1. Mapping Basics MUPGRET Workshop June 18, 2004

2. Randomly Intermated P1 x P2  F1  SELF F2 12 3 4 5 6 7 …… One seed from each used for next generation Recombination. After recombination self to create line.

3. Randomly Intermated. Very high resolution. Accumulates recombination events across generations and fixes them. Excellent for fine mapping Only homozygous genotypes.

4. Population Size Dependent on type of population Generally 200-300 individuals If doing trait analysis, the number of individuals determines the maximum number of QTL you can find. Two samples from the same population will produce different maps because they sample different gametes.

5. Genetic Mapping Basics Gene: a particular sequence of nucleotides among a molecule of DNA which represents a functional unit of inheritance. (Johannsen, 1909) Locus: the position of a gene on a chromosome or a genetic map. (Morgan, Sturtevant, Muller, and Bridges, 1915)

6. More terminology Linkage: the association in inheritance of certain genes and their associated phenotypes due to their being localized in the same chromosome. (Morgan, 1910) Linked: two genes showing less than 50% recombination.

7. More terms Recombination: Any process which gives rise to cells or individuals (recombinants) associating the alleles of two or more genes in new ways. (Bridges and Morgan, 1923) Recombinants are the end products of exchange of alleles from parental types as a result of crossing-over.

8. Terminology Phenotype: the observable properties of an organism, produced by the interaction between the organism’s genotype and the environment (Johannsen, 1909). Genotype: the genetic constitution in respect to the alleles at one or a few genetic loci under observation. (Johannsen, 1909).

9. Recombination Parental Recombinant

10. Recombination and Mapping Assume the frequency of crossing-over is equal along the chromosome. Two genes that are very close to one another will have a lower likelihood of having a cross-over between them than two genes that are far apart.

11. Recombination and Mapping So, we can determine the relative distance between genes by counting the number of recombinant genotypes for each pair of genes. – Lots of recombinants = far apart – Fewer recombinants = close together

12. Two Point Analysis Parental Types Tall, Green 42 Short, White 39 =81% Recombinant Types Tall, White 7 Short, Green 12 =19%

13. Map Units 1 map unit is equal to 1% recombination. Map units are also called centimorgans after geneticist Thomas Hunt Morgan who won the Nobel Prize for discovering how chromosomes govern inheritance.

14. Challenge How do we merge the information about each pair of genes together into one common framework? How do we order the genes relative to one another?

15. Three-Point Analysis Single cross-over ABC ab c Double cross-over

16. Double cross-overs and Map Distance If we only look at the outer markers A and C on the previous slide, we will underestimate the true distance between them because we have not accounted for the double cross- overs.

17. Three-Point Analysis Distance = # Singles +2 * Doubles Total If cross-overs are equally likely along the chromosome and closer genes have few cross-overs, then the likelihood of two cross-overs close to one another would be small.

18. Double cross-overs So mapping algorithms can order genes by minimizing the number of double cross- overs.

19. Maximum Likelihood Method Gives an estimate of the distances and the relative orders of the loci which would maximize the probability that the observed data would have occurred.

20. BHBBAHBHHBHHBHB umc157 HHBBABBHHBBBBAB umc76 BHBBABHAHHBHBAB asg45 BHBBABBAHHBHBAB zb4 BHBBHBHAHHBHBAB csu3 How Maximum Likelihood Works

21. BHBBAHBHHBHHBHB umc157 BHBBABHAHHBHBAB asg45 HHBBABBHHBBBBAB umc76 BHBBABBAHHBHBAB zb4 BHBBHBHAHHBHBAB csu3

22. MapMaker Mapping program that uses maximum likelihood method. Initially calculates what is linked (< 50% recombination).

23. MapMaker Works one linkage group at a time. Randomly picks two genes with the group and calculates the distance between them. Adds another gene from the group and determines the correct placement by using maximum likelihood to minimize the double cross-overs.

24. MapMaker Does this by calculating a LOD value for the placement of the gene in each of the intervals. Accepts the placement with the highest LOD value. Can be used for molecular markers or for trait data.

25. LOD Log likelihood. LOD = log 10 (Probability that the observed data would have occurred /probability that the gene is unlinked).