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How to Make a Genetic Map

How to Make a Genetic Map. Jason Morales Department of Agronomy Purdue University. Review. What is the difference between a genetic map and a physical map? A physical map is the sequence of nucleotides in the genome.

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How to Make a Genetic Map

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  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 Distance A a A a X 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 Distance a A A a a A a A X 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: http://www.rqtl.org/tutorials/geneticmaps.pdf • Let’s See a Demo!

  9. This powerpoint, the sample data files, and the R code can be found on the journal club wiki. • http://ala.genomics.purdue.edu/User:amorales/Plant_Breeding_and_Genetics_Journal_Club • Any questions?

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