1. An Overview of Mouse Genetics
Mouse Genetics pg14

2. Reference Material
Mouse Genetics, Concepts and Applications Silver, L.M. Oxford University Press, New York, NY, 1995, pp
Genetic Variants and Strains of the Laboratory Mouse, 3rd Edition Edited by M. F. Lyon, S. Rastan and S.D.M. Brown. Oxford University Press,New York, NY, 2 Volumes, pp
F Rev RO-2

3. Reference Material (Out of Print; Often in Libraries)
The Mouse in Biomedical Research Edited by H.L. Foster, J.D. Small and J.G. Fox.Academic Press, New York,NY.4 Volumes.
Inbred Strains in Biomedical Research Festing, M.F.W. Oxford University Press, New York, NY.
Origins of Inbred Mice Morse III,H.C. Academic Press, New York, NY.
F Rev RO-2

4. Genetics I: From Fancy Mice to Mendel
Brief History of the Laboratory Mouse
Details and Definitions
Genetic Resources
Gene Mapping
Annotating the Mouse Genome
F Rev RO-2

5. Origin of the House Mouse
Mouse Genetics pg4

6. Geographical Ranges of Subspecies
Mouse Genetics pg21

7. Mouse Genetics pg19

8. Evolutionary Relationships Among Commonly Used Model Organisms

9. Mouse as a Model System
Small size: 25-40g (2, fold lighter than an average human)
Short gestation time: ~10 weeks from being born to giving birth
Breed well: ~5-10 pups/litter and an immediate postpartum estrus
Fathers do not harm young
Vaginal plug: timed pregnancies
F Rev RO-2

10. Mouse Genome 3 x 109 base pairs ~1450 cM ~2Mb/cM ~25,000 genes
Organized into 19 autosomes and the X and Y Chromosome
Chromosomes are acrocentric and show a continual decrease in size
F Rev RO-2

11. Biomedical p106

12. Genetic Resources Outbred Stocks Inbred Strains and Substrains
F1 Hybrids
Mutant Strains
F Rev RO-2

13. Outbred Stocks Genetically undefined
Bred to maintain a maximal level of heterozygosity in all animals
Long life spans, high disease resistance, large and frequent litters, low neonatal mortality, rapid growth, large size, CHEAP
Examples: CD1, Swiss Webster, ICR, NIH
Useful in experiments where genotype does NOT matter (biochemical purification, stud males)
Should NEVER be used in any breeding experiment because of the genetic uncertainty
F Rev RO-2

14. Inbred Strains All members of a strain are genetically identical
Bred by strict brother X sister matings for at least 20 generations (Note: ~3-4 generations/year; at least 5 years)
F Rev RO-2

16. Consequences of Inbreeding up to 20 Generations

17. Inbred pg 16
Beck J. A. Nat. Genet. 2000;21:23-25

18. Inbred pg 17

20. 26724 White Mice.

21. FVB/NJ
AKR/J
f26724 white Mice.
NOD/LtJ
BALB/cWt
MRL/MpJ

22. BALB/cWt Y- chromosome non- disjuction
AKR/J Lymphatic leukemia
BALB/cWt Y- chromosome non- disjuction
FVB/NJ Male pronucleus in fertilized egg is large
MRL/MpJ Lymphoproliferation
NOD/LtJ Diabetes

23. Substrains
Inbred pg 18

24. Simpson E. M. Nat. Genet. 1997;16:19-27
Nature Genetics May p21
Simpson E. M. Nat. Genet. 1997;16:19-27

25. Distribution of SNPs and Haplotypes on Chromosome 4
Job #35693.

26. F1 Hybrid Mice
Produced by crossing mice of two different inbred strains
Can be repeatedly produced as long as the parental strains exist
Heterozygous at all loci at which the parental strains differ
Genetically and phenotypically uniform
Do not breed true (F2 generation mice undergo recombination)
F Rev RO-2

27. Desirable Features and Uses of F1 Hybrid Mice
Hybrid vigor: Increased disease resistance, better survival under stress, greater longevity and larger litters than inbred mice
Useful for carrying deleterious mutations, in radiation research, and for bioassays of pathogens, hormones, drugs, etc……….
Accept transplants of tissue (tumors, skin, ovaries) from mice of either parental strain.
F Rev RO-2

28. Some Common F1 Hybrid Strains
Handbook ..Jak Mice p49

29. 26724 Blk Mice.

30. bgJ
26724 Blk Mice.
white
nose
Aw-J me
c2J

31. “A Mutation” What is it?: A variation from wild-type at a single locus
Mode of origin: Spontaneous or induced (Chemicals, Radiation, Gene Modification)
Mode of inheritance: dominant, semidominant, recessive (or not heritable)
Penetrance: complete or incomplete
Interaction with other mutations
F Rev RO-2

32. Some Practical Information about Mutations
Mouse Gene Symbols: always italicized (or underlined), assigned by the International Mouse Genetics Nomenclature Committee, change often
Example: Dom; rec
Serialization: Dom1, Dom2; rec1, rec2
Alleles of the Same Locus: Dom1a, Dom1b
Special rules for pseudogenes, transgenics, etc..
F Rev RO-2

33. A Wealth of Information at….
The Jackson Laboratory Home Page:
F Rev RO-2

34. Mutant Strains
Coisogenic/Isogenic: mutation arose on an inbred strain and is still maintained on the strain of origin (C57BL/6J-M)
Congenic: constructed by transferring a chromosomal segment carrying a locus, phenotypic trait, or mutation of interest from one strain to another by 10 or more successive backcross matings (B6.C-H-2d)
F Rev RO-2

35. Mouse Genetics pg35

36. Biomedical p98

37. Genomic Homogeneity and Heterogeneity During the Creation of a Congenic Strain

38. Average Length of the Differential Chromosomal Segment During the Creation of a Congenic Strain

39. Why Make Congenic Strains?
Evaluate phenotype of a mutation (single gene trait) on one or more well defined genetic backgrounds
Can be very useful in the analysis of complex traits
F Rev RO-2

40. The Egfr (ko/ko) Example- Phenotype Dependent on Genetic Background
Peri-implantation lethal on a CF background due to degeneration of the inner cell mass
Mid-gestation lethal on a 129/Sv background due to placental defects
Survive up to weaning with abnormalities in many organs on a CD-1 background
Treadgill et al., Science:269, ,
F Rev RO-2

41. Nature Genetics Nov p280a

42. Nature Genetics Nov p281

43. Nature Genetics Nov p280a
Markel P. Nat. Genet. 1997;17:

44. Consomic Strains
Very similar to congenic strains except that selection is for a whole chromosome instead of a chromosomal segment
A set of consomic strains with each A/J chromosome on a C57BL/6J background have been constructed
Particularly useful for the analysis quantitative trait loci (QTL’s) and modifier loci
Singer et al., Science: 304, , 2004
F Rev RO-2

45. Recombinant Inbred Strains
Inbred pg 7

46. Recombinant Congenic (RC) Strains
Similar to RI strains, initial cross is between two distinct inbred strains
Next two generations are made by backcrossing without selection to one of the parental stains
Next 14 generations of brother x sister matings are performed
Mosaic genomes skewed in the direction of the backcross parent (7/8 versus 1/8)
F Rev RO-2

47. Gene Mapping-Definitions
Locus - a DNA segment that is distinguishable in some way by some form of genetic analysis (gene, anonymous DNA, etc…)
Genetic map - a representation of the distribution of a set of loci within a genome (linkage, chromosomal, and physical)
F Rev RO-2

48. Why Map Genes
Facilitate moving from disease phenotype to cloning the causative gene(s) (positional cloning)
Can provide function for a recently cloned gene
Can be used to dissect out the heritable and nonheritable components of complex traits
Comparative genetics
F Rev RO-2

49. Linkage Maps Also known as recombination (meiotic) maps
Can only be constructed for loci that occur in two or more heritable forms or alleles
Are generated by counting the number of offspring that receive either the parental or recombinant allele combinations at two or more loci
F Rev RO-2

50. Where Genetic Recombinants Come From

51. Independent Assortment of Alleles from Unlinked Loci
Mouse Genetics pg138 F-7.2

52. Non-independent Assortment of Alleles from Linked Loci
Mouse Genetics pg139 F-7.3

53. Gene Order A more popular way of looking at it:
White, circling, not pudgy
Pigmented, circling, not pudgy
Pigmented, not circling, pudgy
Gene order pu - c/Tyr - sh1 is derived from this
multipoint cross by parsimony (I.e., that in which there are few or not double-crossover events)
A more popular way of looking at it:
non- recombinant
recombinant pu
c, Tyr sh1
# mice 46 51 1 1 1
Heterozygous, or “b” allele inherited from F1 parent
Homozygous, or “a” allele inherited from pigmented parent

57. Live Linkage Map of the Mouse
10th International Congress of Genetics
Montreal, Canada

58. Inbred pg 40

59. Non-Meiotic Mapping Methods
Somatic cell hybrids
Radiation hybrids
in situ hybridization
F Rev RO-2

61. Biomedical p106

62. The Ultimate Physical Map
The sequence of the mouse genome
Public draft sequence (~96% of the euchromatic genome of C57BL/6J excluding the Y chromosome) released in December
Sanger Center is completing the sequence of chromosomes 2, 4, 11, and X
Page lab has sequenced part of the mouse Y
The rest?
F Rev RO-2

63. Functional Annotation of the Mouse Genome
Need: One or more independent mutations in every gene
Approach: Genotype to phenotype
Approach: Phenotype to Genotype
F Rev RO-2

64. Genotype to Phenotype Targeted mutations in each gene
Gene trap mutagenesis
Chemical mutagenesis of ES cells
Ultimately, must determine the phenotypic affect of the mutation, in vivo
F Rev RO-2

65. Targeted mutations Homologous recombination in ES cells
Advantages: can create exactly what you want;conditional or null allele, temporal regulation, point mutations, small deletions, etc.; tend to know a lot about the gene which can help with interpreting phenotype
Disadvantages: time-consuming and very expensive if all ~25,000 genes are to be mutated; must make assumptions about important functional domains
F Rev RO-2

66. Targeted mutations the future?
Development of simpler/faster methods for construct building-”recombineering” and high throughput analysis
The Sanger Plan--generate 10, , targeted mutations (probably conditional, not null) in a five year period; A FEW THOUSAND IN THE GERMLINE
Part of a larger European effort that will include a collection of null alleles, total exact numbers are unclear
US effort--discussion stage
F Rev RO-2

67. Gene Trap Mutagenesis A form of insertional mutagenesis in ES cells
Various vectors have been developed but all are designed to report the expression of the endogenous gene at the site of integration and provide a DNA tag for rapid identification of the disrupted gene
Lexicon:60% coverage of the mouse genome from 200,000 sequence tags
International Gene Trap Consortium (IGTC):32% coverage in 27,000 tags (variety of vectors may overcome insertion site preference); 20% do not overlap with Lexicon
F Rev RO-2

68. Gene Trap Mutagenesis
Advantages: IGTC clones are available without restriction (see Nature Genet. 36, , 2004); high throughput (1 new gene added every 35 tags); combination of vectors helps overcome integration site preference; like targeted mutations, insertions can be archived as ES cells, which is inexpensive
Disadvantages: Unclear what you have:null, hypomorphic, or neomorphic allele; most of the existing insertions have not been examined for phenotype, in vivo
F Rev RO-2

69. Gene Trap Mutagenesis the Future?
IGTC plans to add additional tags ( until ~ saturation)) to expand the pool of tagged genes freely available
IGTC plans on additional refinement of the technology (new vectors, post-insertional modification of trapped loci to create additional/desired alleles of a tagged gene)
Likely will be up to individual investigators to put the mutations in the germ line and phenotype mice
Toronto Component of the IGTC has done phenotyping on some of the animals
F Rev RO-2

70. Chemical Mutagenesis of ES Cells
Induce mutations in ES cells with ENU
A powerful chemical mutagen that primarily induces point mutations or small deletions
Correlate mutant phenotype with the affected gene
F Rev RO-2

71. Chemical Mutagenesis in ES Cells
Advantages: can directly screen for mutations in gene of interest and then make mice from the mutant cells;can create an allelic series of mutations, can also vary the mutagen to induce different types of lesions
Disadvantages: like gene traps, it takes some work to determine what type of mutation you have-null or hypomorphic
F Rev RO-2

72. Phenotype to Genotype Induce and select for a mutant phenotype
Map the position of the mutation-genome scan
Positionally clone the mutation
Correlate mutant phenotype with the affected gene
F Rev RO-2

73. ENU Mutagenesis, in vivo
A powerful chemical mutagen of spermatogonial stem cells
Primarily induces point mutations or small deletions
Can select for dominant, semidominant or recessive mutations; mutations can be gain or partial or complete loss of function
One mutation/locus in ~ gametes
F Rev RO-2

74. Enu Mutagenesis Projects
International effort-large scale, genome wide
Centers in England, Germany, Japan, Toronto (
Jax, Northwestern, Oak Ridge, Baylor and others
A few smaller genome wide efforts, as well-Sloan Kettering
F Rev RO-2

75. ENU Mutagenesis
Advantages-always have a phenotype, can select for particular organ system/stage of development/tissue type; can get hypomorphic alleles (new alleles of existing mutations)
Disadvantages-time consuming especially for recessive screens; works best with robust phenotypes;must go through a round of mapping but positional cloning is greatly simplified with the sequence of the genome;archiving and distributing the mutation is much more work than with ES cells
F Rev RO-2

76. Issues for both Approaches
Phenotyping
Databases
Distribution
F Rev RO-2