Lab 3: Mendelian Genetics and Statistics

BIOL 212 Genetics Lab Spring 2007 Lab 3: Mendelian Genetics and Statistics

Purpose:

1. To determine phenotypic ratios caused by some simple one and two locus genetic systems. Be able to use such ratios to predict the underlying genetic bases for the observed traits.

2. To understand the nature of statistical hypothesis testing and learn to apply a common statistical test.

Readings:

Chap. 2 pp. 34-51, 53-55

Materials: corn ears corn or other plant seedlings calculator--bring, if you have one worksheets--4 total, one for each corn ear or seedling type

Procedure:

Corn plant seedlings: Examine one type of seedlings.

The corn seedlings are grown up from seeds resulting from either F1 or F2 crosses.

1. Examine at least 4 separate pots of the same seedling type (Better yet, count all pots available of the same type). Record the codes for the seedlings on a worksheet.

2. Identify the phenotypes (for example, tall and short). Phenotypes are the physical characteristics of an organism. Are there two, three or four different phenotypes? Count the number of individual plants of each type you observe and record on the worksheet.

3. Devise possible genotypes and use appropriate symbols for the genotypes you propose. For example, you might use G=green (a dominant trait), g=white (a recessive trait). Genotypes of plants displaying the dominant trait might then be GG (homozygous dominant) or Gg (heterozygous). Before you hand in the worksheet, change any symbol shorthand (like G-) and designate exactly the genotypes of the seedlings.

4. Propose and test a genetic hypothesis using a Chi-square test. Here you would suggest the possible genotypes and phenotypes of the parental plants and propose the genetic

1 cross that produced these offspring. For example, you might propose a cross between two heterozygous green (Gg x Gg) F1 plants to produce a 3: 1 ratio of green (GG and Gg) to white (gg) plants in the F2 offspring. Based on the total number of progeny you observe, calculate how many progeny of each type you would predict, based on your hypothesis. Use the Chi-square test (formulas are given on the next page and a table to work through the calculations is provided on the worksheet) to determine whether the number of progeny deviates significantly from what you would expect if your hypothesis were correct.

5. Compare your calculated Chi-square to the Chi-square critical value at probability (p)=0.05 and the appropriate degrees of freedom (df=1 for a cross with two phenotypes) to determine whether or accept or reject your hypothesis.

6. If you accept the hypothesis, complete or revise the worksheet as needed and hand in. If you reject the hypothesis, begin again with step two on a new worksheet. You should either collect more data and retest your hypothesis or propose and test a different hypothesis.

Ear of corn: Examine three ears of different types

1. Record the symbols for each of the ears on separate worksheets (3 different ones).

2. Identify the phenotypes of the different kernels on each ear. There will generally either be two phenotypes representing alleles of a single gene or four phenotypes representing two alleles each for two genes.

3. Count 4 or 5 rows of kernels (about 200 kernels) and record the number of each phenotype on the worksheet. Exclude from your analysis damaged kernels or those whose phenotype is unclear.

4. Determine the Mendelian ratio that is closest to the ratio of kernels you observed, for example a 1:1 ratio of two kernel phenotypes or a 9:3:3:1 ratio of four kernel phenotypes. Hypothesize what sort of genetic factors could account for the ratio. For example, are one or two genes involved? Which traits are dominant and which recessive? What were the genotypes and phenotypes of the parents of the cross? Whenever possible, first test the simplest hypothesis you can think of which might be consistent with your data.

5. Use a Chi-square test (formulas given on next page) to determine whether your observed data adequately fit the Mendelian ratio. Do you accept or reject your hypothesis at 0.05 probability?

6. If you reject your hypothesis, test other possible ratios to see if they may fit your data, using additional worksheets as needed or include additional data in your analysis. Assignment: (20 pts) Please hand in one of your completed worksheets today, so I can give you immediate feedback. Turn in worksheets for all four samples (at least 4

2 different pages) by next week’s lab. If more than one hypothesis was tested for a sample, complete separate worksheets for each and number in sequence.

Formulas:

Chi-square = sum of (observed-expected)2 for all classes expected

Note: difference of observed-expected = d for worksheets

degrees of freedom = (number of phenotypic classes - 1)

Test null hypothesis at probability = 0.05 level of significance.

Table 5-4 Critical Values of the X2 distribution degrees of freedom (df) probability=0.05 1 3.841 2 5.991 3 7.815 4 9.488 5 11.070

Sample Hypothesis and Chi-Square Test

1. Observe plants are yellow or green—single trait for color 2. Observe more yellow plants than green 3. Develop a hypothesis  one gene is involved  Y=yellow allele  y=green allele  yellow leaves are dominant to green  The plants observed are in a 3:1 ratio of yellow to green 4. Collect data and test hypothesis with a Chi-Square test

Leaf color # observed # expected Obs-Exp (Obs-Exp)2 (Obs-Exp)2 (phenotype) Expected Yellow 33 30 3 9 0.3 Green 7 10 -3 9 0.9 40 40 χ2 1.2

Degrees of freedom=2-1=1

χ2 critical value at p=0.05, 1 df=3.841

5. Interpret result; accept hypothesis if calculated Chi-Square is less than critical value.

3 6. If you accept hypothesis, deduce what the parental and offspring genotypes and phenotypes must have been. Parents were Yy and Yy (both yellow); offspring were YY, 2Yy (yellow) and yy (green).