Transcript Bio290-04-Week3-Mapping Eukaryotic Chromosomes

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
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!
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!