 1330
s + + 144
SCO 1 + e c 147
s e + 171
SCO 2 + + c 169
s + c 2
DCO + e + 2
Compare the DCO s + c to the parental s e c ; this shows that e is in the middle.
Calculate RF s ↔ e = (144 + 147 + 2 + 2)/3288 = 9.0 cM; RF e ↔ c = (171 + 169
+ 2 + 2)/3288 = 10.5 cM.
c. Interference = 1 - coefficient of coincidence

coc = observed DCO frequency / expected DCO frequency = (4/3288) / (0.09 ×
0.105) = 0.001 / 0.009 = 0.11.
I = 1− 0.11 = 0.89; yes, there is interference.
28. a. Recombination does not occur in male Drosophila. Therefore, in the cross A b / a B
♀ × A b / a B ♂ → F1, the females will make 4 types of gametes (parental A b
and a B; recombinant A B and a b). The frequencies of the 2 parental gametes will
be equal to each other, and the frequency of the A B recombinant will be equal to the
frequency of its reciprocal recombinant, a b. Males, however, will make only two
(parental) gamete types in equal numbers: A b and a B. The Punnett square that
follows shows how this will play out; the relative sizes of the boxes do not affect
the ultimate answer.
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There is a ratio of 1/4 A– bb (orange boxes): 1/2 A– B– (blue boxes): 1/4 aa B–

(purple boxes) for the progeny receiving the parental gametes AND the same ratio
among the progeny receiving the recombinant gametes. Thus, the overall
phenotypic dihybrid ratio will always be 1/4 A– bb : 1/2 A– B– : 1/4 aa B–,
independent of the recombination frequency between the A and B genes.
This will not be true of the cross A B / a b ♀ × A B / a b ♂ (see Table
on the following page). The male will make the parental gametes, A B and a b, while
the female will make 4 types of gametes: parental A B and a b; recombinant A b and
a B. In this case, half of the progeny will look A– B– because they received the A B
gamete from the male parent irrespective of the gamete from the female parent. When
the male parent donates the a b gamete, then it is the gamete from the female parent
that determines the phenotype of the offspring. The progeny that are A– bb and aa
B– have received a recombinant gamete from the female parent (and the a b gamete
from the male). These classes of progeny can then be used to estimate the
recombination frequency between the A and B genes: RF = 2(# of A– bb +
# of aa B–)/total progeny. (The factor of 2 is included because you cannot see
half of the recombinants.)
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b. In mice, recombination occurs in both females and males. Therefore, in the cross
A b / a B ♀ × A b / a B ♂ both sexes will make the same array of gametes
(parental A b and a B; recombinant A B and a b). In this case, the only phenotype
of progeny with a singular genotype will be aa bb. In the cross under consideration
here, the aa bb phenotype can only arise if both parents donate the a b recombinant
gamete. Of course, the other recombinant gamete, A B, occurs with equal
frequency. The probability of the aa bb genotype = (probability of an a b recombinant
gamete)2. If you know the frequency of the aa bb phenotypic class in the progeny,
recombination frequency (frequency of recombinant products) between the A
and B genes = 2(√#aa bb/# total progeny).
In the case of the A B / a b ♀ × A B / a b ♂ cross in mice, both sexes are
making the same parental gametes (A B and a b) and recombinant gametes (A b and
a B) gametes. Again, the only phenotype of progeny with a singular genotype will be
aa bb. In this example, this phenotype is the result of the fusion of the a b parental
gamete from each parent. The frequency of the aa bb phenotype = (the frequency
of the a b gamete) × (the frequency of the a b gamete). If you know the frequency
of the aa bb phenotypic class in the progeny, the frequency of nonrecombinant
products between the A and B genes = 2(√#aa bb/# total progeny).
Recombination frequency = 1 - frequency of nonrecombinant products
between the A and B genes.
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M C S / M C S (Virginia strain) × m c s / m c s (Carolina strain) → F1 M C S / m c s ×
mcs/mcs →?
Assume no interference, and remember the map of these 3 genes:
You are being asked to calculate the proportion of the testcross progeny that will have
the Virginia parental phenotype. In Chapter 3 we could answer this question by calculating
the monohybrid ratios for each pair of alleles (M : m, C : c and S : s) in the heterozygous
parent. The testcross parent can provide only the recessive alleles for each gene, so the
probabilities of the various phenotypes can be determined by applying the product rule.
Unfortunately, this method of arriving at the probability of the progeny phenotypes only
works when the genes under discussion are assorting independently. When the 3 genes
are linked, as in this problem, to calculate the frequency of a parental class we must
calculate first calculate the frequencies of all of the phenotypes expected in the testcross
progeny.
A parent that is heterozygous for 3 genes will give 8 classes of gametes. In a test
cross, the gamete from the heterozygous parent determines the phenotype of the progeny.
When the 3 genes are genetically linked, these 8 classes will be found as 4 reciprocal pairs.
In other words, each meiosis in the heterozygous parent must give 2 reciprocal products
that occur at equal frequency. For instance, a meiosis with no recombination will produce
the parental gametes, M C S and m c s at equal frequency. This particular reciprocal pair
will also be the most likely event and so the most frequent pair of products. The
least probable meiotic event is a double crossover which is a recombination event in the
region between M and C (region 1) and simultaneously in the region between C and S
(region 2). The remaining gametes are produced by a single crossover in region 1 (the
reciprocal pair known as single crossovers in region 1 or SCO 1) and a single crossover
in region 2 (the reciprocal pair known as single crossovers in region 2 or SCO 2).
The numbers shown on the map of this region of the chromosome represent the
recombination frequencies in the gene-gene intervals. There are 6 mu between the M
and C genes, so 6% (RF = 0.06) of the progeny of this cross will have had a recombination
event in region 1. This recombination frequency includes all detectable recombination
events between these 2 genes - both SCO in region 1 and DCO. Likewise, 17% of
all the progeny will be the result of a recombination event in region 2. The DCO class is
the result of a simultaneous crossover in region 1 and region 2. Recombination in two
separate regions of the chromosome should be independent of each other, so we can
apply the product rule to calculate the expected frequency of DCOs. Thus, the frequency
of DCO = (0.06) × (0.17) = 0.01. Remember that the recombination frequency between
M and C (region 1) includes both SCO 1 and DCO. Thus, 0.06 = SCO 1 + 0.01; solve
for SCO 1 = 0.06 - 0.01 = 0.05. The same calculation
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for region 2 shows that SCO 2 = 0.16. The parental class = 1 - (SCO 1 + SCO 2 + DCO).
Also remember that each class of gametes (parental, etc.) is made up of a reciprocal pair.
If the frequency of the DCO class is 0.01, then the frequency of the M c S gamete is
half of that = 0.005. This logic is summarized in the table below.
Classes Frequency
Frequency of
of Genotype Numbers of each
reciprocal
gametes class
pair
Parental MCS 1 - (0.05 + 0.16 + 0.39
(P) mcs 1 - all else 0.01) = 0.78 0.39
RF in region 1
Mcs SCO 1 = 0.06 - 0.01 = 0.025
SCO 1 mCS = SCO 1 + 0.05 0.025
DCO
RF in region 2
MCs SCO 2 = 0.17 - 0.01 = 0.08
SCO 2 mcS = SCO 2 + 0.16 0.08
DCO
(RF in region
McS 0.005
DCO mCs 1) x (RF in (0.06) x (0.17) = 0.01 0.005
region 2)
a. The proportion of backcross progeny resembling Virginia (parental, M C S)

= 0.39.
b. Progeny resembling m c s (P) = 0.39.
c. Progeny with M c S (DCO) = 0.005.
d. Progeny with M C s (SCO 2) = 0.8.
30. On the basis of a recombination frequency (RF) of 5%, the physical distance between
the HD gene and the G8 marker was estimated to be 5 million bp, but when the human
genome was sequenced, the actual physical distance between the gene and the marker was
found to be only 500,000 bp. Why is the actual distance much lower than the estimated
distance? The reason is that the estimate of the distance on the basis of the RF assumes
that recombination is uniform over the entire genome. This assumption is not true.
Although over the whole genome the average relationship is that 1% RF corresponds to 1
million bp everywhere in the genome, this value hides a great deal of variation in the
relationship in different regions of the genome.
In this particular case, it appears that about 10× more crossovers occur in the
interval between the HD gene and the G8 marker than in the average 500,000 bp
interval in the genome. Clearly then, the genomic DNA between HD and G8
contains a recombination hotspot.
31. In cross #1the criss-cross inheritance of the recessive alleles for dwarp and rumpled from
mother to son tells you that all these genes are X-linked. In cross #2, you see the same
pattern of inheritance for pallid and raven, so these genes are X-linked as well. The fact that
the F1 females in both crosses were wild type tells you that the wild-type allele of all four
genes is dominant to the mutant allele. Designate alleles: dwp+ and dwp for the dwarp
gene, rmp+ and rmp for the rumpled gene, pld+ and pld for the pallid gene, and rv+
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and rv for the raven gene. Assign the genes an arbitrary order to write the genotypes. If
you keep the order the same throughout the problem, it is sufficient to represent the wild-
type allele of a gene with +.
Cross 1: dwp rmp + + / dwp rmp + + × + + pld rv / Y → dwp rmp + + / + + pld rv
(wild-type females) and dwp rmp + + / Y (dwarp rumpled males).
Cross 2: + + pld rv /+ + pld rv × dwp rmp + + / Y → + + pld rv / dwp rmp + +
(wild-type females) and + + pld rv / Y (pallid raven males).
Final cross: dwp rmp + + / + + pld rv (cross 1 F1 females) × dwp rmp pld rv / Y → 428
+ + pld rv, 427 dwp rmp + +, 48 + rmp pld rv, 47 dwp + + +, 23 + rmp pld +, 22 dwp + +
rv, 3 + + pld +, 2 dwp rmp + rv.
All 4 genes might be genetically linked, as they are all on the X chromosome. If so, you
expect 16 classes of progeny (2 × 2 × 2 × 2) in 8 genetic and numeric pairs. Notice that
there are only 8 classes of progeny. The data that is seen shows exactly the pattern you
expect for a female that is heterozygous for 3 linked genes. If 2 of the 4 genes never
recombine then you would expect the pattern of data that is seen. If 2 genes never
recombine, they will always show the parental configuration of alleles. Thus, examine
the various pairs of genes for the presence or absence of recombinants. Note that you
never see recombinants between pallid and dwarp: all the progeny are either pallid or dwarp,
but never pallid and dwarp nor wild type for both traits. This suggests that the two genes
are so close together that there is essentially no recombination between the loci. If a much
larger number of progeny were examined, you might observe recombinants. Treat dwp
and pld as 2 genes at the same location, so one of them (dwp, for instance) can be
ignored, and this problem becomes a three-point cross between pld, rv and rmp.
Classes of
Genotype Numbers
gametes
dwp rmp + + 427
Parental (P) + + pld rv 428
+ rmp pld rv 48
SCO 1 dwp + + + 47
dwp + + rv 22
SCO 2 + rmp pld + 23
+ + pld + 3
DCO dwp rmp + rv 2
When the rmp + rv DCO class is compared to the rmp + + parental class, you can see
that rv is in the middle. The rmp ↔ rv RF = (48 + 47 + 3 + 2)/1000 = 10 cM; the
pld ↔ rv RF = (22 + 23 + 3 + 2)/1000 = 5 cM. I = 1 - coc; coc = observed
frequency of DCO/expected frequency of DCO. Thus, coc = (5/1000)/(0.05)(0.1) =
0.005/0.005 = 1; I = 1 - 1 = 0, so there is no interference.
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32. a. Interference is a phenomenon by which the occurrence of one crossover prevents

the occurrence of a second crossover in a nearby region of the same chromosome.
Scientists think that the existence of interference helps ensure that each bivalent has
at least one crossover, which is necessary in turn to ensure that homologous
chromosomes segregate from each other properly during the first meiotic division.
One way of thinking about the utility of interference is the following: If you assume
that only a limited amount of recombination enzymes are available in primary
spermatocytes or primary oocytes, the limited number of crossovers that can occur
will be apportioned among all the bivalents.
Fig. 5.7a on p. 134 shows a preparation of chromosomes from a primary
spermatocyte. Note that each bivalent shows at least one green recombination
nodule (a few may be hard to see, but they are present). The existence of
interference is suggested by the fact that even on the bivalents that show
more than one spot of recombination nodules, these nodules are far away from
each other. That is, one recombination event prevents the occurrence of a nearby
recombination event on the same bivalent.
b. Figure 5.7a merely suggests that two crossover events do not occur often at nearby
positions on the same bivalent. To show that this conclusion about the existence of
interference actually hold up from this type of evidence, you would have to look at
many meiotic figures from many spermatocytes and/or oocytes. You would then
have to ask: If recombination nodules can occur at any position in the genome
with equal likelihood (that is, if interference did not exist), how likely
would it be that two recombination nodules would occur in a given specified
distance on one bivalent. (You could calculate this probability by totaling the
average number of recombination nodules from many meiotic figures and
dividing by the total length of all the chromosomes to find the average distance
between nodules. You could then see if the space between nodules can be
graphed as a normal (Gaussian) distribution around this average. If the data
did not resemble the expected bell-shaped curve, then the distribution is not random.
If interference did exist, you would expect to see the data shifted over from a bell-
shaped curve so as to favor larger-than-average distances between adjacent nodules.
33. To answer this question, you need first to count the number of recombination nodules
visible in the whole genome depicted in Fig. 5.7a on p. 134. There is at least one nodule
per bivalent, and there are 20 bivalents in mice. By our own count, we see 29 nodules, but
you may see (or imagine you see) a few more or less. We will take 29 as the proper count
here. In this meiotic figure, the 29 nodules are distributed among 1,386 cM in the male
genetic map. If the same mouse genome corresponds to 1,817 cM in the female genetic
map, this must be because more recombination events take place in the average primary
oocyte than in the average primary spermatocyte. So you would multiply 29 times the ratio
of the cM in the female : male genetic maps (1,817 / 1,386) = ~38 recombination
nodules in the average prophase I primary oocytes. [Your final answer may vary
depending on how many nodules you counted in Fig. 5.7a, but your answer must be more
than 20 × (1,817 / 1,386) = 26.]
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Section 5.4
34. The null hypothesis is that there is independent assortment of 2 genes yielding a
dihybrid phenotypic ratio of 9/16 R– Y– : 3/16 R– yy : 3/16 rr Y– : 1/16 rr yy. Use
the chi square (Χ2) test to compare Mendel's observed data with the 9:3:3:1 ratio expected
for two genes that assort independently.
Genotypes Observed # Expected # Χ2 equation Sum of Χ2

R– Y – 9/16 (556) =
315
313 (315 − 313)2/313 0.01
R– yy 3/16 (556) =
108
104 (108 − 104)2/104 0.15
rr Y– 3/16 (556) =
101
104 (101 − 104)2/104 0.09
rr yy 32 1/16 (556) = 35 (32 − 35)2/35 0.26
0.51
The number of classes is 4, so the degrees of freedom is 4−1 or 3. Using Table 5.2 on p.
147 of the text, the probability of having obtained this level of deviation by chance
alone is between 0.9 and 0.99 (90 - 99%). Thus we cannot reject the null hypothesis. In
other words, the data are consistent with independent assortment and we
therefore conclude that Mendel's data could indeed result from the independent
assortment of the 2 genes.
You should note, however, that although Mendel’s data are consistent with
independent assortment, this chi square analysis does not prove that these genes assort
independently. This analysis did not exclude any hypothesis. We could not formulate
the null hypothesis as stating that the genes do not assort independently; we cannot
predict the expected number of progeny under this hypothesis given that linked genes can
have RF anywhere from 0% to just under 50%.
35. a. Diagram the cross.
orange (O– bb) × black (oo B–) → F1 brown (O– B–) → 100 brown (O– B–) :
25 orange (O– bb) : 22 black (oo B–) : 13 albino (oo bb)
Because the F1 snakes were all brown, we know that the orange snake could not
have contributed an o allele, or there would have been some black snakes. The
orange snake must be OO bb. The black snake could not have contributed a b allele
or there would have been some orange snakes, so the black parent must be oo BB.
Therefore the F1 snakes must be Oo Bb.
b. The F1 snakes are heterozygous for both genes (Oo Bb). If the two loci assort
independently, we expect the F2 snakes to show a 9 brown : 3 orange : 3 black : 1
albino ratio. The total number of F2 progeny is 160. We expect 90 (160 × 9/16) of
these progeny to be brown, 30 (160 × 3/16) to be orange, 30 to be black and
10 (160 × 1/16) to be albino.
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c.
Observed Expected
Genotypes
# # Χ2 equation Sum of Χ2
O– B– 100 90 (100−90)2/90 1.11
O– bb 25 30 (25−30)2/30 0.83
Oo B– 22 30 (22−30)2/30 2.13
oo bb 13 10 (13−10)2/10 0.9
4.97
There are three degrees of freedom (4 classes − 1) and the p value is between 0.5
and 0.1. The observed values do not differ significantly from the expected.
d. There is a 10% - 50% probability that these results would have been obtained by
chance if the null hypothesis were true; this is simply another way of writing the
meaning of the p value.
36. a. The cross is:
normal (DD) × dancer (dd) → F1 normal (Dd) F2 3/4 D– (normal) : 1/4 dd
(dancer)
1/4 of the F2 mice will be dancers if the trait is determined by a single gene
with complete dominance.
b. Diagram the cross:
normal (AA BB) × dancer (aa bb) → F1 normal (Aa Bb) F2 15/16 normal (A–
B– + A– bb + aa B–) : 1/16 dancer (aa bb)
1/16 of the mice would be expected to be dancers given the second hypothesis
that dancing mice must be homozygous for the recessive alleles of two genes.
c. Calculate the chi square values for each situation. Null hypothesis #1: Dancing is
caused by the homozygous recessive allele of one gene, so 1/4 of the F2 mice
should be dancers. Calculating the expected numbers, 1/4 × 50 mice or 13 should
have been dancers, 37 should have been nondancers.
Observed Expected
Genotypes
(3/4) x 50 =
nondancers 42
37 (42−37)2/37 0.68
(1/4) x 50 =
dancers 8
13 (8−13)2/13 1.92
2.60
With one degree of freedom the p value is between 0.5 and 0.1 and we cannot reject
the null hypothesis. The hypothesis that dancing is caused by the homozygous
recessive allele of one gene is therefore a good fit with the data. Null hypothesis #2:
Dancing is caused by being homozygous for the recessive alleles of two genes
(aa bb), so 1/16 of the F2 mice should be dancers.
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Observed Expected
Genotypes
nondancers 42 47 (42−47)2/47 0.53
dancers 8 3 (8−3)2/3 8.33
8.86
With one degree of freedom, the p value is < 0.005, so the null hypothesis that two
genes control the dancer phenotype is not a good fit; in fact, the hypothesis can be
rejected by the criteria employed by most geneticists. The one gene hypothesis is
a better fit with the data.
Section 5.5
37. a. The number of meioses represented here is the total of the number of asci = 334.
Each ascus contains the 4 products of one meiosis.
b. Diagram the cross: a + c × + b +
To map these genes, use the Three Easy Rules for Tetrad Analysis. First designate
the type of asci represented. This has to be done for each pair of loci as PD (P),
NPD (N) and T refer exclusively to the relationship between two genes. In the table
below, the top row shows the designations for all three pairs: the a-b comparison is
at the lower left, the b-c comparison is at the lower right and the a-c comparison is at
the top of the pyramid.
P P T T N P
P P N N T P T N N P T T
a + c a b c + + c + b c a b + a + c
a + c a b c a + c a b c a b + a b c
+ b + + + + + b + + + + + + c + + +
+ b + + + + a b + a + + + + c + b +
137 141 26 25 2 3
I I I I I I II I I II I I I I I I II I
Rule #1: For genes a and b PD = NPD, so these two genes are not linked. For
genes b and c PD = NPD, so genes b and c are not linked. For genes a and c,
PD>>NPD, so the genes are linked. Calculate RF between a and c = 2 + (1/2)(26
+ 25)/334 = 8.2 cM (Rule #2).
Gene-centromere distances can be calculated in Neurospora (Rule #3), so analyze
the data for MI and MII segregation patterns for the alleles of each gene in each ascus
type. This analysis is done separately for each gene, unlike the gene↔gene analysis
done above. The designation for each gene is presented under that gene at
the bottom row of the table (I - MI, II = MII). Rule #3 shows that the distance
between a and the centromere = (1/2)(26 + 25)/334 = 7.6 mu; the distance
between b and the centromere = (1/2)(3)/334 = 0.4 mu; the distance between c and
the centromere = (1/2)(0)/334 = 0.
Now compile all of these pieces of data into one map. Rule #1 shows that gene
b is 0.4 mu from the centromere and is on a different chromosome from genes a
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and c. Genes a and c are on the same chromosome, so the a↔centromere distance
and the c↔centromere distance refer to the same centromere. Gene c is 0 mu from
the centromere. As you can see from the map, there are 2 slightly different distances
for the gene a↔gene c region. The gene↔gene distance is 8.2 mu and the
a↔centromere distance is 7.6 mu. In this case the longer gene↔gene distance is
more accurate as it includes the SCOs between a and c as well as some of the DCOs
between a and c (the 4-strand DCO, Fig. 5.23 on p. 153).
c. Carefully consider the information you have for the different chromosomes in the
ascus type chosen (the group with 3 members). The a and c genes show PD
segregation, which can mean either no crossing-over between them or a 2-strand
DCO. Both genes show MI segregation, which means there haven't been any single
crossovers between either gene and the centromere. Gene b shows MII
segregation, which means there has been an SCO between the gene and the
centromere. This crossover also means the a-b and c-b comparisons in this class will
show the tetratype pattern (T are due to crossovers between either gene and its
centromere when the genes are on separate chromosomes).
38. a. These data are presented as phenotypes of individual spores. Because the data are
presented for 3 genes, they may be analyzed as a 3-point cross. Organize the data into
reciprocal pairs of spores.
Classes
of Genotype Numbers
gametes
Parental α + + 31
(P) a f g 29
a + g 6
SCO 1 α f + 6
α + g 13
SCO 2 a f + 14
a + + 1
DCO α f g 1
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The α f g DCO spore type is most similar to the a f g parental spore type. Thus,
the mating type (a/α) is the gene in the middle. The distances are: f ↔a/α = (6 + 6
+ 1 + 1)/101 = 13.9 cM and a/α↔ g = (13 + 14 + 1 + 1)/101 = 28.7 cM.
b. This problem says you have an ascus with an α f g spore. This spore is the result of
a double crossover [see part (a)]. The reciprocal product would be the a + + spore,
but this is not seen in the ascus. Remember that there are 3 different types of
double crossovers: 2-strand DCOs, 3-strand DCOs, and 4-strand DCOs. Each of
these types of DCOs gives a different array of spores in the resulting ascus (Fig.
5.23 on p. 153). Draw a meiotic figure of this chromosome and try some different
types of DCOs. A 3-strand DCO gives the desired result.
39. Diagram the cross and summarize the data: met- lys- × met+ lys+
P T
met+ lys+ met+ lys+
met+ lys+ met- lys+
met- lys- met+ lys-
met- lys- met- lys-
89 11
a. The two types of cells in the first group of 89 asci are met + lys + (could grow
on all four types of media) and met - lys - (require the addition of met and lys
to minimal medium). These asci are parental ditypes (PD). The four types of cells
in the second group of 11 asci are met + lys + ; met + lys - (grew on min + lys and
on min + lys + met); met - lys + (grew on min + met and on min + lys + met);
and met - lys - . These are tetratype (T) asci.
b. Because the number of PD>>> NPD, the genes are linked. The distance
between them is:
[NPD + (1/2)T] / total tetrads = [0 + (1/2)(11)]/100 × 100 = 5.5 m.u.
c. NPD should be seen eventually and would result from four-strand double
crossovers. There would be two types of spores: met - lys+ (could grow on min +
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met and on min + met + lys) and met+ lys- (could grow on min + lys and on min +
met + lys).
40. Use the Three Easy Rules for Tetrad Analysis to help you solve this problem.
a. In cross 1, the number of PD (parental ditypes) = NPD (nonparental ditypes) so
the ad gene and the mating type locus assort independently. In cross 2 the number
of PD >> NPD so we can conclude the p gene and the mating locus are linked; RF
p↔mating type = [NPD + (1/2)T]/ total tetrads = (3) + (1/2)(27)/54 =16.5/54= .31
× 100 = 31 cM between the two genes.
b. To calculate gene↔centromere distances you need information on the order

of ascospores in each ascus type. Only with this information can you calculate
gene↔centromere distances based on 1/2(# of asci showing MII segregation for
the gene)/total asci.
41. a. The genotype of a true-breeding wild-type diploid strain of Saccharomyces can be
written + / +. If this diploid undergoes meiosis, all (100%) of the asci will have 4
viable spores.
b. The genotype of this strain is + / n, where n = a null activity allele of an essential gene.
The diploid cells will be viable, because they have functional enzyme for this essential
gene from the + allele. If this diploid undergoes meiosis, then all (100%) of the
tetrads will have 2 + : 2 n spores (that is, only 2 spores in each tetrad will be
viable).
c. Gene a and gene b are different essential genes; a and b represent temperature-
sensitive alleles of these genes. When you diagram a cross you must write complete
genotypes for both haploid parents: a b+ (strain a) × a+ b (strain b) → aa+ bb+.
Each haploid parent strain will die when grown under restrictive conditions because
they cannot produce a required product, while the diploid cells are viable because they
have a wild-type allele for both genes.
If these genes are unlinked, then after meiosis PD asci = NPD asci (Three Easy
Rules for Tetrad Analysis: Rule #1). When the genes are unlinked, also remember
that T tetrads (asci) arise from SCOs between either gene and the centromere.
Because each of these genes is 0 mu from the centromere, you will not see T asci.
Thus, after meiosis, you will have 50% PD (2 a b+ spores : 2 a+ b spores) : 50%
NPD (2 a+ b+ : 2 a b). None of the spores in the PD tetrads are viable under
restrictive conditions, while 2 of the 4 spores in the NPD asci are viable (a+ b+).
Thus, 50% of the asci will have 0 viable spores (PD) and 50% of the asci will
have 2 viable spores (NPD).
d. Again genes a and b are unlinked essential genes, but now gene a↔centromere = 0
mu and gene b↔centromere = 10 mu. A SCO between gene b and the centromere
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will happen in 20% of the asci (because only half of the ascospores of an SCO are
recombinant) and will give T asci. A T ascus will have a spore ratio of 1 a+ b+ : 1 a
b : 1 a b+ : 1 a+ b. There is 1 viable spore (a+ b+) in a T ascus. The remaining 80%
of the asci will be divided equally between PD and NPD because the genes are
unlinked. Thus, 40% of the asci will have 0 viable spores (PD), 40% of the asci
will have 2 viable spores (NPD) and 20% of the asci will have 1 viable spore
(T).
e. Because both genes are on the same chromosome, you can diagram this cross: a b+
(strain a) × a+ b (strain b) → a b+ / a+ b. When the genes are linked, SCO and 3-
strand DCO between the genes give T asci and 4-strand DCO between the genes
gives NPD asci. The remainder of the asci are PD (no crossover and 2-strand
DCO). If the recombination frequency between gene a and gene b = 0 mu, then the
only possible result will be PD asci (2 a b+ : 2 a+ b) in which none of the spores are
viable. Thus, 100% of the asci will have 0 viable spores.
f. Now the genes are 10 mu apart and there are no DCO events. This means that 20%
of the asci produced will be T [see part (d)] and the remaining 80% will be PD.
Therefore, 80% of the asci will have 0 viable spores (PD) and 20% of the asci
will have 1 viable spore (T).
g. A 4-strand DCO gives an NPD ascus. The genotypes of the spores will be 2 a+ b+ :
2 a b. Thus, 2 of the 4 spores will be viable.
42. Genes a, b, and c are all on different chromosomes. [For simplicity, we will refer to the
centromere of the chromosome on which a gene is found with the possessive (that is, as
the gene’s centromere.)] Thus, all crosses between these genes are expected to give an
equal number of PD and NPD asci. The fact that the cross involving genes a and b
yields no T indicates that genes a and b are both very close to their respective
centromeres. If two genes are on separate chromosomes, tetratypes arise when a
crossover occurs between one of the genes and its centromere, or between the other gene
and its centromere. In the crosses involving genes a and c or genes b and c, many T asci
are seen. Because genes a and b are tightly centromere-linked, gene c must be very far
from its centromere in order to generate these T asci.
43. Diagram the yeast cross:
his- lys+ × his+ lys- → his- lys+/ his+ lys- → 233 PD, 11 NPD, 156 T.
a. The PD asci must have 2 his - lys + : 2 his + lys - spores, the NPD asci have 2
his + lys + : 2 his - lys - spores and the T asci have 1 his - lys + : 1 his + lys - : 1
his + lys + : 1 his - lys - spores.
b. PD>>NPD so the genes are linked; RF between 2 genes = [11 +
(1/2)(156)]/400 = 22.3 mu.
c. Because the genes are linked, you know that NPD asci are the result of 4-strand
DCOs. This sort of DCO is 1/4 of all the DCO events. The 3-strand DCOs (1/2
of all DCOs) give T while 2-strand DCOs (1/4 of all DCOs) give PD. In the data you
see 11 NPD tetrads, or 11 meioses that underwent 4-strand DCOs. There are another
22 tetrads that are the result of 3-strand DCOs (and are Ts), and another 11
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asci that underwent 2-strand DCOs (and are PDs), for a total of (11 + 22 + 11 =)
44 asci that underwent 2 crossovers. The remaining (156 - 22 =) 134 T asci
underwent a SCO, or 1 crossover, and the remaining (233 – 11 =) 222 PD asci
underwent 0 crossovers (NCOs). From this analysis, you can see that a general
equation for the number of SCO meioses is SCO = T-2NPD. Likewise, a general
equation for the number of DCO meioses is DCO = 4NPD.
d. There are 44 asci that underwent DCOs for a total of 88 crossover events. There were
another 134 asci that underwent SCOs. Thus, there were 134 + 88 = 222 crossover
events / 400 meioses = 0.555 crossovers/meiosis. We have just calculated “m”, the
mean number of crossovers between his and lys per meiosis. A general equation for m
is: m = [(SCO + 2 (DCO)]/total asci.
e. The equation for recombination frequency between 2 genes used in the textbook
and in part (b) above only includes 4-strand DCO (NPD). This formula ignores 3-
strand and 2-strand DCOs. This calculation for recombination frequency assumes
that all T asci are due to SCOs. Though this is true for the majority of T asci, some
T asci are due to 3-strand DCO events; the larger the distance between the 2 genes
in question, the more Ts are due to DCOs. Also, it is an oversimplification to
assume that all PD asci are nonrecombinant, because some of them are due to 2-
strand DCOs; the fraction of PDs due to DCOs also increases with the distance
between the two genes in question. Remember that the 3 types of DCO events
occur in a ratio of 1 (2-strand DCOs) : 2 (3-strand DCOs) : 1 (4-strand DCOs)(see
Fig. 5.23 on p. 153).
A more accurate formula for RF between two genes that takes into account
all crossovers is: RF = m/2, where m is the mean number of crossovers per
meiosis, as defined in part (d) above. The reason is that every meiosis that occurs with
a single crossover (every SCO) results in 2 recombinant chromosomes and 2
nonrecombinants. You can prove to yourself that this equation makes sense by
imagining two theoretical situations. First, suppose that every meiosis were an SCO
(m = 1); then RF = 1/2 or 50%, as expected when no NCOs occur. Second,
suppose that half of all meioses occurred as SCOs (m = 1/2) and the other half
were NCOs; then RF = 25%, which makes sense as 1/4 of all resulting chromosomes
would be recombinants. (Note that the equation for the green line in Fig. 5.15 on p.
142 is m/2.)
With this understanding, and also the relationships we determined in parts (c)
and (d), we can derive a more accurate formula for recombination frequency: RF =
m/2 = (1/2 SCO + DCO)/total asci = [1/2 (T – 2NPD) + (4NPD)]/total
asci = [(1/2)T + 3NPD]/total asci. Many yeast geneticists use this more accurate
formula in preference to the one in your textbook.
f. RF = [(1/2)(156 – 22) + 4(11)]/400 = [(1/2)(134) + 44]/400 = 111/400 = 0.278 =
27.8 mu. As you can see, this value is somewhat larger than the distance calculated
in part (b). As expected, this corrected RF value = m/2, where m = 0.555 [see part
(d)].
44. This problem can be solved only if you make assumptions about interference in the 22
m.u. interval between genes C and D. The reason that interference is important is that the
degree of interference determines the number of double crossovers (DCOs) that
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occur, and this will of course influence the proportion of tetrads that are PD, NPD, and
T. The solution is by far easiest to calculate if interference = 1, because no DCOs occur
in this situation. We will thus discuss each of the two parts of this problem first under the
assumption that interference = 1. We then consider each part of the problem at the other
extreme, in which interference = 0. If interference is greater than 0 but less than
1, the proportions of the three types of tetrads would vary between these extremes.
a1. Situation: Cross in Saccharomyces cerevisiae; Interference = 1. Because there are no
double crossovers (DCOs) between genes C and D; there can be no NPD
tetrads. All the recombinants between the 2 genes are due to single crossovers (SCO).
If two genes are linked, then SCOs between the genes give T asci. Remember
that the RF between C and D is (.07 + .15 = 0.22), and that the formula for
recombination frequency between 2 genes = [NPD + (1/2)T]/total asci. Solve for T:
0.22 = 0 + (1/2)T so T = 2(0.22) = 0.44. Therefore, 44% of the asci will be Ts and
the remaining 56% will be PDs. In Problem 43 above you just derived a more
accurate formula for RF = [3NPD + (1/2)T]/total asci. This new formula accounts
for the Ts and NPDs produced by DCOs, and you can see that when there are
no DCOs, both formulas are equally accurate.
b1. Situation: Cross in Neurospora crassa; Interference = 1. In Neurospora the recombination
events that underlie the formation of PD, NPD, and T are the same as in yeast. The
difference is that the ordered tetrads allow you to distinguish whether a SCO
event occurs between C and the centromere or between D and the centromere. If the
SCO occurs between C and the centromere, then you will see MII segregation for
the alleles of the C gene and MI segregation for the alleles of the D gene. If the
SCO occurs between D and the centromere then you will see the reverse - MI
segregation for C and MII segregation for D.
Here, I = 1, so there are no DCOs. Therefore, as in part (a), T = 0.44 and PD =
0.56. However 7/22 of the SCO events occur between gene C and the centromere,
while the remaining 15/22 of the SCOs occur between D and the centromere. The
expected results are summarized in the table below.
NCO (no
Crossover type
crossover) SCO C↔cent. SCO D↔cent
and location:
ascus type: PD T T
MI or MII gene C: MI MII MI
MI or MII gene D: MI MI MII
15/22 x 0.44 =
frequency: 0.56 7/22 x 0.44 = 0.14
0.30
Before looking at the math for situations where the interference is not equal to 1, you
should think about this problem qualitatively. As interference decreases, a higher
proportion of meioses will have two or more crossovers. Because NPDs can be produced
only by meioses with more than one crossover (in the parts of the problem solved above
for interference = 1, there were no NPDs), as interference decreases you will see more
NPD tetrads. Because in the corrected equation for RF in tetrad analysis from Problem
43 {where RF = [3NPD + (1/2)T]/total asci}, if the RF was constant, the proportion
of T tetrads would have to decrease to compensate for the NPDs. This
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equation also sets limits on the proportions of the total tetrads that would be T and NPD.
Understanding the qualitative relationship of interference with the proportions of tetrads
is more important than obtaining numerical values for these proportions, as we next
describe.
a2. Situation: Cross in Saccharomyces cerevisiae; Interference = 0. You should note at the
outset that the figure accompanying this problem is somewhat ambiguous: Do the
map units shown correspond to the measured recombination frequency (RF) in an
experiment, or are they instead corrected map units corresponding to the physical
distance between the genes (as in Fig. 5.15 on p. 142)? To match all the other problems
in this chapter, we assume that the map units shown on the figure represent
RFs measured in an experiment. (This ambiguity does not exist when the interference
= 1 because the two definitions are then identical.)
If there is no interference, then the likelihood that crossovers occur
anywhere on the chromosome is given by a Poisson distribution. Although
mathematical methods exist to predict the frequencies of single, double, and higher
level crossovers in chromosomal intervals of given lengths from the Poisson
distribution, we will simplify the discussion by using an approximation for the
expected frequencies of DCOs based on the idea that the two single crossovers
occurred independently. That is, the expected frequency of DCO = (recombination
frequency in the C↔D region) × (recombination frequency in the C↔D region) =
(0.22) × (0.22) = 0.0484. [You may ask why you could not estimate the expected
frequencies of DCOs by multiplying the C↔centromere and centromere↔D
distances (0.07) x (0.15). The reason is that such a calculation would ignore all the
DCOs in which two crossovers take place either in the C↔centromere or in the
centromere↔D intervals.]
The RF between C↔D = SCO + DCO (looking at individual spores). [The
reason this is true is that even though DCOs have two crossovers, on average, only
half of the spores from meioses with double crossovers could be recognized as
recombinants.] Thus, 0.22 = SCO + 0.0484; SCO = 0.22 - 0.0484 = 0.1716. If SCO
frequency between C and D = 0.1716 then T due to SCO = 0.3432 (see the case above
where Interference = 1).
Remember that when analyzing tetrads the three different types of DCOs can
be distinguished: 2-strand DCOs, which give PD asci; 3 strand DCOs, which give T
asci; and 4-strand DCOs, which give NPD asci (Fig. 5.23b-f on p. 153). These
DCOs occur in the ratio of 1/4 (2 strand DCOs) : 1/2 (3-strand DCOs) : 1/4 (4-
strand DCOs). If the total DCO frequency = 0.0484 then 1/4 (0.0484) = 0.0121 is
the frequency of 4-strand DCOs (NPD), 1/2 (0.0484) = 0.0242 is the frequency of
3-strand DCOs (T) and the remaining 1/4 of the DCOs (0.0121) are 2-strand
DCOs, which will be PD tetrads.
In total, NPD = 0.0121, T = 0.0242 (due to DCO) + 0.3674 (due to SCO) =
0.3795 and the remainder are PD = 0.6205.
b2.Situation: Cross in Neurospora crassa; Interference = 0. Here, the proportions of PD,
NPD, and T tetrads will be the same as in part (a2) above. However, several
patterns of MI and MII segregation patterns for the two genes are possible depending
upon where the SCO and DCO events are occurring. Let’s first consider
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the NCO and SCO meiosis (this is the same table as shown in part [b] above but
without the frequencies):
crossover no SCO SCO

type and crossover C↔cent. cent.↔D
ascus type:
location: PD T T
gene C (MI/MII) MI MII MI
gene D (MI/MII) MI MI MII
Next we consider DCO meioses in which both crossovers occur in the same
interval: either C↔centromere or centromere↔D. In either case, the DCO could
either involve 2, 3, or 4 strands.
DCO DCO DCO DCO DCO DCO

crossover
C↔cent. C↔cent. C↔cent. cent.↔D cent.↔D cent.↔D
type and
2-strand 3-strand 4-strand 2-strand 3-strand 4-strand
location:
ascus type: PD T NPD PD T NPD
gene C (MI/MII) MI MII MI MI MI MI
gene D (MI/MII) MI MI MI MI MII MI
Finally, let’s look at the DCO meioses in which one crossover occurs in
C↔centromere and the other crossover occurs in centromere↔D. Such DCOs
could again involve either 2, 3, or 4 strands.
DCO DCO DCO

crossover C↔cent. C↔cent. C↔cent.
type and cent.↔D cent.↔D cent.↔D
location: 2-strand 3-strand 4-strand
ascus type: PD T NPD
gene C (MI/MII) MII MII MII
gene D (MI/MII) MII MII MII
1/4 x 1/2 x 1/4 x
frequency: 0.0105 0.0105 0.0105
= 0.003 = 0.005 = 0.003
Note that in these tables, we have calculated the frequencies only for the DCOs in
which one crossover occurs in C↔centromere and the other crossover occurs in
centromere↔D. In this situation, the expected number of simultaneous crossovers
in both regions is easy to calculate as the product of the map distances in the two
intervals (0.07) x (0.15) = 0.0105. The number of meioses with 3-strand DCOs will
be twice that of the meioses with either 2-strand or 4-strand DCOs. The
frequencies for the classes shown in the two previous tables are complex to
calculate (for example, you would have to determine the expected number of DCOs
with both crossovers in each interval) and are not worth the effort. What is worthwhile
is to look at the patterns of PD, NPD, and T superimposed with the
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patterns for MI and MII segregation for the two genes, as these patterns tell us what
occurred during meiosis in each case.
45. a. If at least one crossover, and often multiple crossovers, occurred between a gene
the centromere in every meiosis, the MI or MII configuration of octads would be
randomized. As there are 2 different types of MIs (4a+ : 4a- and 4a- : 4a+), and 4
different types of MII octads (2a+ : 2a- : 2a+ : 2a- and 2a+ : 2a- : 2a- : 2a+ and 2a- :
2a+: 2a+ : 2a- and 2a- : 2a+ : 2a- : 2a+), when MI and MII octads are produced
randomly, 2/6 will be MI, and 4/6 will be MII. As the RF between a gene
and the centromere is (1/2)(# MII octads)/(total # octads), the maximal RF
between a gene the centromere is (1/2)(4/6) = 1/3 = 33%.
b. Yes – a gene and the centromere can be unlinked. This simply means that at
least one crossover occurs between them in every meiosis, and so the fraction
of MII octads is 33% [see part (b)]. Of course a gene is always physically
connected to a centromere through a DNA strand; however, it need not be linked
to the centromere genetically.
c. A distance of 30 m.u. between a gene and the centromere is close to the maximal
RF that can be measured by ordered tetrad analysis, indicating that the gene is far
from the centromere. This map distance is unlikely to be accurate; the reason is that
DCOs between the gene and the centromere will ignored because they result in MI
octads.
46. a. Refer to the three strains as trp1, trp2 and trp3. Remember that in Neurospora the 4
meiotic products undergo a subsequent mitosis to give 8 spores in the ascus.
Consequently, the first 2 spores are identical to each other (they are mitotic
products of the same initial spore), the 3d and 4th spores are the same as each
other, and so on. For the purposes of discussing the results, assume that the ascus is
made up of the 4 original spores prior to this extra mitosis. You cross trp1- × wild
type → diploid → 2 wild type : 2 trp1-. You are seeing a monohybrid ratio of 1:1,
which means there is only one gene controlling the Trp- phenotype in strain trp1. Each
of the strains gives the same result, so in each haploid strain a single mutant
gene is responsible for the Trp- phenotype.
b. First consider the cross between trp3 and wild type. The diploid is trp3- / trp3+.
After meiosis the first 2 spores were either both trp3+ (could grow on minimal
media) or they were both trp3- (could not grow on minimal media). Thus, all the asci
were 2 trp3- : 2 trp3+, and the order of the alleles was either - - + + or + + - -. In other
words, all the asci showed MI segregation for the trp3 gene. In the case of the crosses
with trp1- × wild type and trp2- × wild type, the resultant diploids gave some asci that
gave a different result - only one spore of the top 2 was trp+ while the other one
was trp-. In other words, these asci showed MII segregation for the trp gene in
question. In summary, the trp3 gene is very closely linked to its centromere (no
T = no crossovers between the gene and the centromere), while the trp1 and
trp2 mutations are further from their centromere(s). (Note that we are again using
the possessive “its centromere” or “their centromeres” to indicate the centromere of
the chromosome on which the gene is found.)
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c. If two strains have mutations in the same gene, then the resulting diploid (trpx - /
trpx -) would be unable to grow on minimal media and would give asci where all 4
spores were trpx - (0 spores viable on minimial media). This result is never seen, so
each mutant strain must have a mutation in a different gene, for a total of 3
different trp - genes in the 3 strains. Diagram the cross between trp1 and trp2:
trp1- trp2+ × trp1+ trp2 - → trp1- trp1+ trp2+ trp2 -
When this diploid is allowed to undergo meiosis you see 78 asci with 0 viable
spores (2 trp1- trp2+ : 2 trp1+ trp2 - = PD and 22 asci with 2/8 or 1/4 viable spores
(1 trp1+trp2+ : 1 trp1-trp2- : 1 trp1- trp2+ : 1 trp1+ trp2- = T).
In the trp1 × trp3 cross you see a new class of asci, those with 2 viable spores
(2 trp1+trp3+ : 2 trp1- trp2 - = NPD). In this cross there are 46 PD, 48 NPD, and
6 T asci.
In the last cross, trp2 × trp3, there are 42 PD, 42 NPD and 16 T asci.
d. In trp1 × trp2, PD>>NPD (NPD= 0) so the genes are linked. The T asci are caused
by SCOs between the 2 genes. The recombination frequency between trp1 and trp2
= [0 + (1/2)(22)]/100 = 0.11 = 11 mu. In trp1 × trp3 there are 46 PD = 48 NPD so
the genes are unlinked; the 6 T asci arise from SCOs between trp1 and its centromere.
None of these T asci can arise from crossovers between trp3 and its centromere
because you found in part (b) that they were very tightly linked. Thus, trp1 is 3 mu
from its centromere. In the cross between trp2 x trp3, PD = NPD so the genes are
unlinked. There are 16 T asci, so gene 2 must be 8 mu from its centromere. The map
is shown in the following diagram.
e. Ordered octads show the segregation pattern for each gene separately. In this example,
both mutant genes give the same phenotype (Trp-). Thus, it is impossible to
determine if a Trp- spore is + - or - - or - +. If you cannot distinguish these
different types of spores, then you cannot determine the segregation pattern (MI
vs MII) for the individual genes.
f. You can calculate gene↔centromere distances because you discovered that
one of the genes (trp3) is tightly linked to its own centromere. Therefore,
when trp3- is crossed with either of the other mutants, any T asci must be due to SCO
between the other gene and its centromere, and these T asci can then be used to
calculate a distance between the other gene and its centromere. This same sort of
analysis can also be used in yeast to map gene↔centromere distances if a strain is
available with a mutation known to be right at a centromere.
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Section 5.6
47. a. The colony is mostly white because the cells are heterozygotes (ade2 + / ade2 -) and
the ade2 + allele is dominant. Red sectors arise when one cell in the growing colony
becomes homozygous ade2 - / ade2 -. As all the cells continue to grow, the colony
continues to expand and the ade2 - / ade2 -- cells form a red sector within the white
colony (Fig. 5.29 on p. 159). Red cells of the ade2 - / ade2 - genotype could arise
by mitotic recombination (Fig. 5.28 on p. 158), by loss of the entire
chromosome containing the ade2 + allele, by a deletion of the portion of the
chromosome containing the ade2 + allele, or by spontaneous mutation of the
ade2 + allele to an ade2 - allele. (Note: Using the usual genetic nomenclature in
yeast, the ade2 + allele could be written as ADE2 and the ade2- allele as ade2. These
are alternative ways of representing the same things.)
b. The size of the red sectors depends on when in the formation of the colony the
event occurred to form the initial ade2 - / ade2 - cell. If the event occurred early in the
formation of the colony there will be a larger red sector than if the event occurred
near the end of colony formation. All of the events mentioned in part (a) are rare,
so in general they will occur later in colony formation when there are more cells in
which they could occur. As a result, most of the red sectors will be small. (The
colonies in Fig. 5.29 on p. 159 actually contain several very small sectors that are too
tiny to show up in the photograph.)
48. In a normal mitosis (with no recombination), all of the daughter cells produced are
genotypically a b c leth d e / a+ b+ c+ leth+ d+ e+ and are phenotypically wild type, like
the original cell. Rarely, however, after the chromosomes have replicated into sister
chromatids, recombination can occur between nonsister chromatids. The figure below
shows the possible locations for such recombination events; these are indicated by Roman
numerals I-V. Assume that no crossovers can occur between gene a and the centromere
because they are so closely linked.
If you review Fig. 5.28 on p. 158, you will see that after mitotic recombination, only
one orientation of the chromatids on the homologous chromosomes will segregate to
yield progeny genotypically different from the parents, and we will only discuss this
orientation here. The important rule to keep in mind is that daughter cells of an
originally heterozygous parental cell will become homozygous for an allele only if the
mitotic crossover occurs between the centromere and the gene. If the mitotic crossover
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occurs further away from the centromere than the gene, all daughter cells will remain
heterozygotes for that gene (see again Fig. 5.28 on p. 158).
Consider now the results of a crossover in region I of the figure. In the segregation
pattern of interest, one daughter cell will be homozygous for the b+ allele and
heterozygous for the rest of the genes on the chromosome. Thus, this cell will be
phenotypically wild type and indistinguishable from the nonrecombinant cells
surrounding it. However, the reciprocal product of this mitosis will be a daughter cell
whose genotype will be homozygous mutant for gene b and heterozygous wild type for
everything else. This cell will continue to divide mitotically and yield a patch of b mutant
tissue in a sea of wild-type tissue.
Next consider a crossover in region II. In this case, the segregation pattern of
interest will yield one wild-type cell and a reciprocal daughter cell which will be b+ a+ c
leth d e / b a c leth d e. Because this cell is homozygous for the recessive lethal mutation, it
will die and you will never see it. A crossover in region III will also give a lethal
recombinant product (genotypically b+ a+ c+ leth d e / b a c leth d e) that again you will
never see.
A crossover in region IV will give a d e patch of mutant tissue (genotypically b+ a+
c+ leth+ d e / b a c leth d e), while a crossover in region V will give a patch of e mutant
tissue (genotypically b+ a+ c+ leth+ d+ e / b a c leth d e).
Thus, the only phenotypes that will be found in sectors as a result of mitotic
recombination will be those associated with b, d, and e (representing crossovers in
regions I, IV, and V, respectively).
49. The genotype of the female fly is y+ sn+ / y sn. A diagram of potential mitotic
crossovers in the cells of this animal is shown in the following figure:
a. The larger patch of yellow tissue arises from a mitotic crossover in region I.
This mitotic recombination will generate a cell of the genotype y sn + / y sn
(Problem 5-48). The smaller patch of yellow and singed tissue must have arisen
from a second mitotic recombination between the centromere and sn, in region
II. This would produce cells that are y sn / y sn. Because the yellow patch is larger,
the recombination in region I occurred earlier in development. The yellow, singed
cells are a small patch within a larger patch of yellow cells, so the mitotic crossover in
region II happened after (later in development than) the crossover in
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region I, and this second crossover happened in a recombinant daughter cell of the
first recombination event. No wonder these patches within patches are rare!
b. If the genotype of the female was y+ sn / y sn+, then a recombination event in
the region I would give you a detectably recombinant cell (yellow phenotype)
with the genotype y sn / y sn + . A subsequent second mitotic crossover in
region II in one of these originally recombinant y sn / y sn + cells will give
you a patch of y sn tissue inside a patch of yellow tissue, as in part (a).
Although the problem did not explicitly ask, you should note that one kind of
mitotic crossover can occur which will give a different result in a y+ sn+ / y sn
female [part (a)] than a y+ sn / y sn+ female [part (b)]. After a recombination event
in region II the female from part (a) will show a y sn patch of tissue. The other
recombinant product will be homozygous y+ sn+, and this cell and its descendants
will be indistinguishable from nonrecombinant cells. The same sort of
recombination event in region II in the female from part (b) will yield one daughter
cell of genotype y+ sn / y+ sn which will give a patch of sn tissue. The reciprocal
product of this mitotic recombination will be y sn+ / y sn+ and will give an adjacent
patch of yellow tissue. This phenomenon is called twin spots and was depicted in
Figs. 5.27 and 5.28 of the text (pp. 157-158).
50. List the phenotypes seen in the normal tissue and the 20 tumors and their frequency of
occurrence:
- normal tissue = AFAS BFBS CFCS DFDS
- tumor type 1 = AF BFBS CFCS DF = 12 tumors
- tumor type 2 = AF BFBS CFCS DFDS = 6 tumors
- tumor type 3 = AF BS CFCS DF = 2 tumors
Remember that all of the tumor tissues were also homozygous for NF1- while the
normal tissue is heterozygous NF1- NF1+.
a. Mitotic recombination could have caused all 3 types of tumors.
b. Remember that mitotic recombination causes genes further from the centromere to
become homozygous, while genes between the recombination event and the
centromere, or those on the other side of the centromere, remain heterozygous
(review Problem 5-48). Notice that all 3 types of tumor cells are homozygous for NF1-
, so by definition all 20 mitotic recombination events that gave rise to the 20 tumors
occurred between the centromere and the NF1 gene. Notice also that all 20
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tumors are homozygous for gene A, specifically the AF allele. Because gene A is
affected by all of the mitotic recombination events, it must be further from the
centromere than the NF1 gene. Because these tumors become homozygous for the
AF allele, that allele must be on the same homolog with the NF1- allele. There are 6
tumors that are homozygous for these 2 genes (tumor type 2).
As you work your way along the chromosome from NF1 toward the
centromere the next gene to also become homozygous is the D gene (tumor type 1),
specifically the DF allele, then the B gene (tumor type 3), the BS allele. Gene C
never becomes homozygous, yet we are told it is on this chromosome as well. Thus
it could either be on the other side of the centromere from NF1, A, D and B or it
could be on the same side of the centromere as the rest of the genes but very closely
linked to the centromere (like the a gene in Problem 5-48). The order of the genes
and coupling of the alleles in normal tissue (prior to mitotic recombination)
is shown in the following figure:
It is possible to use the mitotic recombination frequencies with which the

various genotypes of tumors arose as a rough, relative approximation of the
distances between the genes. These numbers are NOT to be confused with the
meiotic recombination frequency we have been calculating in the other problems in
this and other chapters! In tumor type 2 the mitotic recombination event happened
between gene NF1 and gene D (NF1- is homozygous, and so further from the
centromere than the recombination event while gene D is still heterozygous), and
this occurred in 6/20 tumors = 0.3, so the relative recombination frequency
between NF1 gene D is 0.3. In tumor type 1 the mitotic recombination event
happened between gene B and gene D (B is still heterozygous in these tumors while
D is homozygous DF), and this happened in 12/20 tumors = 0.6, so the relative
recombination frequency between genes B and D is 0.6. In tumor type 3 the
mitotic recombination event happened between the centromere and gene B (or
between gene C and gene B if you place gene C on the same side of the centromere
as the NF1 gene). This event happened in 2/10 tumors = 0.1 so the relative
recombination frequency between the centromere and gene B is 0.1.
c. An entire homolog of one chromosome is lost. If the lost homolog were the one
with the NF1+ allele, then the resulting cell would be hemizygous for the
NF1 - allele, and would develop into a tumor. This did NOT occur here,
because ALL 3 genotypes of tumors are still heterozygous for at least the C
gene.
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d. Yes, deletions of portions of the NF1 + homolog which cause loss of the
NF1 + allele could cause tumors to develop in the resulting NF1- cells. If these
deletions extended to the neighboring genes A, D, or B, the tumor cells could show
the same protein variants as in the problem. Although point mutations which
inactivate the NF1+ allele could cause tumors to develop in the resulting NF1-
cells, this mechanism does not seem to be responsible for any of the particular tumors
seen, because all of the tumors express only one allele of gene A (the AF allele), and
this should not be the case if a point mutation occurred in the NF gene.
51. This problem illustrates how scientists studying the development of multicellular
organisms can use GFP (green fluorescent protein) and mitotic crossing-over to create
mosaic animals in which different cells have different genotypes. This technique has the
additional virtue that the scientists can recognize these different cells within the body of
the animal to see how gene function in various cells influence the organism’s
development.
a. See following diagram:
b. To study the importance of the smc+ gene, scientists want to study what happens when
the gene function is removed; that is, to “knock out” the function of the gene.
Because animals homozygous for the loss-of-function smc mutation die as early
embryos, you cannot obtain any adult mice that completely lack smc function. By
using mitotic recombination, researchers can create animals in which most
cells are heterozygotes (smc + /smc), but some cells are smc/smc homozygotes
without smc function. As long as the lack of the smc-encoded protein in those
particular cells does not prevent mice from being born, scientists can then study
what happens to the animal if the protein is removed from specific cells.
c. The light green cells (most of the cells in the heterozygous animal) are cells
with one copy of the GFP gene. The dark green cells are those with two copies
of GFP that are formed from mitotic recombination (these are homozygous for
GFP+). Because these cells have two copies of this gene, they make more GFP protein
and fluoresce in green more brightly. The cells with no GFP + gene fail to
fluoresce and are shown in white in the figure. These are the other,
reciprocal daughter cells produced from the same mitotic recombination events giving
rise to the bright green cells.
d. As just mentioned in the answer to part (c), the bright green cells (clone 2) and
the white cells (clone 1) are next to each other because they are the reciprocal
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products of the same mitotic recombination events. Right after mitosis, these
cells are adjacent to each other because they were produced from the same parent cell.
If the progeny of these reciprocal daughter cells do not move in the epithelium, they
will stay in the same general area and make the twin spots that are shown.
e. See the mitotic recombination event “e” depicted in the diagram shown in
the solution to part (a). The mitotic crossover must occur in the interval between
the centromere and the GFP gene so as to create daughter cells homozygous for
GFP+ (the bright green cells) or homozygous for no GFP gene (the white cells).
Because the smc gene is further away from the centromere than the GFP gene, the
mitotic crossover shown in the diagram will make a daughter cell that is
homozygous for both d for bright green and normal sized), and a daughter cell that
is homozygous for no GFP gene and for the smc mutation (no fluorescence, small
sized).
f. There are more cells in clone 1 than in clone 2 because the cells in clone 2 are
homozygous for the recessive smc mutation that causes these cells to divide
prematurely before they reach normal size, making the cells smaller than the
normal cells (like those in clone 2) with one or more copies of the smc+ allele.
There will be more of such small white cells because in any given period of time,
they will undergo more rounds of cell division than the normal sized cells.
g. See the mitotic recombination event “g” depicted in the diagram shown in
the solution to part (a). This event occurs in the interval between GFP and smc.
These daughter cells will be light green (one copy of GFP+) and small (because they
are homozygous for smc). No twin spots will result from this type of mitotic crossover
because the reciprocal daughter cell will be light green (GFP+ / no GFP) and normal
sized (smc+ / smc+), just like all the surrounding cells.
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Solution Manual for Genetics From Genes to Genomes

5th Edition by Hartwell Goldberg Fischer ISBN

Three Easy Rules for Tetrad Analysis

Tips for two-point crosses:

Tips for three-point crosses:

Tips for crosses involving 4 genes:

Tips for tetrad analysis problems:

b. We know the John is Bb because he has brachydactyly. His complete genotype

recombinant types A b and a B. The genes are 40 cM apart, so the recombinants

e. In order for the X and Y chromosomes to segregate faithfully so that each

© Dr. Paula Cohen & Dr. Kim

d. Interference (I) = 1 - coefficient of coincidence (coc)

24. Diagram the cross:

b. Diagram the cross: a+ b+ c+ / a b c ♂ × a b c / a b c ♀ → ?. Here, the

c. I = 1 – coefficient of coincidence; coefficient of coincidence = observed DCO /

b. Write the classes out as reciprocal pairs.

c. Interference = 1 - coefficient of coincidence

There is a ratio of 1/4 A– bb (orange boxes): 1/2 A– B– (blue boxes): 1/4 aa B–

29. Diagram the cross:

a. The proportion of backcross progeny resembling Virginia (parental, M C S)

32. a. Interference is a phenomenon by which the occurrence of one crossover prevents

Genotypes Observed # Expected # Χ2 equation Sum of Χ2

b. To calculate gene↔centromere distances you need information on the order

crossover no SCO SCO

DCO DCO DCO DCO DCO DCO

DCO DCO DCO

It is possible to use the mitotic recombination frequencies with which the

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