Welcome to IB 201, Part II

Genetics

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IB 201 Genetics and Evolution

Part 2 Genetics

Dr. Kim Hughes

465B Morrill Hall

kahughes@uiuc.edu

Office hours: Tu/Th after class or by appointment (email for appointment)

Required Texts

Readings from “Essential of Genetics”,

by Klug and Cummings

Today

1. Genetic Data Analysis

2. How to do well in this course

3. Review Questions

Genetic Data Analysis

Does a genetic “model” fit the data?

Genetic experiments are designed to answer this question.

Data analysis and experimental design are intimately related.

Design of Experiments

A friend claims that he will only drink “Sierra Springs” bottled water, because it tastes the best.

How would you decide if he really can tell the difference between brands of bottled water?

Design of Experiments

How many “tests” would you conduct?

What if you conducted 10 tests, and he got it right 7 times?

Could you reject the hypothesis that he was guessing randomly?

Genetic ExampleYou have discovered a new mutation in a fruit fly and you think

it’s a recessive mutation. How do you test this hypothesis?

Female (true-breeding wild-type strain) X Male (true-breeding mutant strain)

P: AA x aa (presumed)F1: Aa (presumed)Testcross: Aa (presumed) x aa (presumed)

Expected offspring ratio: 1 wild type : 1 mutant

If your genetic model is correct, then you predict a 1:1 ratio in the offspring of the testcross.

Genetic Example

If your genetic model is correct, then you predict a 1 : 1 phenotypic ratio.

What if the phenotypic ratio is 1.2 to 1?

How do you know if this deviation from an expected result is due to chance or due to the fact that your genetic model is wrong?

Simple ExperimentWhat if you were to repeat a simple experiment many times?Toss a fair coin 100 times and count how many heads are

thrown. Repeat this experiment 100 times.

What is the most likely outcome of a single experiment (if coin is fair)?

Will all 100 experiments have the same outcome?

100 Tosses of a Fair Coin

0123456789

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100

Number of Heads

Times out of 100

The most likely outcome is the expected value, which is the same as the average or mean.

100 Tosses of a Fair Coin

0123456789

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100

Number of Heads

Times out of 100

What is the probability that you would get 55 or more heads in a single experiment?

What is the probability that you would get 65 or more heads?

P = 18.4/100 = 0.184. So, 55 is different from expected, but close enough that the differences is likely due to chance.

P = 0.18/100 = 0.0018. So, 65 is different from expected, and the difference is unlikely to be due to chance.

Genetic example

Q: You cross a dark moth and a light moth, and the F1 offspring are all dark. You then inter-cross the F1 with each other to produce the F2. In the F2, you get 70 of the dark moths and and 30 light moths. Can you reject the hypothesis that the dark parent was AA and the light parent was aa?

What is your hypothesized genetic model? AA x aa

Genetic example

Q: You cross a dark moth and a light moth, and the F1 offspring are all dark. You then inter-cross the F1 with each other to produce the F2. In the F2, you get 70 of the dark moths and and 30 light moths. Can you reject the hypothesis that the dark parent was AA and the light parent was aa?

What is your hypothesized genetic model?

If this model is correct, what are the expected number of dark and light moths in the F2?

AA x aa

3 : 1 ratio, or 75 dark : 25 light

Genetic example

Q: You cross a dark moth and a light moth, and the F1 offspring are all dark. You then inter-cross the F1 with each other to produce the F2. In the F2, you get 70 of the dark moths and and 30 light moths. Can you reject the hypothesis that the dark parent was AA and the light parent was aa?

What is your hypothesized genetic model?

If this model is correct, what are the expected number of dark and light moths in the F2?

What is the observed result?

How could we measure the difference between the expected and observed results?

AA x aa

3 : 1 ratio, or 75 dark : 25 light

70 dark : 30 light

Genetic ModelP (phenotypes) dark x light

P (genotypes) AA x aa

F1: Aa

F2: 1/4 AA 1/2 Aa 1/4 aa

F2 phenotypes: 3/4 dark : 1/4 light

Expected numbers (phenotypes)?

(100 offspring)

Observed result?

75 dark: 25 light

(Null) Hypothesis: observed results do not deviate from expected results more than expected by chance.

70 dark: 30 light

2 TestA way to tell if the difference between observed results and expected results is too big to be due to chance.

Observed number (O) in each category is compared to the expected number (E) in each category under the null hypothesis (the hypothesized genetic model): (Obs - Exp).

Use the square of the difference between observed and expected numbers : (O - E)2

Correct for the size of the experiment by dividing by the expected number in each category: (O - E)2 /E

2 Test

= [(O-E)2]/E = ∑ (d2/E)

(O-E) is the “difference” (d).

symbol means to sum the values over each category or “class” of the data.

€

# classes∑

2 TableProbabilities

= 1.33, d.f. = 1

df 0.90 0.50 0.20 0.05 0.01 0.001

1 0.02 0.46 1.64 3.84 6.64 10.83

2 0.21 1.39 3.22 5.99 9.21 13.82

3 0.58 2.37 4.64 7.82 11.4 16.27

4 1.06 3.36 5.99 9.49 13.3 18.47

A Real ExperimentYou have crossed two plants with purple flowers and have

166 offspring. Your hypothesis is that both plants are heterozygous for a dominant allele at a single locus controlling flower color. Genetic Model

P: (Ww X Ww) F1: 3/4 W- (purple) and 1/4 ww (white)

Expected: If model is true, you expect 3/4 purple and 1/4 white. Out of 166 offspring: 124.5 purple: 41.5 white.

Observed Data: 166 progeny: 110 purple & 56 white.

Q: Is the deviation from expected too big to be due to chance?

Test

Class O E (O-E) (O-E)2 = d2 d2 /E

PurpleWhite

110 56

124.5 41.5

-14.5 14.5

210.25210.25

1.69 5.07

= 6.76

df 0.90 0.50 0.20 0.05 0.01 0.0011 0.02 0.46 1.64 3.84 6.64 10.832 0.21 1.39 3.22 5.99 9.21 13.823 0.58 2.37 4.64 7.82 11.35 16.274 1.06 3.36 5.99 9.49 13.28 18.47

Table

df = 1

Probabilities

Problem: An ear of corn has a total of 381 grains, including 216 purple, smooth, 79 purple, shrunken, 65 yellow, smooth, and 21 yellow, shrunken.

Your Hypothesis: This ear of corn was produced by a dihybrid cross (PpSs x PpSs) involving two pairs of heterozygous genes resulting in an expected ratio of 9:3:3:1. Purple dominant to yellow; smooth dominant to shrunken.

d.f. = 3 2 = 1.80

Class Obs Exp O-E (O-E)2/E

Purple

Smooth

216 214 2 4/214 = 0.019

Purple

Shrunk

79 71 8 64/71 = 0.901

Yellow

Smooth

65 71 6 36/71 = 0.507

Yellow

Shrunk

21 24 3 9/24 = 0.375

df 0.90 0.50 0.20 0.05 0.01 0.0011 0.02 0.46 1.64 3.84 6.64 10.832 0.21 1.39 3.22 5.99 9.21 13.823 0.58 2.37 4.64 7.82 11.35 16.274 1.06 3.36 5.99 9.49 13.28 18.47

Probabilities

d.f. = 3 2 = 1.80

How to do well in this course

Course Web Sitehttp://www.life.uiuc.edu/ib/201Class scheduleAssigned readingsHomework assignmentsLecture notesPowerpoint slidesRecommended problemsOther

Course Pre-requisites

IB 150: Organismal and Evolutionary Biology

MCB 150: Molecular and Cellular Basis of Life

Review material available on the course web site: Basic Mendelian and Molecular Genetics

How is this course different?Memorization is less important. Learning and applying concepts is more important.

You need to be able to think about and analyze genetic data.

Most homework and exam questions will require you to examine and analyze data, and to make conclusions based on your analysis.

In this way, the work you do in this course is very similar to work done by professional geneticists.

How to succeed in this course Come to class! Read the assigned material before class Download lecture notes before class. Bring a calculator and scrap paper to class. Do recommended problems and the problems in

lecture notes/slides: you will see them again! Posted to Lecture Schedule web page. Use your resource groups, TAs, and me for help!

Participate in class activities

Don’t

• Furiously take notes during class

• Put off the homework until the last minute

• Put off doing recommended problems until just before the exam

Review Questions1. A round-seeded pea was crossed to a wrinkle-seeded

pea, and all the offspring were round. Diagram the cross and predict the ratio of wrinkled to round offspring in the F2 generation.

2. A round-seeded pea is crossed to a wrinkle-seeded pea. Half the offspring were round and half were wrinkled. What were the genotypes of the parents, the round F1 offspring, and the wrinkled F1 offspring?

3. True-breeding yellow and round seeded plants were crossed to true breeding green and wrinkled ones. All F1 offspring had yellow and round seeds. What were the genotypes of the parents and the F1 offspring? What phenotypes, and in what proportions, do you expect in the F2 generation?

4. A red snapdragon is crossed to a white snapdragon and all the offspring are pink. This is an example of what genetic property?

Review Questions5. A woman homozygous for the A allele of the ABO blood

group marries a man who is homozygous for the B locus. What is the blood group phenotype of their child? This is an example of what genetic property?

6. What is the most likely mode of inheritance illustrated by this pedigree?

7. If a couple want to have two children, what is the probability that the first will be a girl, and the second will be a boy?

8. If a couple want to have two children, what is the probability that they will have one girl and one boy?

Answers1. P: WW x ww

F1: WwF2: 3/4 round (W-) to 1/4 wrinkled (ww)

2. P: Ww x wwF1: 1/2 Ww (round) and 1/2 ww (wrinkled)

3. P: GG WW x gg wwF1: Gg WwF2: 9/16 yellow, round (G- W-); 3/16 yellow, wrinkled (G- ww); 3/16 green, round (gg W-); 1/16 green, wrinkled (gg ww)

4. Incomplete dominance5. AB; Codominance6. X-linked recessive7. 0.258. 0.5

Terms you should know GeneLocusAlleleDominanceRecessivenessWild typeMutationGenotypePhenotypeHomozygoteHeterozygoteMonohybridDihybrid

PleiotropyEpistasisAutosomeSex chromosomeHemizygousPleiotropyEpistasisHaploidDiploidNuclear DNAMitochondrial DNAChloroplast DNAChromosome

Homologous chromosomesSister chromatidsTetradMitosisMeoisisIndependent assortmentRecombinationCrossing overTranscriptionTranslation

If you found these questions easy

You’re prepared to start this portion of the class

If these questions were not easy

You should attend the review session and study review material

Review session: Today, 5 pm, 140 Burrill Hall