1. Molecular Mapping

2. Terminology Gene: a particular sequence of nucleotides along 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)

3. Terminology Allele: one of two or more alternate forms of a gene occupying the same locus on a particular chromosome or linkage structure and differing from other alleles of that locus at one or more sites. ( Johannsen, 1909 ).

4. 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.

5. Terminology 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 product of exchange of alleles from parental types as a result of crossing-over.

6. Terminology Phenotype: the observable properties of an organism, produced by the interaction between the organism’s genotype and the environment. ( Johannsen, 1909 )

7. Terminology Genotype: the genetic constitution in respect to the alleles at one or a few genetic loci under observation. ( Johannsen, 1909 ) AA Aa aa

8. A a B b AB ab Ab a B Parental Type Recombinant

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

10. 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.

11. 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?

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

13. 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.

14. Three-point analysis Distance = # Singles + 2 ( # Doubles) Total

15. Double cross-overs If cross-overs are equally likely along the chromosome and closer genes have few cross-overs, then the likelihood of two crossovers close to one another would be small.

16. Double cross-overs If cross-overs are equally likely along the chromosome and closer genes have few cross-overs, then the likelihood of two crossovers close to one another would be small. So, mapping algorithms can order genes by minimizing the number of double cross-overs.

17. Mapping Maize at UMC Genetic mapping is based on DNA fingerprint data of offspring from two parents which differ in their appearance. Genetic mapping is based on DNA fingerprint data of offspring from two parents which differ in their appearance. Similar fingerprint data for two gene indicates they are physically close together on a chromosome. Similar fingerprint data for two gene indicates they are physically close together on a chromosome.

18. Scoring your gel Each parent A and B have different size DNA fragments. Progeny are either: A (homozygous parent A) H (heterozygous) B (homozygous parent B) Can also use a – if missing or not clear.

19. Molecular mapping Digest DNA Electrophorese - + Southern blot Hybridize with probe

20. Scoring data A B H H A B A H

21. Recombination and Mapping P Assume that the frequency of crossing- over is equal along the chromosome. P 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 very far apart.

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

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

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

25. SSR gel scoring ABAABAAAAABABBBBBABABBAB BAABAAABAAAAGBABAABBBBAA ABBGAABABABAABABBAAABBAB ABBBBAABBAAAABBBGBABABAB