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Appendix D: Student Lab Activities - University of Wisconsin - Madison
Genetic Analysis of a Population
of Organisms
Overview
This lab uses the Classical Genetics Simulator developed by Ben Adamczyk, PhD Botany.
The Classical Genetics Simulator (CGS) is a computer simulation which allows you to conduct
classical genetics laboratory experiments. The program provides you with populations of organisms
with unknown patterns of inheritance and gives you the tools to design and perform experiments to
discover these inheritance patterns. You will be able to mate or cross the unknown organisms and
analyze your crosses in ways similar to those used by practicing geneticists and genetics counselors.
This will give you the opportunity to develop the logic and thought processes needed to solve reallife problems in genetics.
Before Coming to Lab:
1. Read all of this lab exercise.
2. Read all of the Reading Assignment associated with this exercise.
3. Answer the Pre-Lab Questions.
a) Week 1 – Questions 1 to 10.
b) Week 2 – Questions 11 to 15.
PRE-LAB QUESTIONS – Week 1
Answer questions 1 through 10 before coming to lab Week 1. In lab, we will give you some time to compare
your answers and problem solving strategies before asking you to demonstrate how to solve these.
DEFINITIONS:
Sex-linked: Genes that are said to be sex-linked are physically located on the sex chromosomes. Compared
to the X chromosome, the Y chromosome is very small and contains many fewer genes. As a result, most
sex-linked genes are X-linked. For these females (XX) have two copies of every gene on the X
chromosome, males (XY) most often only have one copy.
Autosomal: All genes not on sex chromosomes are said to be autosomal, i.e. are located physically on
autosomes. Autosomes are all chromosomes except the sex chromosomes. Diploid males and females both
carry two alleles for each gene on the autosomes.
QUESTIONS 1 through 10 are due at the beginning of lab -- Week 1:
1) Matching:
___ heterozygous
a. blue eyed blonde mates with brown eyed
brunette
___ homozygous
b. blonde mates with brunette
___ sex-linked
c. BB or bb
___ autosomal
d. not on sex chromosomes
___ genotype
e. blue or brown eyes
___ phenotype
f. Bb
___ gene
___ allele
g. locus on a chromosome that codes for a
given RNA
___ dihybrid cross
h. genes located on the X chromosome
___ monohybrid cross
i. BB, Bb or bb
j. males have only one for each gene on the
X chromosome
For all genetics problems:
a) Unless otherwise indicated, assume that a capital letter indicates a dominant allele and a
small (or lower case) letter indicates a recessive allele.
b) Include information on how you solved each problem, i.e. the method you used to solve each
problem.
2. How many genetically different kinds of gametes can an individual with each of the following
genotypes produce?
a. AA
e. AaBb
b. aa
f. AaBbCC
c. Aa
g. AaBbCc
d. AaBB
h. AaBbCcDdEeFf
i. Given the information above, what general rule exists for determining the number of different
gametes an organism of a given genotype can produce? Explain.
3. For a given autosomal gene with two alleles, A and a, there are three possible genotypes: AA,
Aa and aa. Use a Punnett square to show all of the possible matings among these three
genotypes. Once you have done this, how would you determine the ratios of the phenotypes
which will result from each of the matings? Explain.
4. In a cross between two individuals of the genotype AABbCcddEE:
a. how many different kinds of gametes can each individual produce?
b. what is the probability that any of the offspring will have the genotype,
AABBCCddEE?
c. what is the probability that any of the offspring will have the genotype AABBccDdEE?
5. In a monohybrid cross of a brown male hamster (from a very long line of brown only
hamsters) and a black female hamster (from a very long line of black only hamsters) all the
offspring produced are brown.
a. What are the genotypes of the male and female parents?
b. What are the genotypes of the offspring?
c. If you mate 2 of the F1 offspring with each other, what phenotypes of offspring will be
expected in the F2 and in what proportions would you expect them? Explain.
6. Length of fur is also genetically determined. The allele L produces long fur and its
corresponding allele, l, produces short fur. Long fur is dominant to short.
a. You mate 2 hamsters. Both are heterozygous for brown long fur. Would you expect any
of the offspring to have black short fur? If yes, what proportion would have black short
fur?
b. What proportion would have black long fur?
7. In cats, yellow coat color is due to a gene, b, and black coat color is due to its allele, B. The
alleles b and B are X-linked (located on the X chromosome). Because of Barr body formation,
the heterozygous condition results in tortoise shell colored cats (with both black and yellow
patches of fur).
a. What kinds of offspring would be expected from the mating of a black male with a
yellow female?
b. What kinds of offspring would be expected from the mating of a yellow male with a
tortoise shell female?
8. In poultry, a gene C produces creeper (very short legs) in the heterozygous condition and is
lethal in the homozygous condition. The c allele of the gene produces normal legs in the
homozygous condition. Barring is due to a dominant sex-linked gene, B, and nonbarred to its
recessive allele, b. In chickens, males are ZZ (similar to XX) and females are ZW (similar to
XY) and the barring gene is on the Z chromosome.
A creeper male homozygous for barring is mated with a creeper female who is nonbarred. What
kinds of offspring can be expected from this cross and in what proportions will each kind occur?
9. In cattle, polled (absence of horns) is dominant over horned and roan is the result of the
heterozygous condition of the genes for red and white coat color. (Neither red nor white is
dominant so in the heterozygote, both are expressed, e.g. half of the hairs on the coat are white
and half are red.) Assume both traits are on separate pairs of autosomes.
What proportion of the offspring of a roan, heterozygous polled bull and a roan, horned cow
would be expected to be roan and horned?
10. You want to know whether the gene for hair color in hamsters is autosomal or sex-linked.
Assume:
a. only one gene controls hair color in hamsters
b. there are only 2 alleles of this gene: B for brown and b for blonde.
c. in the heterozygous condition, brown is dominant.
You are given a blonde female hamster from a very long line of blonde (only) hamsters and a
brown male from a very long line of brown (only) hamsters.
1) Outline the breeding experiment you would set up to determine how the hair color gene is
inherited.
2) What information does the F1 generation give you?
3) What further information do you get from the F2 generation results?
PRE-LAB QUESTIONS -- Week 2
11. Two black female mice are crossed with a brown male. In several litters female ‟1”
produced 19 black young and 17 brown young; female ‟2” produced 37 black young.
a. What deductions can you make concerning inheritance of black and brown coat color
in these mice?
b. What are the most likely genotypes of the parents in these cases?
12. In humans, one type of color-blindness, an inability to distinguish between red and green, is
inherited as a sex-linked gene on the X chromosome. It is recessive.
a. If a color-blind man marries a homozygous normal woman, what chance is there for
any of the children to be color-blind?
b. A normal man marries a color-blind woman. Which, if any, of their children are likely
to be color-blind?
c. Why is it so commonly believed that women cannot be color-blind?
13. A color-blind man has a color-blind sister and his mother has normal vision.
a. What are the genotypes, for color vision, of this man’s mother and father?
b. If he marries a woman identical in genotype to his mother, what phenotypes for color
vision will be observed (theoretically) among his sons and daughters and in what ratios
will each of these occur?
14. In humans, hemophilia is a recessive and sex-linked characteristic. A man and a woman
(grandparents), both normal with respect to blood clotting have:
(a) a hemophilic son who has a daughter who is normal;
(b) a daughter who has normal blood and who has one hemophilic and one normal son; and
(c) another daughter with normal blood who has five sons, all normal.
What are the probable genotypes of the grandparents, their children, and their grandchildren?
15. Purebred lines of fruit flies with wild type (tan) body color and stubby bristles are mated to
flies with ebony bodies and normal bristles. The resulting F1 offspring all have a normal wildtype body color and stubby bristles. The F1 flies are crossed with flies recessive for both traits
(i.e. ebony bodies and normal bristles).
a. What phenotypes and ratios of phenotypes would you expect to find among the
offspring produced by crossing the F1 with flies recessive for both traits?
b. Assume you found the following results among the offspring.
Wild type body, Stubby bristles
430
Ebony body, Stubby bristles
55
Wild type body, Normal bristles
65
Ebony body, Normal bristles
450
How could you explain these results.
Genetic Analysis of a Population
of Organisms
I. What is pedigree analysis?
In many of the genetics problems in the Pre-Lab Questions you were given the characteristics of
the genes. For example in question 2, you were to assume that capital letters were dominant and
lowercase letters or genes, recessive. In many of the problems you were also told if the traits
were autosomal or sex-linked. Given this information, you could solve the problems without
much difficulty. However, what happens if you are presented with a new or previously unknown
mutation in a population? How do you determine the genetic characteristics of this new
mutation? The mechanism used most commonly is pedigree analysis.
Pedigree analysis requires knowledge of the phenotypes of several generations of individuals
and their offspring. Among humans, most genetic information comes from analysis of family
trees or pedigrees. Among other organisms, for example, fruit flies (Drosophila melanogaster)
or moue ear cress (Arabidopsis thaliana), we can perform controlled crosses to determine the
genetics. By analyzing the results of the matings, we can determine the genetics behind a given
trait - for example, its mode of inheritance.
A. Working in small groups, analyze the pedigree in Figure 1 (on the next page)
to determine the:
1. probable mode of inheritance of the trait (e.g. autosomal, sex-linked, dominant,
recessive)
2. probability that individual III5 will pass the allele for the trait on to her offspring.
Figure 1 below illustrates a hypothetical family pedigree for a trait.
•
Affected individuals are represented as shaded symbols.
•
Males are represented as squares; and females, as circles.
•
A diamond indicates the sex of the individual is not known (e.g. II2).
•
Parents are connected by a marriage line and their children (sibs or siblings) are
connected to each other by a sibship line.
•
The children are listed in order of birth from left to right.
•
Separate generations are indicated by Roman numerals (I, II, etc.). Individuals
within a generation are identified by Arabic numerals (1, 2, etc.).
•
Identical twins (e.g. II6 and II7) share a single connection to the sibship line;
fraternal twins have separate connections to the line (e.g. III3 and III4).
•
A number inside a symbol (e.g. II8 to II10) indicates sibs with similar
characteristics who are not individually listed.
Figure 1. A sample human pedigree.
B. Answer the following questions.
1. What kinds of crosses provide evidence that a trait or gene is dominant versus recessive?
2. What kinds of crosses provide evidence that a trait or gene is autosomal versus sex-linked?
3. What is the probable mode of inheritance of the trait indicated by the shaded symbols in
Figure 1 (e.g. autosomal, sex-linked, dominant, recessive)?
4. What is the probability that individual III5 will pass the allele for this trait on to her
offspring?
II. What is the research project?
Are specific traits in a newly identified population of Drosophila or Arabidopsis
genetically determined?
Drosophila – Assume you are a geneticist. You have just returned from one of the more remote
areas of the Hawaiian Islands. On the islands you collected specimens from different
populations of fruit flies that were endemic (found only in this area). In this initial wild or fieldcaught population, the genotypes of the individual fruit flies and the mode of inheritance of the
phenotypic traits displayed by the flies are not known.
Arabidopsis – Assume you are a geneticist. You are trying to learn more about the genes that
control specific aspects of development in plants. Using Arabidopsis as a model plant organism,
you add a mutagen to wild-type seeds in the hope of altering genes important for normal growth
and development. When you grow the seeds and allow the plants to self-fertilize, you find
several new phenotypes in the next generation that may be the result of genetic mutations.
You need to do controlled crosses in order to determine whether the new phenotypes (fruit fly or
Arabidopsis) are genetically determined. If the traits are genetic, you also need to determine the
mode of inheritance (sex-linked, autosomal, etc.). Please note that while fruit flies must outcross,
i.e. mate with others of the opposite sex, Arabidopsis can either self-fertilize or be outcrossed.
Remember that not all phenotypic traits are genetically determined. For example, the colors of
some animals, e.g. flamingos, are the result of the foods they eat. High levels of foods rich in
orange pigments, for example, beta carotene, can produce an orange body color. Similarly,
growth of plants in soils of differing chemical composition can lead to changes in growth pattern
or color.
III. How do we get started?
A. What do we get when we open a problem using the CGS program?
Each time you open a new problem in CGS, you are given a new field-caught population of fruit
flies or the offspring of a self-fertilized Arabidopsis plant.You will use these organisms to
perform a series of crosses (or matings) to determine whether or not their phenotypic traits are
genetically determined.
If the results of your crosses indicate the trait(s) are genetically inherited, you will then
determine the probable mode of inheritance of each phenotypic trait.
For example, is/are the trait(s):
- dominant or recessive
- sex-linked or autosomal
- the result of linked or unlinked genes
- the result of 2 alleles of a given gene or more than 2 alleles
You will also determine the genotypes associated with each phenotype and the ratios of
genotypes and phenotypes expected in crosses between individuals of given genotypes.
Refer to the “Quick Start” information for CGS and the handout titled,
“Solving Genetics Problems” as you work on the problems. Copies of
these are available in lab and on the course web site.
B. How do we use the Practice Problems?
The practice problems are designed to help you learn how to use the CGS program. They also
give you experience developing strategies for determining inheritance patterns.
As noted above, the goals in this (and all) problems are to determine:
• the probable mode of inheritance of each phenotypic trait.
• the genotypes associated with each phenotype.
• the ratios of genotypes and phenotypes expected in crosses if your model is correct.
In order to determine the mode of inheritance, you will work in a group of 3 to 4 students and
keep a detailed record of:
1) the crosses you did (including details such as sex, phenotype, vial/cross number, etc.)
2) what you wanted to learn by doing the cross. For example, did you do the cross to
eliminate the possibility that the gene was sex-linked?
3) the actual results you got and what these indicate about what you wanted to learn. (For
example, do the results allow you to state that the gene cannot be sex-linked, etc.?)
You must record all crosses and results as noted on the log
sheets provided in this lab.
You can use the log sheets themselves or you can include this
information in the “Notes” feature of the CGS program.
Completed log sheets (hand written or printed from “Notes” in CGS must
be attached to your final PowerPoint presentation, poster or report as an
Appendix.
Classical Genetics Simulator
Record of crosses for the Practice problem.
Vial#
What cross did you do?
What did you want to learn by doing
the cross and what (if any)
assumptions did you make?
What did the results indicate about your
assumptions and the genetics of the trait?
IV. Which research problems do we investigate?
After completing the practice problem you and your partner(s) will determine
the inheritance patterns for three additional problems.
Solve one problem from each of the following categories available in the CGS program.
A. Mendel
B. Morgan
C. McClintock
Note: The names of the categories do not imply anything about the genetics in each category.
V. What problem solving strategies do we use?
Using the data sheets provided, answer the following questions for EACH cross
you perform.
Hints: It will help to:
• work on one trait at a time.
• determine which phenotype is dominant and which is recessive.
• find homozygotes.
For each cross answer the following questions.
1. What cross did you perform? Include details such as sex, phenotype, vial/cross number, etc.
2. What did you want to learn by doing the cross? In other words, what information could the
proposed cross provide (e.g. about whether it is autosomal or sex-linked, etc.)?
3. What did the results of your crosses indicate about your assumptions and the genetics of the
trait?
a.What were the actual results of your cross? Include the original data. [You can save and
print these using the “Notes” function in CGS and paste these into your lab notebook.]
b. What do these results tell you about the genotypes of the flies/plants you used in the
cross as well as the inheritance pattern of the trait? [Be sure to indicate what the results tell
you as well as what they leave unanswered.]
c. How does your hypothesis change in light of these results? Do you need to develop a
new hypothesis.
d. What additional crosses do you need to perform to support your new hypothesis?
Use all of this information to help you develop a strategy to solve the problems as well as
to assist you in writing your lab report.
Classical Genetics Simulator - Record of crosses for the problem titled:
☐ Mendel ☐ Morgan ☐ McClintock
Vial#
What cross did you
do?
What did you want to learn by
doing the cross and what (if
any) assumptions did you
make?
What did the results indicate about your
assumptions and the genetics of the trait?
Classical Genetics Simulator - Record of crosses for the problem titled:
☐ Mendel ☐ Morgan ☐ McClintock
Vial#
What cross did you
do?
What did you want to learn by
doing the cross and what (if
any) assumptions did you
make?
What did the results indicate about your
assumptions and the genetics of the trait?
VI. How do we communicate our findings?
Scientists, by definition, do research. However, if they want the results of their research to have
meaning outside their own labs, they must communicate their findings to others. This can be done by
publishing articles, formally presenting a talk at a Professional Society meeting, or presenting a poster
at a Professional Society meeting. Discoveries that may change the way we think about science can go
totally unrecognized and unrewarded if they are not communicated effectively to others.
To communicate the results of your genetics research, you will prepare either a short lab report or a
PowerPoint presentation. If you do a PowerPoint presentation it should include both:

the individual PowerPoint slides and

the narrative that would accompany each slide.
Your instructor will let you know which format to use.
A. Your report or PowerPoint presentation should contain the following.
Title
The title of your project should be descriptive and indicate to the reader the “reasons” for doing
the research (e.g. what you hoped to discover). See the example below.
Authors’/researchers’ names and their affiliations (where they are from) should follow.
For example:
Calcium Transients in Hamster and Bovine Oocytes and their Relation to Bull Fertility
Benjamin M. and Smith S. (The researchers’ names)
Introductory Biology 151, UW, Madison, Wis. 53706 ( your professional affiliation)
Abstract (Your TA will let you know if you need to do an abstract.)
This is a 100-200 word paragraph that summarized the important findings of your research. The
abstract begins with a general statement that introduces the reader to the purpose, objective
and/or importance of the study. It presents major results and major conclusions, both in just a
few sentences. It discusses the methods used only if needed to give the reader an understanding
of how and why the study was done.
Introduction
The introduction contains a description of the hypothesis/problem/topic you have been
researching and a statement of the rationale (reason) for the project. Any discussion of the
history that led up to the current project should be very condensed and limited to the essentials
required to understand the rationale.
Methods
This section should contain a highly condensed version of what you would write for a full
scientific paper. Concentration should be on a general description of the strategy and logic used
to gather and analyze the data. (See example on next page.)
Results
This section should be subdivided into sections one for each major research problem (e.g.
Mendel, Morgan and McClintock). In each subsection you should summarize the key crosses
required to solve the research problem. The significance of these key crosses should be stated.
For example,what do these indicate about the mode of inheritance. Where needed use statistical
evidence to support the conclusions. For example, when at least two logical alternative
explanations exist use statistical analysis to try to eliminate one of the alternatives.
Any Figures and Tables should appear in this section in support of the results stated in the text.
Remember all figures and tables require figure numbers, titles and legends.
Discussion
The Discussion should highlight the main conclusions which can be drawn from the experiment.
The Discussion should also address what still needs to be done to answer any questions which
remain. If additional questions arose as a result of your study, these should be included.
References (12 point, bold, single-spaced)
Include any references you cited. See Appendix A for more information on what should be in
the reference list and what format this information should take.
Appendix (can be handwritten)
At a minimum, this should contain a description or diagram of the logic you used to come to the
conclusions you state in the discussion. It should also include your log sheets (or “Notes” pages
from CGS) for each “Research Problem”. Key crosses on the logs should be highlighted and
annotated.
B. How do we write the Methods section?
In this section the general methods for solving all problems are summarized and presented together.
The following is an illustration of the beginning of a well written Methods section. Note: Bullet points
indicate information that would appear on the slides. Text in italics would be presented orally, but
would not appear on the slides.
Methods:
Three separate sets of field caught Drosophila were examined: Mendel, Morgan and
McClintock. In each experiment, we first examined the inheritance of each phenotype
separately.
To determine which of the phenotypes was dominant versus recessive, we crossed ___ and
looked for ___ in the F1 generation. This indicated that . . ..
To determine if the phenotypes resulted from autosomal versus sex-linked traits, we . . .
VII. How will our presentations be graded?
All presentations will be graded using the following basic guidelines.
Authors’ names:
Lab #____________
Title:
Introduction:
___ Does the introduction include a clear statement of the overall (larger) goal(s) of this type of
research?
___ Does the introduction include a clear statement of the specific goal(s) of the research and the
rationale behind these goals?
Methods:
___ Do the authors provide an overall summary of the logic used to determine the patterns of
inheritance?
___ Do the authors provide an explanation of any differences involved in analyzing the results
from the three different problems/fly populations?
Results:
___ For each problem, do the authors indicate which key crosses provided evidence allowing
them to make their conclusions?
___ Where needed, do the authors present statistical evidence to support their conclusions? For
example, when at least two logical alternative explanations exist do the authors use statistical
analysis to try to eliminate one of the alternatives?
Discussion:
___ Do the authors relate their results to the specific purpose(s) stated in the introduction?
___ Do the authors state the limitations of the data, or indicate the studies they recommend to
clarify any unanswered questions?
Overall Quality:
___ Does the presentation have a logical flow to it?
___ Is all information presented in a clear and concise manner?
Reading Assignment
Genetic Analysis of a Population
of Organisms
I. How do mitosis and meiosis compare?
II. How can we determine expected ratios of offspring?
What rules can we learn from Mendel’s work with
pea genetics?
III. How do we know if our observed results support the
genetics proposed?
How does the Chi Square Test help?
IV. What do we know about the Drosophila life cycle?
V. What do we know about the Arabidopsis life cycle?
I. How do mitosis and meiosis compare?
Read the sections in your text book which describe the cell cycle and the stages of mitosis
and meiosis.
After reading these you should know:
1) Which cells in your body undergo mitosis and for what reasons they undergo mitosis.
2) The various stages of mitosis and how each can be recognized.
3) Which cells undergo meiosis and for what reasons they undergo meiosis rather than
mitosis.
4) The stages of meiosis and how each can be recognized.
5) The major differences between mitosis and meiosis.
6) What relationship(s) Mendel's laws of independent assortment and segregation have with
specific meiotic events.
A. Based on your reading, develop and complete a table similar to that below.
1. Fill in the major events which occur in each phase of mitosis, meiosis I and meiosis II.
2. In the last row of the table indicate which events in a given stage (e.g. metaphase) are
common across all three of the division cycles: mitosis, meiosis I and meiosis II and which are
different or unique; that is, which occur in only one of these division cycles. Then answer the
following questions.
Interphase
Prophase
Metaphase
Anaphase
Telophase
Cytokinesis
Mitosis
Meiosis I
Meiosis II
Common
events
Differences
B. Include your answers to the following summary questions.
1. How does mitosis differ from meiosis?
2. What are the major differences between meiosis I and meiosis II?
3. Why is it essential that the resulting cell products of meiosis (which will become gametes)
have half the number of chromosomes of the parental cells? Which specific half of the
chromosomes do the cell products contain?
II. How can we determine expected ratios of offspring?
What rules can we learn from Mendel’s work with pea genetics?
A. Who was Mendel?
Genetics, as a field of scientific inquiry, began with the studies of Gregor Mendel, an Austrian
monk. In 1865, he reported the results of eight years of breeding experiments with plants to the
Naturalist Society of Brun. Mendel's experiments, and those of many scientists since,
demonstrated that many characteristics of individuals are inherited as individual units, now
referred to as genes. Mendel's analysis is especially impressive since the importance of
chromosomes and the mechanics of mitosis and meiosis had yet to be discovered.
B. What kinds of research did Mendel do?
Mendel discovered the genetics of specific traits by doing controlled crosses of known parents.
He began by establishing pure breeding lines (or populations) of plants which displayed
contrasting genetic characteristics such as tall vs. short plants, yellow vs. green seeds, smooth vs.
wrinkled seeds. A pure breeding line of tall plants mated with each other will (by definition)
always produce tall offspring. Similarly, a pure breeding line of plants with red flowers, when
crossed with each other, always produces offspring with red flowers. Today we would say that
these lines are homozygous for the gene in question.
In one set of experiments, Mendel crossed a pure breeding tall line of peas to a pure breeding
short line and made the following observations.
1. Parental generation (P) -- Tall plants crossed with short plants
First filial generation (F1) -- All offspring are tall
2. Tall F1 offspring crossed with each other
Second filial generation (F2) -- 787 tall plants and 277 short plants
Similar results were obtained for all seven pairs of characteristics Mendel studied. He concluded
that:
a. Inherited characteristics were controlled by pairs of factors (alleles of genes).
b. Each individual contains a pair of such factors (alleles) for a particular gene.
c. During the formation of gametes, this pair is separated or segregated, so that only one
member of the pair appears in any one gamete.
d. At fertilization, the single allele in the sperm and the single allele in the egg are
combined so that the new individual (offspring) again has a pair of alleles for that gene or
trait.
In the example above, each of the pure breeding tall plants contained a pair of alleles for tall
stature and the purebreeding short plants contained a pair of alleles for short stature. When the
mating occurred, each parent (the P generation) contributed a single allele of the gene for height
to the offspring. The tall plant, TT, contributed one T allele. The short plant (tt) contributed one
t allele. The F1 plants therefore had the genotype, Tt. These plants appeared tall because, in this
case, the tall allele (T) was dominant over the short allele (t) which is then said to be recessive.
When two F1 plants are crossed, in this case Tt crossed to Tt, each parent will contribute a T
allele half of the time and a t allele the other half of the time. This will result in three different
genotypes, but two different phenotypes as shown in the table of offspring types below:
Sperm
(½) T
Eggs
(½) t
(½) T
TT (1/4)
Tt (1/4)
(½) t
Tt (1/4)
tt (1/4)
This results in 1/4 TT, (1/4 + 1/4) Tt, and 1/4 tt.
Since TT and Tt individuals are phenotypically indistinguishable (all look alike; all are tall), the
tall offspring would make up 3/4 of the total and the short, 1/4. This was just what Mendel
observed.
This is an illustration of what is now known as Mendel’s law of segregation. In this example, it
is the individual alleles of a gene which are segregated. We know now that this occurs during
anaphase I of meiosis when homologous chromosomes migrate to opposite poles of the spindle.
As a result, the two alleles of each gene are physically separated or compartmentalized into
gametes.
C. Dihybrid Crosses
Go one step further, as Mendel did, and deal with two specific traits, size and color, e.g. tall vs.
short and yellow vs. green. Here, tall is dominant to short and yellow is dominant to green.
In this dihybrid cross the purebreeding parental genotypes would be TTYY and ttyy. The F1
genotypes would all be TtYy. We can predict the number of different genotypes that should
appear in the F2 by using a Punnet square. To do this we must first determine how many
different kinds of sex cells (gametes) an individual with the genotype, TtYy, can produce. The
answer is four, because each gamete must have one allele from each pair but it makes no
difference which one. The number of possible gametes can be calculated from the formula: 2n =
number of possible gametes. Here n = the number of heterozygous allele pairs (genes on
separate chromosome pairs) under consideration.
The four possible gamete combinations for this example would be TY, tY, Ty and ty.
T
t
Y
TY
tY
y
Ty
ty
Next we use a Punnet square to determine expected types and probabilities of offspring for the
cross. A Punnet square lists male gametes on one side and female gametes on the other. This
allows you to visualize all possible combinations of male and female gametes. Therefore, the
hypothetical or expected proportions of offspring genotypes and phenotypes can be determined.
SAMPLE PUNNET SQUARE :
Sperm
TY
Ty
tY
ty
TY
Ty
Eggs
tY
ty
1. Use this Punnet square to combine the gametes in all possible combinations.
2. What expected phenotypic and genotypic ratios result in the offspring?
3. How were you able to determine this?
This illustrates Mendel's Law of Independent Assortment. This law states that the alleles of
different pairs of genes will assort (segregate) independently of each other during gamete
formation. (Note: This is true, only if the genes in question are on different pairs of homologous
chromosomes, i.e. are not linked on the same chromosome. One exception: genes that are very
far apart on the same chromosome and therefore have a high probability (0.5) of cross over will
appear to be unlinked and to segregate independently.)
If the genes in question assort independently, we can also solve problems like this by solving for
each gene separately. For example, we can treat the cross of TtYy X TtYy as two separate
crosses: Tt X Tt and Yy X Yy. We know that these crosses will produce:
Tt X Tt –
Yy X Yy –
3/4 tall
+ 1/4 short
3/4 yellow + 1/4 green
In combination, these would yield:
3/4 tall
1/4 short
3/4 yellow
3/4 x 3/4 = 9/16 tall, yellow
1/4 x 3/4 = 3/16 short, yellow
1/4 green
3/4 x 1/4 = 3/16 tall, green
1/4 x 1/4 = 1/16 short, green
Keep in mind that every offspring has to have both size and color and that the most frequent size
and most frequent color will be observed together most often.
Terms to Know:
Phenotype - The expression of the genes in an individual organism; what the individual looks
like, e.g. tall, green, blonde.
Genotype - The combination of genes found in an individual organism, e.g. TT, Tt or tt. If T
(tall) is dominant, both TT and Tt individuals will be tall (have the same phenotype), even
though their genotypes differ.
Allele - Different or contrasting forms of the same gene. For example, T (tall) and t (short) are
alleles of the gene for overall height of the organism.
Homozygous - An individual is said to be homozygous for a given gene when the two alleles in
the genotype are the same. For example, TT is homozygous tall and tt is homozygous short.
Heterozygous - An individual is said to be heterozygous for a given gene when the two alleles in
the genotype are different, e.g. Tt. If T (tall) is dominant, this individual would display the tall
phenotype.
Hemizygous - The special condition seen when an otherwise diploid organism has only one
representation (allele) of certain genes. For example, in mammals, females are XX (have two X
chromosomes) and males are XY (have an X and a Y chromosome). For most genes on the X
chromosome, there is no corresponding allele on the Y. For these genes, males would be
hemizygous, i.e. have only one allele of these genes.
III. How do we know if our observed results support the
genetics proposed? How does the Chi Square Test help?
Expected ratios from a given genetic cross can be calculated. For example, if two genes are
assorting independently, the offspring of individuals heterozygous for both genes are expected to
occur in a 9:3:3:1 phenotypic ratio. However, observed ratios of offspring often differ from
expected ratios. This occurs because each cross, like each flip of a coin, is subject to errors of
sampling, or chance deviation from ideal or expected values.
If you think about it, the significance of a given deviation is clearly related to sample size. If
chance alone is causing the observed deviation from expected, larger samples should result in
less deviation than smaller samples. For example, you are more likely to come closer to 500
heads and 500 tails out of 1000 flips of a coin than you are to 5 heads and 5 tails out of 10 flips
of the same coin. When a deviation from expected is consistently large, it is likely that
something other than chance alone is operating. For example, if you flipped a coin 100 times
and turned up 90 heads (a deviation of 40 from the expected 50), you would suspect a biased
coin.
Chance variation can also affect the outcome of genetics experiments. In a cross of Tt
(heterozygous tall) by tt (homozygous recessive short) you would expect a 1:1 ratio of tall to
short in the offspring. In Experiment 1, if you evaluate only 40 offspring, and find 30 tall and 10
short, the deviation of 10 may seem significant.
Experiment 1: Tt X tt
Observed:
Expected:
Tall
30
20
Deviation:
10
(Tt)
Short (tt)
10
20
10
In Experiment 2, if you evaluate 200 offspring from the same cross, a deviation of 10 may seem
less significant.
Experiment 2: Tt X tt
Observed:
Expected:
Tall
90
100
Deviation:
10
(Tt)
Short (tt)
110
100
10
Using the Chi Square statistical test allows you to determine if the deviation you observe is
significantly different from that expected given chance deviation alone.
The Chi Square test is calculated as follows.
Χ2 = ∑(d2/e)
Here ∑ means “the sum of”; d = deviation = (observed - expected) and e = expected.
1. Observed values (number of actual offspring from a cross) are counted and expected values
are calculated based on the assumed genetics. If you assume you are crossing a heterozygote
with a homozygous recessive you would expect ½ the offspring to be dominant and ½ to be
recessive for phenotype. To calculate the expected values multiply the total number of offspring
actually counted by ½ to get each expected value.
2. Subtract the observed number of offspring from the expected number then square the resulting
difference or deviation and divide by the expected number.
For Experiments 1and 2 above the Chi square calculations would be:
Experiment 1 - Χ2 =∑(d2/e) = (30 - 20)2 /20 + (10 - 20)2 /20 = (10)2 /20 + (-10)2/20 = 100/20 +
100/20 = 5 + 5 = 10
Experiment 2 – Χ2 = ∑(d2/e) = (90 - 100)2/100 + (110 - 100)2 /100= (-10)2 /100 + (10)2 /100 = 2
To determine whether the deviations from expected are significant we need both the Chi square
value and the degrees of freedom. The number of degrees of freedom in tests of genetic ratios is
almost always one less than the number of classes possible.
In these experiments only two types (classes) of offspring were possible (tall vs short). This
means that there is only one degree of freedom here.
To help you understand why degrees of freedom are calculated as they are, consider the situation
encountered when you put your shoes on. You have two shoes, but only one degree of freedom.
This occurs because you have one decision to make, that is, which shoe to put on the first foot.
Once that decision is made, right or wrong, the other shoe has to go on the remaining foot; there
is no other option. The first decision (or value) can be thought of as arbitrary; the last, as fixed
by assigning a value (foot) to the first.
After calculating Χ2 and determining degrees of freedom, you can consult a Χ2 Table to
determine the probability that the experimental deviation from expected is due to chance alone.
To use the table, look down the column of degrees of freedom to locate the calculated degrees of
freedom for your problem. The values in the row next to your value for degrees of freedom are
the Χ2 values which have been calculated for that number of degrees of freedom. At the top of
the table you will see column headings which indicate the probability that a given Χ2 value could
result from chance deviation alone.
Χ2 TABLE
Degrees
of
Freedom
p = 0.99
0.95
0.80
0.50
0.20
0.05
0.01
1
0.0001
0.004
0.064
0.455
1.642
3.811
6.635
2
0.020
0.103
0.446
1.386
3.219
5.991
9.210
3
0.155
0.352
1.005
2.366
4.642
7.815
11.341
4
0.297
0.711
1.649
3.357
5.989
9.488
13.277
5
0.554
1.145
2.343
4.351
7.289
11.070
15.086
What are the p values for Experiment 1 and Experiment 2 above?
To find the p values:
a. Go to the degrees of freedom column and read down it until you find “1”.
b. Read across the row for 1 degree of freedom to determine where your calculated Χ2
value would fall. For Experiment 1, the Χ2 value, 2, falls between 1.642 and 3.811.
c. Read up the columns which contain the numbers 1.386 and 3.219. These correspond to p
values of 0.5 and 0.2 respectively.
d. This indicates that between 20 and 50% of the time, the deviation you observed in
Experiment 1 could be accounted for by chance alone. Such a deviation is generally
considered “not significant” enough to indicate anything other than chance is operating to
cause the deviation.
In most scientific investigations, p values must be less than 0.05 to be considered significant
and less than 0.01 to be considered highly significant. Another way of looking at this is a p
value of 0.05 indicates that only 5% of the time can the observed deviation be expected to result
from chance variation alone.

Using this same method, what is the p value for Experiment 2? Is this deviation
significant?
How is the Chi square test adjusted when you have more than two possible classes of offspring
or outcomes?
Where four offspring classes are possible, it becomes reasonable to allow the value of Χ2 to be
larger before questioning the hypothesis that chance alone explains the deviation. As noted
above, the number of degrees of freedom in tests of genetic ratios is almost always one less than
the number of classes possible.
Thus, in tests of 1:1 or 3:1 ratios, there would be one degree of freedom (two possible classes of
offspring minus one = 1 degree of freedom). A test of a 1:2:1 offspring ratio would have two
degrees of freedom and so on.
Examine the Χ2 Table again. Choose one of the probability (p) value columns.
 What relationship do you see between degrees of freedom and Chi square values in this
column?
X2 ANALYSIS - SAMPLE FORM
CLASS OR
PHENOTYPE
OBS
EXP
O-E
(O-E)2/E
(O-E)2
Total:
X2 =
Degrees of
Freedom =
p=
IV. What do we know about the Drosophila life cycle?
The life cycle of the fruit fly (Drosophila melanogaster) is completed in 10 days at 25 °C, the
optimal temperature. There are four stages in the life cycle: egg, larva, pupa and adult (see
figure below). The duration of each of these stages depends on many environmental factors,
especially temperature. The life cycle is completed more quickly at higher temperatures and
more slowly at lower temperatures.
During the larval stage, there are two molts and three larval periods or instars. Pupation usually
occurs on a dry surface. Upon emerging, the adults appear lightly colored with folded wings.
Within a short time, they darken, their exoskeletons harden and their wings expand. Males can
be distinguished from females because males are usually shorter with the posterior region of the
abdomen rounded. Females have a more pointed posterior abdomen. On the female’s dorsal
abdominal surface, there are alternating dark and light color bands which extend to the tip of the
abdomen. In the male the posterior third of the abdomen is a solid dark color.
Female fruit flies can store sperm for relatively long periods of time. Therefore, it is important
that females used in genetics experiments be virgins to control for the source of the sperm or
paternal genotype. Newly emerged males will not mate for 12 hours. This allows us to collect
virgin females for mating experiments by removing all flies from breeding vials at time t = 0.
Eight hours later, the flies which have hatched are collected and separated by sex. Using this
technique, these hatchlings will all be virgins.
V. What do we know about the Arabidopsis life cycle?
Over 750 different varieties (or ecotypes) of Arabidopsis thaliana have been discovered
worldwide. Arabidopsis is a small weedy dicot in the family Brassicaceae. Arabidopsis has a
very small diploid genome (115,000 kb of DNA, 2n = 10) and a relatively short life cycle (6
weeks from seed to seed).
In 2000, Aradidopsis became the first dicot plant to have its complete genome sequenced. The
small relative size of Arabidopsis (a full-sized mature adult plant that has not yet flowered
typically occupies less space than a golf ball) means that many individuals can be grown in a
very small area. Arabidopsis normally self-fertilizes, but can also be crossed manually with
other flowering individuals. Each mature plant can produce 100s to 1000s of seed (offspring).
Together, all these characteristics have made Arabidopsis the most commonly used model
organism in plant research. For example, studying the differences found in the750 varieties has
allowed us to identify specific genes and gene interactions involved in morphology, physiology
and evolution. What we cannot learn by studying these naturally occurring variations, we can
often learn by inducing new variations using mutagenesis. Following the mutagenesis, we
screen (look) for particular changes in growth, form or function. We can then use these
mutations to identify specific genes and to study the effects of these mutations/genes at the
physiological and molecular levels.