1. How to Make a Genetic Map
Jason Morales
Department of Agronomy
Purdue University

2. Review
What is the difference between a genetic map and a physical map?
A physical map is the sequence of nucleotides in the genome.
A genetic map is the position of markers relative to one another based on recombination frequencies.

3. Genetic Maps What do you need to make a genetic map?
Polymorphic markers
Genotypes of individuals at a given set of markers
What units are used to measure genetic distance?
Centimorgans

4. Calculating Genetic DistanceX X B b B b a A A a a A a A X X B b B b B b B b
Recombinant
Parental
Recombinant
Parental

5. Calculating Genetic DistanceX X B b B b B b B b
Recombinant
Parental
Recombinant
Parental 73 77 21
129
73/150 = 0.49
0.49 x 100 = 49 cM
21/150 = 0.14
0.14 x 100 = 14 cM
What is the highest cM value?
Why fewer recombinants?

6. Other Considerations Which mapping function should you use?
Haldane and Kosambi are the most popular
Haldane corrects for double crossovers (which can’t be detected using recombination data alone)
Kosambi corrects for double crossovers AND interference (the physical space required for one crossover prevents another crossover from occurring in close proximity)
What is the maximum distance between pairs of markers that should be used to consider two markers “linked”?
The paper used 50cM or less. What do you think?

7. Mapping Software
Calculating recombination ratios for hundreds of markers is extremely complex!
Several software tools are available
Joinmap – great software but expensive
QTL Cartographer
R/qtl

8. QTL Cartographer & R/qtl
R/qtl has a great tutorial for constructing a genetic map:
Let’s See a Demo!

9. This powerpoint, the sample data files, and the R code can be found on the journal club wiki.
Any questions?