Solution Manual for Genetics Analysis and Principles

5th Edition by Brooker ISBN 0073525340

9780073525341
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Chapter 6: Genetic Linkage and Mapping in Eukaryotes

Key Terms

Ascus Nonparental ditype

Bivalent Nonrecombinant offspring
CentiMorgans Null hypothesis
Crossing over Octad
Dihybrid cross Ordered tetrad (octrad)
First-division segregation Parental ditype
Genetic linkage Parental offspring
Genetic linkage map Positive interference
Genetic map Recombinant cells
Genetic mapping Second-division segregation
Genetic recombination Spores
Linkage groups Synteny
Locus Testcross
Map distance Tetrad
Map units Tetratype
Mitotic recombination Trihybrid cross
Nonparental cells Unordered tetrad (octad)

Chapter Outline

6.1 Overview of Linkage

Learning Outcomes:
1. Define genetic linkage.
2. Explain how linkage affects the outcome of crosses.

Synteny refers to two or more genes that are located on the same chromosome.
1. Chromosomes consist of more than one gene, typically in the hundreds to
thousands.
2. The term genetic linkage is use to indicate two genes that are located on the same
chromosome.
a. Genes that are close together tend to be transmitted from parent to
 offspring as a group.
b. Genes that are farther apart have a greater chance of being separated
during crossing over.
3. Chromosomes are often called linkage groups, since the genes on a chromosome
are physically connected to one another.
a. In humans there are 22 autosomal linkage groups, an X linkage group, and
a Y linkage group.
4. When geneticists follow traits they rely upon dihybrid (two-factor) and trihybrid
(three-factor) crosses.
Bateson and Punnett Discovered Two Traits That Did Not Assort Independently
1. Bateson and Punnett were the first researchers (1905) to demonstrate that not all
traits assort independently.
2. In crosses involving flower color and pollen length in the sweet pea, the
researchers noticed that the offspring did not display a 9:3:3:1 phenotypic ratio as
expected from a dihybrid cross (Figure 6.1).
3. They suggested that their traits were coupled to one another in some manner.

6.2 Relationship between Linkage and Crossing Over

Learning Outcomes:
1. Describe how crossing over can change the arrangements of alleles along a
chromosome.
2. Explain how the distance between linked genes affects the proportions of
recombinant and nonrecombinant offspring.
3. Apply a chi square analysis to distinguish between linkage and independent
assortment.
4. Analyze the data of Creighton and McClintock, and explain how it indicated that
recombinant offspring carry chromosomes that are the result of crossing over.

Crossing Over May Produce Recombinant Genotypes

1. Crossing over may alter linkage of genes.
a. The bivalent chromosomes consist of two homologous chromosomes with a pair
of sister-chromatids each.
2. Genetic recombination by crossing over can produce new combinations of alleles on
chromosomes (Figure 6.2).
a. The cells that contain the new allelic combinations are called nonparental or
recombinant cells.
b. The cells that contain the original combination of alleles are called parental
offspring or nonrecombinant offspring.

Morgan Provided Evidence for the Linkage of X-linked Genes and Proposed That
Crossing Over Between X Chromosomes Can Occur
1. The first direct evidence that different genes are physically located on the same
chromosome was provided by Thomas Hunt Morgan (Figure 6.3).
a. Morgan studied X-linked patterns of inheritance.
b. His experimental proof used three traits: body color, eye color, and wing
shape.
 2. With three traits assorting independently, it was expected that there would be
eight phenotypic classes, each in equal proportion.
a. Morgan’s results (Figure 6.3) indicated that the parental combinations
were the most prevalent in the offspring. Morgan correctly suggested that
these three traits are found on the X chromosome and are inherited
together as a unit.
b. For offspring that did not contain the parental combinations, Morgan
suggested that there was crossing over between the homologous X
chromosomes.
c. The concept of homologous crossing over had been previously introduced
by the French cytologist F. A. Janssens.
3. Morgan suggested three hypotheses to explain his results:
a. All three genes are located on the same chromosome (the X chromosome).
b. Crossing over produces new combinations of alleles.
c. The likelihood of crossing over depends on the distance between the two
genes. Genes that are far apart are more likely to cross over than genes
that are close together.
4. Figure 6.4 demonstrates what Morgan was viewing at the chromosomal level.

The Likelihood of Crossing Over Between Two Genes Depends on the Distance Between
Them
1. On order to explain the different proportions of nonparental offspring in his
crosses, Morgan proposed that the likelihood of crossing over depends on the
distance between two genes. The further the genes are apart, the more likely
crossing over will occur. Thus, the more nonparental offspring present, the
further apart the genes are.
2. Double crossovers between two genes which are far apart can rarely occur as
well.

A Chi Square Analysis Can Be Used to Distinguish Between Linkage and Independent
Assortment
1. Researchers need a mechanism of testing whether two genes are linked or
assorting independently.
2. The chi square test allows a researcher to test the goodness of fit between the
observed and expected data.
3. To test for linkage using a chi square analysis:
a. Propose a hypothesis. The usual hypothesis is that the traits are assorting
independently. This is known as the null hypothesis, since it assumes
there is no real difference between the observed and expected values.
b. Calculate the expected values for each of the phenotypes that are possible
with the hypothesis.
c. Perform a chi square analysis using the expected values from above and
the observed phenotypic data.
d. Interpret the chi-square. A rejected hypothesis that the genes are assorting
independently indicates linkage.
Creighton and McClintock Showed That Crossing Over Produced New Combinations of
Alleles and Resulted in the Exchange of Segments Between Homologous
Chromosomes
1. Creighton and McClintock are responsible for providing the first direct evidence
that crossing over is associated with genetic recombination.
2. In their work they identified two chromosomal abnormalities (Figure 6.6) that
allowed them to track the movement of specific chromosomes during meiosis.
a. The chromosomes consisted of unusual staining patterns or translocations.
b. They used these abnormalities to trace the movement of alleles for kernel
color and the texture of the kernel endosperm.
3. Their experimental system (Figure 6.7) indicated that the process of crossing over
was responsible for the generation of genetic recombinants (nonparentals) and
that this was due to a physical exchange of material between the homologous
chromosomes.

6.3 Genetic Mapping in Plants and Animals

Learning Outcomes:
1. Describe why genetic mapping is useful.
2. Calculate the map distance between linked genes using data from a testcross.
3. Explain how interference affects the number of double crossovers.

1. Genetic mapping determines the linear order of genes on a chromosome and the
separation of those genes on the chromosome.
a. Genes have a specific place on a chromosome, called a locus.
b. Crossing over can separate alleles found at different loci.
2. Genetic maps serve the following purposes:
a. It allows geneticists to understand the complexity and genetic organization
of the species.
b. It illustrates the underlying basis for the inherited traits of an organism.
c. The location of a gene may allow the use of molecular techniques to clone
and study the gene in greater detail.
d. Comparisons of genetic maps are often used in evolutionary studies.
e. Once the location of disease-causing genes are determined, it may be
possible to diagnose and treat the disease.
f. The location of the gene may allow genetic counselors to predict the
likelihood that parents will produce offspring with a given trait/disease.
g. Genetic maps are becoming common in agriculture to enhance selective
breeding by farmers.
3. The linear order of genes on the chromosome is called a genetic linkage map
(Figure 6.8).

A Testcross is Conducted to Produce a Genetic Linkage Map

1. Genetic mapping allows the determination of relative distances between genes,

since the further two genes on the same chromosome are from one another, the
greater the chance that crossing over will occur between them.
 a. The percent of recombinant offspring is correlated to the distance between
the genes.
2. The construction of a genetic linkage map utilizes a testcross. Testcrosses
typically involve an individual who is heterozygous for the traits being mapped,
and an individual who is homozygous recessive for the traits being mapped.
3. Testcrosses allow a researcher to distinguish between recombinant and
nonrecombinant offspring (Figure 6.9).
a. Recombinant offspring have different combinations of alleles than either
of the parental strains.
b. Nonrecombinant offspring have the same combinations of alleles as one of
the parental strains.
c. Crossing over during meiosis produces recombinant offspring.
d. Recombinant offspring are typically fewer in number than
nonrecombinant offspring.
4. Map distance is defined as the number of recombinant offspring divided by the
total number of offspring, multiplied by 100.
a. Note that the total includes both recombinant and nonrecombinant
offspring.
b. The units for map distance are called map units (mu) or centiMorgans
(cM).
c. One map unit (or centiMorgan) equals a 1% recombination frequency.
5. The first genetic map was constructed by Alfred Sturtevant in 1911.
a. Used Drosophila melanogaster as the model system.
b. Map was constructed of X-linked traits.
6. Sturtevant correctly assumed that the most accurate distances would be those
between genes that are closely linked.
a. At map distances approaching 50.0 (50% recombination), there is a greater
chance that undetected multiple crossover events may be influencing the
results (Figure 6.10).

Trihybrid Crosses Can Be Used to Determine the Order and Distance Between Linked
Genes
1. Trihybrid crosses (three traits) may be used to determine the map distance and
order of genes on a chromosome.
2. The procedure for constructing a trihybrid cross is as follows (pgs. 139 – 141):
a. Cross two true-breeding strains that differ with regard to three alleles.
b. Perform a testcross by mating F1 female heterozygotes to males that are
homozygous recessive for all three alleles.
c. Collect the F2 data. The parental phenotypes should occur with the greatest
frequency in the offspring. The next highest frequency should be the
offspring with a recombination event between one of the genes, followed
by those individuals that display a double-crossover. The double-crossover
phenotypes indicate which of the three genes is in the middle (Table 6.1).
d. Calculate the map distance between pairs of genes.
e. Construct the map.
Interference Can Influence the Number of Double Crossovers That Occur in a Short
Region
1. Since map distances equal recombination frequency, the number of double-
crossovers should be able to be calculated using simple probability.
a. The probability of a double-crossover in a trihybrid cross is equal to the
product of the recombination frequency between the genes.
b. This probability, when multiplied by the total number of offspring, should
equal the observed number of double-crossovers.
2. This rarely occurs due to the phenomenon of positive interference. When a
crossover occurs in an area of a chromosome, it usually decreases the probability
that a second crossover will occur in that area.
3. To calculate interference (pg. 141), it is necessary to first calculate a coefficient of
coincidence (C). C is equal to the observed number of double-crossovers divided
by the expected number of double-crossovers.
4. Interference (I) is then equal to 1-C.
a. If this number is positive, it is called positive interference and indicates a
decrease in the observed number of double-crossovers compared to the
expected.
b. Rarely, this number may be negative (negative interference), which
indicates that a crossover enhances the chances of a second crossover
event occurring in the region.

6.4 Genetic Mapping in Haploid Eukaryotes

Learning Outcomes:
1. Explain the experimental advantage of genetic mapping in fungi.
2. Calculate the map distance between genes in fungi using tetrad analysis.

1. Species of simple eukaryotes, such as the sac fungi and algae, spend a portion of
their life cycle as haploid organisms. These organisms, specifically the fungi,
have played an important role in the understanding of genetic recombination.
2. Fungi are haploid organisms that frequently reproduce asexually, but can
reproduce sexually by the fusion of two haploid cells to produce a diploid zygote
(Figure 6.11).
a. The diploid zygote then proceeds through meiosis to produce four haploid
spores. These spores are collectively called a tetrad.
b. In some species, this is followed immediately by a mitotic division,
producing an octad of cells.
c. These cells are usually contained within a sac called an ascus, which
contains the product of a single mitotic division.

The Arrangement of Spores in an Ascus can be Ordered or Unordered

1. The arrangement of the spores within an ascus is species specific (Figure 6.12).
a. If the spores are randomly mixed together, it is called a unordered tetrad or
octad.
b. If the space in the ascus is limited, the result is an ordered tetrad or octad.
2. In ordered tetrads the position of the spores within the ascus reflects their
 relationship to each other as they were produced by meiosis and mitosis (Figure
6.12).
a. Daughter cells are located alongside of one another in the ascus.
b. This allows the mapping of the distance between a gene and the
centromere of the chromosome.
c. The model organism for these studies in Neurospora crassa.

Unordered Tetrad Analysis Can Be Used to Map Genes in Dihybrid Crosses

1. Using dihybrid cross of organisms with unordered tetrads, it is possible to
determine if two genes are linked or assorting independently.
2. If the tetrad contains four spores with the parental combinations of the alleles, it is
called a parental ditype (PD). Those tetrads that contain four spores with
nonparental combinations are called nonparental ditypes (NPD). If there is a mix
of parental and nonparental genotypes in an ascus, it is called a tetratype (T). This
is shown in Figure 6.13
3. The map distance between two linked genes can be calculated using the number
of NPD and T offspring (formula on pg. 144).
a. This calculation is accurate for short distances, but does not account for
double-crossovers for genes that are further apart.
b. In order to account for double-crossovers over longer distances, the
formula must be modified to the form on pg. 144. Figure 6.14 shows the
relationship between crossing over and the production of the parental
ditype, tetratype, and nonparental ditype for two linked genes.

6.4 Mitotic Recombination

Learning Outcome:
1. Describe the process of mitotic recombination and explain how it can produce a
twin spot.

1. Mitotic crossing-over may produce a pair of recombinant chromosomes that have

new combination of alleles, an event known as mitotic recombination.
2. First studied in Drosophila by Curt Stern who noticed that adjacent areas of the
body in Drosophila may express different alleles for bristle length and body color
(Figure 6.15).
a. These adjacent areas of the same organism that are slightly different in
phenotype are called twin spots.
b. Twin spots are the result of mitotic recombination.