Excelsior BIo300 M4A1: Lab Assignment: Mendelian Pigs

M4A1: Lab Assignment: Mendelian Pigs

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Worksheet

· Complete the work sheet as you work through SimBio lab activities.

· Type answers into the worksheet or copy and paste from the SimBio application.

· Address all parts of each section. You may submit bullet statements or full sentences. Keep statements short and concise (100 words or less).

· The lab has three sections, sections 1 and 2 will each add 50 points to your lab grade. Section 3 will be evaluated as part of the lab report M4A3.

There are two ways to study genetics. Mendelian genetics focuses on the rules of inheritance and the expression of an individual's alleles. Population genetics examines how allele frequencies change in populations. In this lab, you'll use both approaches to explore the genetics of coat color in pigs and how these traits are passed down within families and through populations.

Section 1: Breed your bacon

1. How many generations does it take to have pure breeding brown and black pigs in your selected pens?

2. Summarize first back cross experiment:

Parents	A	B
Genotype
Phenotype

Punnett Square

	Gamete A - 1	Gamete A-2
Gamete B-1			Genotype
		Phenotype
Gamete B-2			Genotype
		Phenotype

Summary of outcome:

Prediction

Genotype
Phenotype

Result:

Genotype
Phenotype

3. Summarize second back cross experiment:

4. Parents	A	B
Genotype
Phenotype

Punnett Square

	Gamete A - 1	Gamete A-2
Gamete B-1			Genotype
		Phenotype
Gamete B-2			Genotype
		Phenotype

Summary of outcome:

Prediction

Genotype
Phenotype

Result:

Genotype
Phenotype

Section 2:

Pigmented Pigs

1. What is the difference between eumelanin and pheomelanin?

2. What is the role of MC1R in the production of each type of melanin?

3. Explain the function of the W Allele

4. Explain the function of the B Allele

5. Explain the function of the R Allele

6. Explain the function of the SAllele

7. What is a loss of function mutation and how does loss of function of S affect coat color of pigs?

8. What type of pigs would you cross to produce light spotted red pigs?

Section 3

(This part of the lab simulation will be graded as the lab report M4A2):

Going Hog Wild

In the previous exercise (Pigmented Pigs), you used the principles of Mendelian inheritance to make predictions about how traits would be passed down in families of pigs based on the genotypes of the parents. In section 3, you will make predictions about inheritance in whole populations, not just families. By studying the genetics of populations, you will discover whether a particular trait such as hair color can disappear over time.

1. Genes in populations

Complete the first simulation. What is your starting allele frequency and ending allele frequency for the alleles you chose?

Phenotype/Allele

Initial frequency

Ending frequency

Phenotype/Allele

Initial frequency

Ending frequency

You founded the first population with a rare dominant allele and a common recessive allele, and you looked at how allele frequencies changed over time (Qu. 37-Qu. 40).

Now consider the following questions:

How are dominance relationships of alleles related to allele frequencies in apopulation? That is, does knowing an allele is dominant tell you whether it iscommon or rare? Does knowing an allele is common tell you whether it is dominant or recessive?

Propose a hypothesis for the questions above as well as describe how you would set up a study to test your hypothesis. Run your experiment and save your results, you will need them later.

Hypothesis:

Experimental Design: What type pigs are you planning to cross? How many generations?

Phenotype/Allele

Initial frequency

Ending frequency

Phenotype/Allele

Initial frequency

Ending frequency

Hypothesis Accepted/Rejected:

How does the starting frequency of an allele affect changes in frequency for that allele over time?

Generate a hypothesis andexperiment for this question. Make sure you keep yourresults forlater.

Hypothesis:

Experimental Design: What type pigs are you planning to cross? How many generations?

Phenotype/Allele

Initial frequency

Ending frequency

Phenotype/Allele

Initial frequency

Ending frequency

Hypothesis Accepted/Rejected:

2. Gene frequencies for populations (Lab tutorial page 7)

Set up a population, with at least 30 pigs, that contains two alleles, with any allele frequencies you like. Record which two alleles you use:

1. Allele (p) Frequency #pigs:

2. Allele (q) Frequency: # pigs:

Predicted frequency after 270 months, we estimate a population of a 1000 pigs:

1. Allele (p) Frequency: # pigs:

2. Allele (q) Frequency: # pigs:

Observed frequency after 270 months, we estimate a population of 1000 pigs:

1. Allele (p) Frequency: # pigs:

2. Allele (q) Frequency: # pigs:

After finishing all parts of this lab simulation, return to your results and check if the alleles for coat color were in Hardy Wein-Berg Equilibrium at the beginning and end ofthe simulation. You will need to compare calculated and observed allele frequencies (see lecture notes and assigned videos) and test results by Chi-Square for significance. You find an example at the end of this worksheet. Results will be part of lab report M4A3.

3. Hungry wolves or Will Blondes Really Disappear (Lab Tutorial p. 12)

Predation

The researchers also believe that so-called bottle blondes may be to blame for the demise of their natural rivals. In terms of pigs and our simulation – this means, certain coat colors are more vulnerable to predation.

• Design and conduct an experiment(s), using the pigs, to test whether this idea could be true.
• In designing your experiment, consider which pig phenotypes to use for representing hair color genetics in people, where bottle blonds are not naturally blond and therefore have a hair color, like brown or black, which is dominant to blond.
• Also consider that being so unattractive that you fail to find a mate is, in an evolutionary sense, the same as being eaten by a wolf before you reach puberty. In both cases you fail to leave descendants. So giving one color of pig a higher death rate is equivalent to making them less attractive to mates.
• When you have finished your experiment(s) and come to a conclusion, your instructor may ask you to write this as a short scientific paper, so take notes on what you do and the results you observe.

Hypothesis:

Set up a population, with at least 100 pigs, that contains three or more alleles to produce the phenotypes you choose. Add to tables as needed. Record which alleles you use:

1. Phenotype: Allele (p) Frequency: #pigs:

2. Phenotype: Allele (q) Frequency: # pigs:

3. Phenotype: Allele (p) Frequency: #pigs:

4. Phenotype: Allele (q) Frequency: # pigs:

Predicted frequency after 270 months, we estimate a population of a 10000 pigs:

1. Phenotype: Allele (p) Frequency: #pigs:

2. Phenotype: Allele (q) Frequency: # pigs:

3. Phenotype: Allele (p) Frequency: #pigs:

4. Phenotype: Allele (q) Frequency: # pigs:

Observed frequency after 270 months, we estimate a population of 10000 pigs:

1. Phenotype: Allele (p) Frequency: #pigs:

2. Phenotype: Allele (q) Frequency: # pigs:

3. Phenotype: Allele (p) Frequency: #pigs:

4. Phenotype: Allele (q) Frequency: # pigs:

Hypothesis Accepted/Rejected:

After finishing all parts of this lab simulation, return to your results and check if the alleles for coat color were in Hardy Wein-Berg Equilibrium at the end of the simulation. You will need to compare calculated and observed allele frequencies (see lecture notes and assigned videos) and test results by Chi-Square for significance. You find an example at the end of this worksheet. Results will be part of lab report M4A3. Double check your math with the online X-square calculator,QuickCalcs.

The alleles and phenotypes in your virtual pigs are all found in real pigs as well. Meiying Fang and colleagues found that wild pigs are virtually all homozygotes for the W allele, whereas genotypes that include the B, S, and R alleles are common among domestic pigs. Could these data help us to determine the history of domestication of pigs?Include this information in the discussion and conclusion of the lab report M4A3.

Resource:

Fang, M., G. Larson, et al. 2009.Contrasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genetics 5:e1000341

Chi-Square Test (Goodness of Fit)

This statistical analysis will test if your data fit gene frequencies under expected conditions, in this case the Hardy-Weinberg equilibrium.

The Chi-square is calculated by the formula:

X²= ?

Observed values are frequencies of coat color alleles in our simulation, and expected values are the calculated values of allele frequencies based on a Hardy-Weinberg distribution (p² + 2pq + q² = 1)

X² test requires degrees of freedom, which is the number of classes of characters -1.

For example:

Set up a population, with at least 30 pigs, that contains two alleles, with any allele frequencies you like. Record which two alleles you use:

4. Allele (p) Frequency: 0.6 # pigs: 18

5. Allele (q) Frequency: 0.4 # pigs: 12

Predicted frequency:

Homozygotes P²: 0.36

Heterozygotes 2pq: 0.48

Homozygotes q²: 0.16

Predicted frequency after 270 months, we estimate a population of a 1000 pigs:

3. Allele (p) Frequency: 0.6 # pigs: 600

4. Allele (q) Frequency: 0.4 # pigs: 400

Observed frequency after 270 months, we estimate a population of 1000 pigs:

3. Allele (p) Frequency: 0.625 # pigs: 625

4. Allele (q) Frequency: 0.375 # pigs: 375

Homozygotes P²: 0.389

Heterozygotes 2pq: 0.424

Homozygotes q²: 0.14

Calculation: X²= = + = 1.04 + 1.56 = 2.6

We have two classes (2 alleles) in our analysis, which means 1 degree of freedom. If our Chi-square value is less than the value at the 0.05 probability level, we accept our hypothesis.

Our X²value (2.6) is smaller than 3.84, so our hypothesis is correct, and the population is in Hardy-Weinberg Equilibrium.

A Chi-Square Table

	Probability
Degrees of Freedom	0.9	0.5	0.1	0.05	0.01
1	0.02	0.46	2.71	3.84	6.64
2	0.21	1.39	4.61	5.99	9.21
3	0.58	2.37	6.25	7.82	11.35
4	1.06	3.36	7.78	9.49	13.28
5	1.61	4.35	9.24	11.07	15.09

Reference:

GraphPad (2016) QuickCalcs. Retrieved from http://graphpad.com/quickcalcs/chisquared1/