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 Countries 4. 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

Why do we need to know where genes are? Building complex genotypes Identifying its structure and function Deciphering evolutionary mechanisms

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!

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/M1 What do you expect to see? (Part 4)

Mapping With Molecular Markers A/a * M1/M2 X a/a * M1/M1 Results: 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!