This document summarizes a genetics experiment conducted on Drosophila melanogaster flies to identify two mutations labeled D and U and determine their inheritance patterns. The D mutation caused small indentations on wings and was termed "cookie-cutter", located on the ckcr gene. The U mutation resulted in shorter, bent bristles and was called "kinked-bristles", located on the kdbr gene. Crosses between mutant and wildtype flies were performed to analyze inheritance, but results were inconclusive as F2 progeny ratios did not match expected sex-linked recessive patterns, though this remains a possibility due to incomplete penetrance.

1.
Genetic analysis of novel mutations on the ​ckcr ​and ​kdbr ​genes in ​Drosophila melanogaster
Zachary Bibb and Kirsten Pierce
Professor Jim Smart
BIOL 350A – Genetics
December 7, 2014
George Fox University

2. Abstract
The objective of this experiment was to identify mutations in ​Drosophila melanogaster ​labeled
D and U, and determine the inheritance patterns for both mutations. ​Drosophila ​has been
considered an ideal model organism due to a large amount of offspring being generated in a short
amount of time. In addition, the ​Drosophila ​genome is remarkably similar to the human
genome, making it a valuable model organism when studying diseases. In this experiment, the D
mutation was determined to cause small dents along the wings was named ​cookie­cutter ​and
determined to be on the ​ckcr ​gene. The U mutation was determined to result in shorter, bent
bristles in mutants, was termed ​kinked­bristles​, and was determined to be located​ ​on the ​kdbr
gene. The results of the crosses made in this experiment led to inconclusive results. While
reciprocal crosses suggested that the ​cookie­cutter ​and ​kinked­bristle ​mutations were sex­linked
recessive, the F2 progeny for both strains (and the unexpected ratios of ​kinked­bristle ​F1s), did
not correspond to the expected ratios for this mode of inheritance. However, it is still likely that
these mutations are sex­linked recessive due to incomplete penetrance.
Introduction
The fruit fly ​Drosophila melanogaster​ is one of the most widely used genetic model organisms
and has been used for a variety of purposes, from complementation testing to comparison of
disease­associated gene sequences to studying the ​p53​ tumor­suppressor gene (2). Numerous
studies have made it clear that the fruit fly is one of the most useful genetic model organisms due
to similarities between genes in its genome and crucial genes in the human genome. In fact, it
has been determined that ​Drosophila ​have the most similar genome to humans, compared to

3. other invertebrates Because of this, fruit flies have served as a valuable model organism for drug
testing (6). The use of ​D. melanogaster​ as a model organism has been crucial to understanding
the human genome and how genes are passed down from one generation to the next.
The first notable use of ​Drosophila ​ as a model organism was by Thomas Hunt Morgan in the
early 1900s, when he demonstrated that the ​white​ gene for eye color was linked to the X
chromosome (7). ​Drosophila ​was the ideal choice of a model organism because hundreds of
progeny could be produced from one female, a new generation could be produced in
approximately 10 days, and the flies were relatively easy to take care of (4). One of Morgan’s
students, A. H. Sturtevant, experimented with ​D. melanogaster​ to show that genes are located
linearly along a chromosome (7). ​D. melanogaster​ has also been used in complementation
testing, specifically with regards to eye color in order to determine which eye color mutations are
located on the same genes (7).
More recently, fruit flies have also been used in a study on disease­associated gene sequences in
humans. It was found that 77% of the 929 genes analyzed had almost identical genes in
Drosophila​, the majority of these counterparts being genes that affected the visual,
cardiovascular, auditory, skeletal, and endocrine systems. In addition, there were genes in which
a mutation caused neurological disorders as well as cancer (5). It has been hypothesized that
these genes can be extremely useful if studied in ​Drosophila​ since the processes involving these
genes are controlled in very similar ways between fruit flies and humans (5). Additionally, a
functional and structural homolog of the human ​p53​ gene has been found in ​Drosophila​, with

4. similarities in the secondary structures as well as the structures of the tetramerization domains of
their respective proteins. This gene was also seen to induce apoptosis (2).
The above experiments have demonstrated that experimenting with ​Drosophila ​as a model
organism can result in findings that have high levels of significance with regard to human health
and well­being. These experiments, as well as the short generation time and the propensity for
Drosophila ​to produce large numbers of offspring, led it to be the model organism of choice for
the conduction of mutation analysis. In this experiment, two ​Drosophila ​mutations were studied
to determine their effect on offspring phenotype as well as their inheritance patterns. These
Drosophila ​were in Group 4, and the mutations were labeled D and U. The first of these
mutations resulted in small chunks taken out of the wings of mutant flies, and was termed
cookie­cutter​ and determined to be on the ​ckcr​ gene. The second, termed ​kinked bristles​, caused
slightly smaller, bent bristles in mutant flies, and was determined to be located on the ​kdbr​ gene.
Materials and Methods
Preparing the ​Drosophila ​culture medium
One full scoop of banana flakes was added to a plastic vial. An equal amount of water was then
added until all of the flakes were saturated, which was signified when they turned blue in color.
Once this had occurred, five grains of baker’s yeast were added on top to prevent contamination.
The vial was then plugged with a foam cork to prevent the flies from escaping, and the flies were
added five minutes later.

5. Checking for new hatches
When checking for parental and F1 progeny, the vials containing the flies were checked four
times a day at approximately six hour intervals. This was due to the fact that female ​Drosophila
are not sexually mature for the first eight hours of adulthood (1). Checking every six hours
reduced the risk of collecting non­virgin females, giving enough time to collect all the flies if a
large number of hatches occurred. The shifts were scheduled around 6:00AM, 12:00PM,
6:00PM, and 10:30 PM (due lab access only being allowed until 11:00PM). Once a substantial
amount of F2 progeny had begun to hatch for D and U strains of ​Drosophila, ​the checks were
reduced to twice a day, with shifts at 10:30 and 6:00. This routine continued until the
experiment’s completion.
Anesthetization of ​Drosophila ​specimens
Two different methods were used to anesthetize ​D. melanogaster​, involving the use of carbon
dioxide (CO​2​) as well as ice when CO​2​ was not available. The first method involved lightly
tapping the tube to be anesthetized against a hard edge to prevent the flies from getting trapped
in the culture medium, and then inserting the nozzle of the CO​2 ​gun into the vial without
removing the foam stopper. The trigger was squeezed until all of the flies were anesthetized, and
the vial was emptied onto either a pad connected to a CO​2​ tank or onto a clean Petri dish on top
of a deeper glass dish filled with ice to sort the flies. When there was no CO​2​ available, the vials
to be analyzed were put in a freezer for 3­4 minutes to sufficiently anesthetize the flies, and were
then emptied onto the Petri dish.

6. Sorting the ​Drosophila​ specimens
After the vial was emptied, the ​Drosophila​ specimens were analyzed under a dissecting
microscope (3x magnification). A small camel hair paintbrush was used to sort the fruit flies by
phenotype and sex. The traits used to distinguish sex were the presence of sex combs on the front
pair of legs in males and the shape of the posterior segment of the abdomen. This body part was
rounder in the males and more pointed in the females. Mutant phenotypes (​kinked bristle​ or
cookie­cutter​) were looked for as well. After sorting, the flies were brushed back into their
respective vials with a camel hairbrush.
Cleaning out the culture medium vials
When it was determined that a vial needed to be cleaned out, all live specimens were
anesthetized with CO​2​ (or frozen as previously described). The flies were then either dumped
into a bottle of ethanol to kill them or were transferred to a new vial. Cleaning out the vials was
done for three different reasons: there were no live specimens remaining, there was
contamination in the vial, or the specimens in the vial were no longer needed for experimental
purposes. Following this step, the culture medium was scraped out of the vial using a plastic
spatula. Any culture medium that could not be cleaned out using this method was rinsed out
using cold water. The clean vials were then put on a tube rack to dry.
Crossing the parental generations to produce F1 flies
A vial with culture medium was prepared, and 3­4 virgin female flies as well as 1­2 male flies
were anesthetized and transferred to the CO​2​ pad to keep them anesthetized. The specimens were

7. then brushed into the previously prepared vial and the vial was labeled with the date and
phenotypes of the male and female specimens. Two different types of crosses were made for this
experiment. One consisted of exclusively wild­type males crossed with mutant virgin female
flies. A reciprocal cross was also made; 3­4 wild­type females were crossed with 1­2 mutant
male flies. Both types of crosses maintained an approximate ratio of 3 female flies to 1 male fly.
Crossing the F1 generation to produce F2 flies
The vials containing F1 eggs were checked 4 times per day for F1 hatches. When it was observed
that the eggs containing F1 flies were at either the second or third instar stage of the fly life
cycle, the parental flies were transferred to a separate vial. This was done to prevent mating
between generations. When F1 flies were observed, a vial was prepared to hold the first hatches.
The newly hatched flies were then anesthetized, sorted by phenotype and sex, and then brushed
into the vial to breed with each other. When it was determined that a specific vial was getting too
full, a new one was prepared.
Results
cookie­cutter ​F1 progeny
To obtain F1 progeny, 2­3 females expressing the ​cookie­cutter ​mutation and 1­2 wild type
males were sorted into the same vial. After the cross was made, the vials were checked for F1
progeny four times a day at approximately six hour intervals. A total of 694 F1 progeny were
bred, with the results displayed in Table 1 below.

8. Table 1: ​cookie­cutter​ ​Drosophila ​F1 progeny
Sex and Phenotype Number of Progeny
Wild­type males 12
Wild­type females 287
ckcr​ males 302
ckcr​ females 53
Unknown males 14
Unknown females 26
T1 displays the different phenotypes present among male and female F1 progeny. The number
of F1’s expressing the various phenotypes are also recorded.
According to T1, the most common phenotype expressed by male ​Drosophila ​was the mutant
cookie­cutter ​phenotype (302). The most common phenotype expressed by female ​Drosophila
was wild type. (287). Other sex­phenotype combinations observed were: wild type males (12)
and ​ckcr​ females (53). Some specimens were categorized as “unknown” due to under developed
wings or their wings being too damaged to distinguish a phenotype upon inspection.
cookie­cutter​ F2 progeny
When the F1 progeny first hatched they were placed in a previously prepared vial. More F1s
were added to the vial as they hatched, and additional crosses were made in a new vial when
overcrowding seemed to occur in the first vial. F2’s were obtained by checking the F1 crosses
four times a day at approximately six hour intervals. The F2s were then separated in a similar

9. matter to the F1s. A total of 302 ​ckcr​ males were crossed with 287 wild­type females to
produce a total of 1210 F2 progeny.
Table 2: ​cookie­cutter​ F2 progeny
Sex and Phenotype Number of Progeny
Wild­type males 207
Wild­type females 228
ckcr​ males 307
ckcr​ females 343
Unknown males 71
Unknown females 54
T2 shows phenotypes present among the ​cookie­cutter​ F2 progeny and the numbers of male or
female ​Drosophila ​with each phenotype. Male and female flies with an unknown phenotype are
also shown.
According to T2, the most common phenotype within​ ​the F2 generation was the ​ckcr ​mutant
phenotype, with 307 males and 343 females exhibiting this phenotype. The remaining
phenotypes were wild type females (228) and wild type males (207). Male and female
Drosophila ​of unknown phenotype occurred at lower frequencies than known phenotypes (71
unknown males and 54 unknown females).

10. cookie­cutter ​reciprocal F1 progeny
The ​cookie­cutter ​reciprocal F1 progeny were bred in a similar manner as the ​cookie­cutter ​F1s.
About 2­3 females expressing wild type phenotype were crossed with 1­2 males expressing the
cookie­cutter ​mutation. More P generation male and female ​Drosophila ​expressing the
previously described phenotypes were also placed into the cross as they hatched, to produce
more reciprocal F1 progeny. A total of 301 ​cookie­cutter ​reciprocal F1 progeny were bred for
this experiment.
Table 3: ​cookie­cutter Drosophila ​reciprocal F1 progeny
Sex and Phenotype Number of Progeny
Wild­type males 133
Wild­type females 150
ckcr​ males 4
ckcr​ females 1
Low expressivity ​ckcr​ female 1
Unknown / under developed winged females 12
T3 indicates the different phenotypes expressed among the F1 progeny of the reciprocal cross,
and indicates whether males or female ​Drosophila ​expressed those phenotypes. ​Drosophila ​of
unknown phenotypes were also observed, due to under developed wings, wings being smashed
prior to inspection, or other reasons.
T3 illustrates that the most common phenotype expressed among both male and female
reciprocal F1 progeny was wild type, with 133 wild type males and 150 wild type females, with

11. the ​ckcr​ mutant phenotype also being expressed. Additional phenotypes that were expressed by
female reciprocal F1 progeny were the ​cookie­cutter ​phenotype, low expressivity ​cookie­cutter
phenotype, and unknown phenotypes due to reasons previously described.
cookie­cutter ​reciprocal​ ​F2 progeny
The ​cookie­cutter​ reciprocal F2 progeny were bred in a similar manner to the ​cookie­cutter ​F2
progeny. As the reciprocal F1s hatched, they were placed into a prepared vial with no other
Drosophila ​present, and their sex was recorded for future reference. The vials were then
checked four times a day at approximately 6 hour intervals. When reciprocal F2 progeny
hatched, they were separated into newly prepared empty vials and their sex was also recorded. A
total of 218 ​cookie­cutter ​reciprocal F2 progeny were bred, expressing wild type, ​ckcr​ (with
various levels of expressivity), as well as unknown phenotypes.
Table 4: ​cookie­cutter Drosophila ​reciprocal F2 progeny results
Sex and Phenotype Number of Progeny
Wild­type males 49
Wild­type females 93
ckcr​ males 36
ckcr​ females 18
Low expressivity males 1
Extremely low expressivity males 1
Unknown / under developed wings: males 10
unknown / under developed wings: females 10

12. T4 displays the phenotypes expressed among the reciprocal F2 progeny, as well as the number of
male and female ​Drosophila ​expressing that phenotype.
As indicated by T4, the most common phenotype expressed by male reciprocal F2 progeny was
wild type with a frequency of 49. The most common phenotype expressed by female reciprocal
F2 offspring was wild type at 93 progeny. Additional phenotypes expressed among male
reciprocal F2 progeny were the ​ckcr​ phenotype (36 progeny), low expressivity ​ckcr ​wings (1),
extremely low expressivity ​ckcr ​wings (1), and unknown / underdeveloped wings (10). Other
phenotypes that were expressed among females were ​ckcr​ females (18 progeny), unknown /
underdeveloped wings (10 progeny), and crumpled wings.
kinked bristle ​F1 progeny
When enough P generation flies had hatched, 2­3 females expressing the ​kinked bristle ​mutation
were crossed with 1­2 wild type males. As more P generation ​Drosophila ​hatched,​ ​they were
added to the cross and additional crosses were made when overcrowding started to occur in the
original cross. These crosses were checked four times a day at approximately 6 hour intervals.
When F1 progeny hatched, their sex was recorded and all F1 progeny were placed into a newly
prepared vial, making a ​kinked bristle ​F1 cross. 97 F1 males were crossed with 121 females to
produce 496 F1 progeny. These progeny expressed wild type, mutant ​kdbr​, and unknown
phenotypes.

13. Table 5: ​kinked bristle Drosophila ​F1 progeny
Sex and Phenotype Number of Progeny
kdbr​ males 189
Wild­type females 305
kdbr​ females 1
Unknowns 1
T5 establishes which phenotypes were expressed among the ​kinked bristle ​F1 progeny, and
whether that phenotype was expressed by male or female ​Drosophila. ​The number of male or
female ​Drosophila ​expressing a particular phenotype is also recorded.
According to T5, the most common phenotype among male F1 progeny was the ​kinked bristle
mutation (189 male F1 progeny expressed), and the most common phenotype expressed among
female F1 progeny was wild type ( 305 female F1 progeny expressed). Other phenotypes present
were ​kdbr​ females (1), and a ​Drosophila ​specimen​ ​of unknown gender and phenotype.
kinked bristle ​F2 progeny
The ​kinked bristle ​F1 crosses that were made were used to produce the ​kinked bristle ​F2
progeny. The F1 crosses were checked 4 times a day at six hour intervals, and F2 progeny were
separated into a newly prepared vials upon hatching. Their sex was recorded but both sexes
were placed into the same vial. A total of 189 male F1s were crossed with 306 female F1s to

14. produce a total of 218 F2 progeny. These F2 progeny expressed wild type, ​kdbr​, and unknown
phenotypes.
Table 6: ​kinked bristle Drosophila ​F2 progeny
Sex and Phenotype Number of Progeny
Wild­type males 64
Wild­type females 69
kdbr​ males 49
kdbr​ females 35
Unknown males 1
T6 displays the various phenotypes expressed by male and female F2 progeny from the ​kinked
bristle ​F1 cross. The number of offspring expressing each phenotype (by gender) is also
displayed.
According to T6 the most common phenotype expressed by the male F2 offspring and the female
F2 offspring from the ​kinked bristle ​F1 cross was wild type (64 male progeny, 69 female
progeny). The other phenotype expressed by male and female F2 offspring was the ​kinked
bristle ​mutation (49 male progeny and 35 female progeny). One male of unknown phenotype
was also observed.
kinked bristle ​reciprocal F1 progeny
Reciprocal F1 progeny for the ​kinked bristle ​mutation​ ​were produced by crossing 2­3 P
generation wild type females with 1­2 P generation ​kinked bristle ​males. As more P generation

15. Drosophila ​with these specific sex­phenotype combination hatched, they were added to the cross
and additional crosses were made when overcrowding occurred. These crosses were checked
four times a day in approximately six hour intervals. When F1s hatched they were placed into a
newly prepared vial and their sex recorded. A total 171 ​kinked bristle ​reciprocal F1 progeny
were bred during the experiment, and exhibiting wild type phenotypes, with the exception of one
kinked bristle ​male.
Table 7: ​kinked bristle Drosophila ​ reciprocal F1 progeny
Sex and Phenotype Number of Progeny
Wild­type males 84
Wild­type females 86
kdbr​ males 1
T7 establishes the phenotypes that were expressed among the reciprocal F1 progeny, and also
displays which sex of ​Drosophila ​had that particular phenotype. The frequency of phenotypic
expression among male and female ​Drosophila ​is also displayed.
According to T7, the most common phenotype expressed by ​kinked bristle ​reciprocal F1s was
wild type, with only 1 male F1 expressing a mutant phenotype.
kinked bristle ​reciprocal ​ ​F2 progeny
There were no reciprocal F2 progeny produced for the ​kinked bristle ​mutation during this
experiment, although ​kinked bristle ​F1 crosses were prepared by placing the reciprocal F1

16. progeny into a newly prepared vial as they hatched, and additional crosses were made as
overcrowding occurred.
Discussion
The original purpose of this experiment was to analyze two different mutations in ​Drosophila ​in
order to determine their inheritance patterns from the phenotypic ratios of the F1s and F2s. The
original hypothesis was that both mutations were sex­linked.
Analysis of the ​cookie­cutter​ F1 generation
Almost all observed hatches for the ​cookie­cutter​ F1 generation were either ​ckcr​ male or
wild­type female flies, strongly suggestive of the sex­linked recessive hypothesis. If
cookie­cutter​ was sex­linked dominant, then it can be expected that at least half of both the males
and females would display the mutant ​ckcr​ phenotype. However, this was not the case, as the
parental cross for this mutation yielded an almost perfect 1:1 ratio of wild­type females to ​ckcr
males, with well under half of the females (53 out of 340, or 15.6%) displaying the mutant ​ckcr
phenotype. It was then reasoned that ​cookie­cutter​ must be sex­linked recessive. A chi­square
analysis of the ​ckcr​ males and wild­type females using this hypothesis yielded a value of 0.38.
With one degree of freedom in this case, this value falls well within the range of acceptable ​p
values and so cannot be rejected.
This hypothesis is further supported by the results of the reciprocal cross. A sex­linked recessive
mutation would be expected to yield a 1:1 ratio of wild­type males to wild­type females. The F1
results of the reciprocal cross in this case almost perfectly conformed to this ratio. In this case, a

17. chi­square analysis yielded a value of 1.02. With one degree of freedom, this value yields a ​p
value within the acceptable range, further supporting the sex­linked recessive hypothesis.
Analysis of the ​cookie­cutter ​F2 generation
Since the results of the F1 generations for both the normal and reciprocal crosses supported the
hypothesis that ​cookie­cutter ​ is sex­linked recessive, it is reasonable to expect equal ratios of all
four possible gender­phenotype combinations in the F2 generation for this mutation. However, it
was at this point in the experiment that results were obtained that did not support the sex­linked
recessive hypothesis. Crossing the F1 generation for this mutation yielded 307 ​ckcr​ males, 207
wild­type males, 343 ​ckcr​ females, and 228 wild­type females, or almost perfect 3:2 ratios
between mutants and wild­types for each sex. While these results appear to disprove the
sex­linked recessive hypothesis, with a chi­square value of 45.81, there may be an alternative
explanation of incomplete penetrance in the wild­type progeny. Since 1085 total offspring
having expected phenotypes were obtained, there should be approximately 271 offspring in each
phenotypic class. This would yield a penetrance of between 76.3% and 84.1%. This is not an
unreasonable expectation, since ​Drosophila ​mutations have previously been observed to display
incomplete penetrance, as seen in a study done by Lachance, et. al in 2013 (2).The original
hypothesis that the novel ​cookie­cutter​ mutation is sex­linked recessive can therefore be
maintained.

18. Analysis of the ​kinked bristles ​F1 generation
The F1 offspring for the ​kinked bristles​ mutation exhibited very different phenotypic ratios than
the ​cookie­cutter​ F1 offspring. 305 wild­type females along with 197 ​kdbr​ males were obtained,
in addition to a single ​kdbr​ female. This could be due to starting the ​kdbr​ female and wild type
male crosses later than originally planned due to difficulty in identifying the ​kinked bristle
mutation. Since females tend to hatch earlier than males, starting these crosses later could have
contributed to a larger proportion of wild­type females compared to ​kdbr ​males in the F1
generation. The original hypothesis was that this mutation was sex­linked recessive, since all the
female offspring (with one exception) were wild­type and all the males displayed the ​kdbr
phenotype. However, a chi­square analysis of the results obtained yields a value of 23.19, well
outside of the range for which the sex­linked recessive hypothesis can be accepted.
Analysis of the ​kinked bristles ​F2 generation
Crossing the F1 offspring for the ​kinked bristles​ mutation yielded a ratio of 4 wild­type males : 4
wild­type females : 3 ​kdbr​ males : 2 ​kdbr​ females, as shown in Table 6. While a chi­square
analysis of these data yields a value of 13.05, which would normally result in the rejection of a
hypothesis, an alternative explanation can be proposed. As was suggested with the ​cookie­cutter
mutation, it is likely that there is incomplete penetrance with both the F1 and F2 generations for
the ​kinked bristles​ mutation. If this is the case, then penetrance levels would be 78.3% for the F1
generation, and between 64.2% and 89.9% for the F2 generation.

19. The results of a reciprocal cross for this mutation also support the sex­linked recessive
hypothesis. If this hypothesis is correct, a reciprocal cross would be expected to yield a 1:1 ratio
of males to females, all wild­type. The reciprocal cross in this experiment yielded 86 wild­type
female and 84 wild­type male flies as well as 1 ​kdbr​ male fly. A chi­square analysis of these
offspring yields a value of 0.024; as such, the sex­linked recessive hypothesis is strongly
supported by the results of this reciprocal cross.
Conclusions
This experiment ultimately yielded inconclusive, yet intriguing results. Some of the offspring
results showed a near perfect conformation to the phenotypic ratios expected of a sex­linked
recessive mutation, while others yielded the expected phenotypes, but in unexpected ratios.
While a possible explanation for these results is incomplete penetrance, the approximate 9:7
phenotypic ratios of the F2 offspring could be suggestive of complementary gene action.
However, while the mechanism behind the unexpected ratios of the F2 offspring is unclear, it is
likely that the ​cookie­cutter​ and the ​kinked bristles​ mutations are both sex­linked recessive. A
sex­linked dominant mutation would cause at least half of the F1 females to display the mutant
phenotype, this number being dependent on whether or not the parent female is homozygous. In
this experiment, essentially all F1 females were wild­type. Additionally, a sex­linked dominant
mutation would result in 3 wild­type : 1 mutant fly among the males and 5 mutant : 3 wild­type
ratios among the F2 offspring. The results of both the F1 and F2 generation in this experiment
strongly suggest that neither the ​cookie­cutter​ nor the ​kinked bristles​ mutation is sex­linked
dominant.

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