1. Experiments in Plant Hybridization (1865) by Gregor Mendel Bad title! People forgot about me and my work!

2. Pedagogical Objectives Bioinformatics/Neuroinformatics Unit Introduce bioinformatic tools Introduce QTL analysis Review of genetics Review/introduction of molecular techniques Review/introduction of statistical analyses and concepts

3. Bioinformatics/Neuroinformatics Unit—Specific steps Quantify phenotype—olfactory bulb volume Remove error variance –Due to differential shrinkage of brains –Due to multiple raters –Due to extraneous variables--demographic characteristics (eg. Sex, age, body weight, brain weight) and other individual differences.

4. Bioinformatics/Neuroinformatics Unit—Specific steps Link remaining variance to chromosomal markers—define region of interest on a chromosome(s) Determine genes at these markers Determine at least one gene that is either highly expressed or quite down-regulated In-depth examination of gene

6. Bioinformatics/Neuroinformatics Unit—Specific steps Link remaining variance to chromosomal markers—define region of interest on a chromosome(s) Determine genes at these markers Determine at least one gene that is either highly expressed or quite down-regulated In-depth examination of gene

8. Bioinformatics/Neuroinformatics Unit Link remaining variance to chromosomal markers—define region of interest on a chromosome(s) Determine genes at these markers Determine at least one gene that is highly expressed In-depth examination of gene

10. Bioinformatics/Neuroinformatics Unit Link remaining variance to chromosomal markers—define region of interest on a chromosome(s) Determine genes at these markers Determine at least one gene that is either highly expressed or quite down-regulated In-depth examination of gene

11. In what cell layers is gene expressed.

12. Entrez gene for sequence info including coding sequence

13. Go find an article on your gene, write up a 1 page summary, and attach article and summary to your lab report

15. This lecture Definition of terms Description of phenotype Description of recombinant inbred strains from which our phenotype will be measured Description of chromosome mapping

16. Phenotype vs. Genotype A phenotype is any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, or behavior. The genotype represents its exact genetic makeup — the particular set of genes it possesses. Two organisms whose genes differ at even one locus (position in their genome) are said to have different genotypes.

17. And now, a little

18. Qualitative vs Quantitative Traits Qualitative Traits Influenced by a single gene Typically follow simple patterns of inheritance Phenotypes fall into distinct categories (nominal scale) Trait expression is typically unaffected by environment Quantitative Traits Influenced by multiple genes, perhaps interacting genes Do not follow simple patterns of inheritance Phenotype is measured on continuous scale (interval scale) Trait expression may be affected by environment

19. Many biological and psychological traits are normally distributed, in other words, polymorphic--influenced by several alleles, possibly by several genes.

20. Definition of an Allele is one member of a pair or series of different forms of a gene Can be one, two or many alleles (different forms) of a gene in the population (individuals can have 2 different forms of a given allele in vertebrates). Homozygous—both chromosomes have same version of gene Heterozygous—chromosomes have different versions of the gene.

21. Hey! You wanna Recombine DNA?

22. Hey! I never saw any evidence of recombination!

23. Gregor Mendel Describes laws of inheritance 1)Segregation of alleles --segregate into different gametes 2) Independent assortment of different genes.

24. F 0 Generation (Grandparents) Highly discrepant trait F 1 Generation Crossing F 1 with F 1 F 2 Generation A Mendelian Split!

25. Some human characteristics obey Mendelian rules, Huntington’s Disease for example.

26. What’s the evidence of recombination!

27. Let’s consider the case where there are more than 2 genes. From “The cartoon guide to genetics” By Larry Gonick, Mark Wheelis

30. During meiosis, the homologous chromosomes pair-up. In the case of the F 1 generation, that means The chromosome from mom gets back together with the chromosome from dad. In structures known as chiasmata, some of the DNA from the mom strain can end up on the dad chromosome and vice-versa-- RECOMBINATION!

31. So, now the gametes of the F 1 have some of the DNA from each F 0 strain. So, the F 2 generation will have a collage of the F 0 DNA

32. And now: how to make a recombinant inbred strain of mouse. Start with two already inbred mouse strains (so that they are homozygous in their alleles), that are quite discrepant (far apart) on the phenotypic trait of interest, and cross them.

34. C57Bl/6J (B strain) are less sensitive to some odors than are DBA (D strain) mice but have larger olfactory bulbs.

35. Now, you cross the F 1 generation together and the F 2 generation will have chromosomes with DNA that are a combination of the grandparental (F 0 ) strains.

36. Coutesy GeneNetwork http://www.webqtl.org/tutorial/ppt/index.html

37. Effects of Inbreeding Reduces heterozygosity Through many generations of inbreeding, alleles for a given gene will become homozygous. Once both alleles of a given gene are identical in both partners, they become trapped with no ability to return to heterozygous state.

38. The heterozygosity that appears in the first F 2 generation will disappear Fig. 2. Genotypes at a microsatellite locus on chromosome 5 (D5Mit294). The left lane is a DNA size standard, and the next two lanes are PCR samples from the parental strains B (higher band at 198 bp) and D (lowest band at 176 bp). Lanes 4 to 25 are the F2 samples. The bottom band—or bands, in the case of heterozygotes—define the genotype of each animal. The bands at the top of the figure are caused by DNA retained in the pipetting wells. Figure from work by G. Zhou (Zhou & Williams, 1997; see Detailed PCR protocols for mapping microsatellites. )

39. Decrease in Heterozygosity from Sibling Matings Generation 0 1 2 3 4 5 10 20 Remaining Heterozygosity 1.000 0.750 0.625 0.500 0.406 0.338 0.114 0.014

40. Now we have to get rid of all of that darn heterozygosity--we will do that by breeding brother-sister pairs together for 20 generations. Then we will have a single allele present for each marker within a given recombinant inbred stain. Across recombinant inbred strains, some will have the B allele and some will have the D allele at any given locus.

41. Ultimately, we will have phenotypic data on 33 different recombinant inbred strains. Several individuals will represent each strain.

42. I need a map to figure all this out, and chromosomes can be mapped!

43. Hey! We have at Least three maps! Chromosomal, linkage, physical.

44. Here’s a use for chromosomal maps: trisomy 21

45. Hey! We have at Least three maps! Chromosomal, linkage, physical.

46. Hey! We have at Least three maps! Chromosomal, linkage, physical. Linkage map is in centimorgans (cM).

47. Now that we have maps, we will examine a representative of each recombinant inbred strain and seeing if they have the B or D marker and placing this location on the map on every chromosome. (Note none of them will be heterozygous like some of these FIRST generation F 2 guys.)

48. QTL is good for detecting the approximate locus of multiple genes affecting a phenotype across all the chromosomes, except Y. This is a graph that displays the likelihood ratio statistic as a function of locus on the various chromosomes, which are numbered at top.

49. This is a PCR product for a marker— or Locus (remember Quantitative Trait Loci?) it is a small stretch of DNA that is different between the two different F0 strains. A marker is usually a microsattelite or a single nucleotide polymorphism (SNP).

50. BUT due to linkage, a given marker ought to be in or close to a given gene(s). A marker MAY be close to a gene on the chromosome where different alleles between the 2 strains that have a differential impact on the phenotype

51. QTL is good for detecting the approximate locus of multiple genes affecting a phenotype across all the chromosomes, except Y. This is a graph that displays the likelihood ratio statistic as a function of locus on the various chromosomes, which are numbered at top.

53. QTL is good for detecting the approximate locus of multiple genes affecting a phenotype across all the chromosomes, except Y. This is a graph that displays the likelihood ratio statistic as a function of locus on the various chromosomes, which are numbered at top.

54. I started with the phenotype, and so shall you. Your phenotype will be olfactory bulb size. (I’ll be back--but for now, I have to take a pea.)

57. This lecture Definition of terms Description of recombinant inbred strains from which our phenotype will be measured Description of chromosome mapping Description of phenotype