Welcome to Week 3!

Today’s Agenda:

1. Reviewing Pedigrees (Part 1)2. Practicing with Chi Square Analysis (Part 2)3. Thinking About Genetics and Agriculture in

Developing Countries4. Introduction to Chromosome Mapping (Part 3)5. Comments on Next Week (Fieldtrip!)

*Don’t forget to turn in your topic statement today!*

Pedigrees….where to begin??

• Look for a pattern in the pedigree– Is the trait present in every generation?– Is the trait inherited from one parent only?

• Some assumptions to make– In most recessive traits the parents will be unaffected and

heterozygous – In recessive traits, anyone married into a family is

considered not a carrier

What type of inheritance is this?

• Which individuals have the trait?

• What type of relationship do III-5 and III-6 have?

• Autosomal Recessive• Ex: Cystic fibrosis

Try One More: What type of inheritance is this?

• What are some of the trends that you notice?

• Autosomal Dominant• Ex: Huntington Disease

Critical Skill: Building and Interpreting Pedigrees

Let’s practice! (Part 1A)

Critical Skill: Building and Interpreting Pedigrees

Working with pedigrees is a key component to understanding genetic diseases and predicting risk.

Meet Dr. Nancy Wexler

Let’s practice! (Part 1B)

Looking Ahead to Next Week: Lifton’s Work on CAD

Practicing Chi-Square Analysis

• Work with your group on Part 2 to investigate shattering and grain color in rice. (Part 2)

Genetics in Context: Agriculture in the Developing World

Our Task:1- What role does this author suggest genetics has

in agriculture in the developing world?2- What are some of the most important

obstacles this author identifies to creating food security in developing countries?

3- What aspect of this paper did you find most interesting? Were there any terms or ideas you found difficult to understand?

Genetics in Context: Agriculture in the Developing World

Your Group Should:1- Have everyone share their interpretation of the role

of genetics and/or one of the most critical obstacles from the text.

2- Have everyone share one aspect they found new, interesting, or challenging.

3- Then, prepare a brief report out on your group’s conclusions and designate a spokesperson (Part 3).

Looking Ahead to Mapping

Eukaryotic Chromosomes

Looking Ahead to Mapping Eukaryotic Chromosomes

Why do we need to know where genes are?

• Building complex genotypes

• Identifying its structure and function

• Deciphering evolutionary mechanisms

Linkage Mapping

Linkage Mapping

How can Morgan explain his results?How can this information be used to build maps?!

Linkage Mapping

Recombination frequencies of less than 50%

suggest linkage!

Recombination frequencies of less than 50%

suggest linkage!

Linkage: Double Crossover?!?

• Crossovers can inhibit one another through an interaction known as interference

• We can quantify interference (I) by subtracting the ratio of observed to expected frequency of double recombinants from 1.

• What does it mean if I = 0? If I = 1?

Mapping With Molecular Markers

• Molecular markers = loci of molecular heterozygosity

• Let’s us take advantage of silent variation!

Try one!

A/a * M1/M2 X a/a * M1/M1What do you expect to see? (Part 4)

Mapping With Molecular Markers

A/a * M1/M2 X a/a * M1/M1Results:

A/a * M1/M2 = 49%A/a * M2/M1 = 49%A/a * M2/M1 = 1%

Aa/a * M1/M1 = 1%

• So original cross must have been A M1/aM2 X aM1/aM1• 2% RF means 2 map units between the A/a locus and the M1/M2 locus

Mapping With Molecular Markers:

SNPS! (Single Nucleotide Polymorphisms) and SNP

Haplotypes

(What does it mean for a SNP to be in Linkage

Disequilibrium??)

Mapping With Molecular Markers:

Other useful markers include variable number tandem repeats (VNTRs),

Minisatellite Markers, and Microsatellite Markers.

Mapping With Molecular Markers:

• Chi-Square Analysis is often required to establish linkage.

• In humans, large sample sizes are rare, so we combine the results of many crosses to calculate Lod scores.

• LOD score >3 represent convincing support for a specific RF Value.

Double Crossover Complicates Linkage Mapping

Two Common Methods to Correct:

1. Mapping Function: RF = ½ (1 - e-m)

2. Perkins Formula

(these formulas aren’t critical for us!)

Final Product: Physical Maps!

Reminders for Next Week

1. CAD- Start Reading! (Pre-class assignment on Review Paper due Thursday at 2)

2. Read Chapter 4: Focus on key points we’ve identified today to help you prepare for the Quiz

3. Quiz 4- Posted by Monday at noon, due by Wednesday at noon.

4. Don’t forget to use our fabulous Discussion Room!

5. Next Week: ~1 hour Class session UW Symposium!