Genetics Lab #3: Review of Mendelian Genetics Objectives In today’s lab you will explore some of the simpler principles of Mendelian genetics using a computer program called CATLAB. By the end of this lab you should be able to demonstrate and interpret the products of monohybrid and dihybrid crosses, design crosses to identify dominant and recessive traits and design crosses to identify the genotype of individuals bearing a dominant trait. Introduction: The genetic cross, or mating, is the bread-and-butter technique of genetic analysis. Mendel derived his particulate theory of inheritance from many crosses involving pea plants. To this day, in thousands of laboratories throughout the world, genetic crosses of experimental organisms are still carried out on a daily basis to test hypotheses of gene inheritance and function. In today’s lab you will use a computer program called CATLAB to simulate genetic crosses of cats in a variety of experimental contexts. You will be approaching genetic analysis the way real geneticists do: you will only be able to see phenotypes but, through selected crosses, you will be able to draw conclusions about genotypes.

Opening up CATLAB 1. Click on the CATLAB icon. 2. Click “OK” on the title screen. This will display the simulation screen and the program’s controls. 3. Note the tabs labled Instructions, Introduction, Usage and Phenotype. Click on and read each to familiarize yourself with CATLAB. 4. Note the menu bar across the top, left of the screen. It consists of File, Cat and Options. You will be working primarily in the Cat menu. The Cat menu includes: Add - this allows you to create a cat with desired characteristics. Set as Parent - this allows you to select a particular cat as a parent. Set Litter Size - allows you to control litter size from 4 to 7. Mate Cats - Produces a litter from the selected parents. Display Phenotype - This shows you the phenotype of any selected.

Exercise #1: Single Gene Inheritance (monohybrid cross) In cats, one gene controls the density (or intensity) of fur color. The different alleles of this gene produce phenotypes in which the color is dense (black fur will be the example of dense coloring used in this simulation) or dilute (gray fur will be the example of dilute coloring used in this simulation). The purpose of this exercise is to explore the inheritance of this gene.

The alleles for color density are: D for dense fur (black fur in this case) d for dilute fur (gray fur in this case) Based on these symbols, which is the dominant trait and which is the recessive trait? The P1 cross: Generate black and gray cats as follows: First click on add under the cat menu. 1. Black female (click on: female, has a tail, not all-white, no white areas, no tabby stripes, black) 2. Gray male (click on: male, has a tail, not all-white, no white areas, no tabby stripes, gray) Check the phenotype: First select a cat by clicking on the cat’s number. Then click on “Display Phenotype” under the Cat menu. What are the possible genotypes for the black cat? What are the possible genotypes for the gray cat? Make a prediction: What kinds of kittens do you expect to get from these parents? Test Your Prediction: Select each cat as a parent. Set the litter size to a constant value of 5. Test your prediction by mating cat #1 and cat #2. Obtain three litters (15 kittens total). This is your F1 generation. Record their colors in the space below:

Analyzing Your Results Based on your results, what do you think the genotype of your black female is? Can you be certain about this conclusion?

All gray kittens from this mating are genotype: All black kittens from this mating are genotype: The F1 x F1 cross: Select a black female and a black male from the group of 15 kittens as your new parents. Re-set the litter size to 6. DO NOT MATE THEM YET. Record the genotype of the new mother and the new father. The mother will produce eggs with allele: ________ or ________. The father will produce sperm with allele: ________ or ________. What is biological process that results in the formation of gametes (sperm and egg cells)? Make a prediction: Predict the possible genotypes and the phenotypic ratio among the offspring of these two cats. Use a Punnett square to make your predictions. Write out all possible genotypes and the corresponding phenotypes.

Test Your Prediction: Set the litter size to a constant value of 6. Test your prediction by mating your two new parents. Obtain four litters (24 kittens total). Record your results in the following table. Color

Observed number

Black Gray Do your results fit your prediction? Why might your results differ from your prediction?

Exercise #2: Determining Genotype In this exercise you will generate three new black cats (follow the instructions for making black cats provided above). The computer program will randomly assign genotypes to each cat. Since black is dominant, the cats will be either DD or Dd. Your mission, should you choose to accept it, is to identify the genotype of each cat. Before you start, decide on a strategy for solving this problem. Cat

Genotype

1 2 3 Describe your strategy and present the results of an experiment that identified a cat with the DD genotype and the results of an experiment that identified a cat with the Dd genotype.

Exercise #3: Dihybrid cross Some breeding experiments require that the experimenter follow more than one trait in a cross. A dihybrid cross involves analyzing the inheritance of two traits. In this exercise you will follow the inheritance of the color density gene and the tabby striping pattern. These genes are located on non-homologous chromosomes (i.e., they are unlinked) and will therefore obey Mendel’s law of independent assortment. The alleles for color density

The alleles for tabby striping

D for dense fur (orange fur in this case) d for dilute fur (cream fur in this case)

T for mackerel striping t for blotched striping

1. Generate an orange/mackerel cat and a cream/blotched cat. These cats will be your P1 generation. To make the cats, select the following: Male or Female (choose one) Has a tail Not all-white No white areas Blotched or Mackerel (choose one) Orange or Cream (choose appropriate color) Once you generate your cats, check their phenotype. Note the difference in the striping pattern between blotched and mackerel. What is the genotype of each cat?

2. Mate the two cats to get an F1 litter. Keep mating these original parents until you get at least two orange/mackerel cats in the F1 generation. 3. Select two orange/mackerel cats from the F1 generation as parents. DO NOT MATE THEM YET. Answer the following questions. What is the genotype of orange/mackerel cats in the F1 generation? What is the genotype of the gametes produced by the F1 orange/mackerel kitten? In the space below, use the Forkline method to predict the F2 genotypes. What is the predicted ratio of phenotypes among the F2? If the F1 cats produced 50 kittens, how many of each phenotypic class do expect to get? (round to whole numbers) Diagram the Forkline for the Dihybrid cross in the space below

4. Set the litter size to 7. Mate the F1 cats and produce 7 litters (a total of 49 kittens in the F2 generation). Note the number of kittens with each phenotype. Do these numbers agree with your predictions? orange/mackerel orange/blotched cream/mackerel cream/blotched

Lab #3: Take-home Quiz (due March 2, 2007) 1. From which of the following crosses could offspring be produced that have a genotype different from either parent? Cross 1: Cross 2: Cross 3: Cross 4:

aa x aa AA x aa Aa x aa Aa x Aa

2. For exercise #2, present the results of an experiment that identified a cat with the DD genotype and the results of an experiment that identified a cat with the Dd genotype.

3. The gametes produced by parent #1 all carried the F allele. The gametes produced by parent #2 carried either the F allele or the f allele. What is the genotype of each parent?

4. Consider the cross of two heterozygous parents: Dd x dd i) What is the chance that the right parent will produce a gamete carrying the D allele? ii) What is the chance that the left parent will produce a gamete carrying the d allele? iii) What is the chance of an offspring of genotype dd? iv) What is the chance of an offspring of genotype DD? v) What is the chance of an offspring of genotype Dd? 5. Flower color in pea plants is controlled by a single gene with two alleles, designated “P” and “p”. The “P” allele is dominant and determines the purple flower color phenotype and the “p” allele is recessive and determines the white flower color phenotype. Seed shape is controlled by a single gene with two alleles, designated “R” and “r”. The “R” allele is dominant and determines the round seed shape phenotype and the

“r” allele is recessive and determines the wrinkled seed shape phenotype. Consider a cross of two pea plants, one with purple flowers and round seeds and one with purple flowers and wrinkled seeds. In genotypic terms the cross is: Pp/RR x Pp/rr. (show Punnet squares to support your answer) a) Out of 1000 progeny from this cross, how many plants do you expect to have white flowers and wrinkled seeds? b) Out of 1000 progeny from this cross, how many plants do you expect to have white flowers and round seeds? c) What is the chance of having an F2 plant with the genotype of pp/Rr

5. What was the genotype of your P1 orange/mackerel cat in exercise #3? What is your evidence for assigning this genotype?