Topic 6, Linkage, crossing-over, and mapping in eukaryotes

1. Types of segregation of alleles of two loci
   A. Independent assortment
       1) Alleles of two loci are unlinked, they are transmitted independently of each other
       2) Segregation follows Mendel's fourth postulate (independent assortment)
       3) A dihybrid produces 4 types of gametes in equal frequencies
           a. Two gametes are parental types (non-recombinant types)
           b. Two gametes are non-parental types (recombinant types)
           c. The parental (non-recombinant) gametes and non-parental (recombinant
               gametes occur in equal frequencies.
       4) This is interchromosomal recombiantion
   B. Complete linkage
       1) Alleles of two loci are always transmitted together
       2) Segregation does not follow Mendel's fourth postulate
       3) A dihybrid produces only 2 types of gametes, both are parental types
       4) Symbolism:
           a. Commas are placed between genes that are linked
           b. Semicolons are placed between genes that are unlinked (assort independently)
       5) Cis configuration (coupling): in a dihybrid, both domiannt alleles are on one homolog
       6) Trans configuration (repulsion), in a dihybrid, one dominant allele is on each homolog
   C. Partial (incomplete) linkage
       1) Alleles of two loci are usually (greater than 50%) transmitted together
       2) Segregation does not follow Mendel's fourth postulate
       3) A dihybrid produces 4 types of gametes; however,
           a. The two parental types occur more frequently than the non-parental types
           b. This is intrachromosomal recombiantion
   D. Results of Bateson, Saunders, and Punnett (1905) in which they first observed incomplete linkage
   
2. Two-point linkage
   A. Thomas Hunt Morgan's dihybrid crosses in Drosophila melanogaster with X-linked loci
       1) Yellow body and white eye
       2) White-eye and miniature wing
   B. Mapping genes
       1) Alfred Sturtevant (1913), an undergraduate in Morgan's lab., used pre-existing data to construct the first genetic map
       2) Importance of genetic maps
   C. Mapping two autosomal loci in Drosophila melanogaster, purple eye and vestigial wing
   D. 1 % recombinants = 1 map unit = 1 centimorgan (cM)
   
   
3. Definitions:
   A. Chiasma (chiasmata = plural), what you see with a microscope
   B. Exchange (crossing-over), the process
   C. Crossover chromatid (crossover), the product
   D. Recombinant chromatid (recombinant); product with a new combinations of genes
   
   
4. Relationship between frequencies of recombinants and single-exchange tetrads
   A. The frequency of single exchange tetrads is twice the frequency of recombinants
   B. The frequency of recombinants is half the frequency of tetrads with a single exchange
   
   
5. Three-point testcrosses
   A. Three-point testcross #1 (with maize): Gl, Va, V
   B. Determining the order of the genes
       1) Method 1, determining the amount of recombination between each pair of genetic loci
       2) Method 2
           a. The most frequent two classes are usually the parental types
           b. The least frequent two classes are usually the double crossover types
           c. Comparing the alleles in the parental and DCO classes
               (1) The gene that is transposed (changed from dominant to recessive or vice-versa) is the middle gene
   C. Interference (the tendency for a crossover to inhibit the occurrence of other crossovers nearby)
       1) Determining the expected frequency of DCOs
       2) Determining the actual frequency of DCOs
       3) Types of interference:
           a. If there are fewer DCOs than expected, positive interference is present
           b. If there are more DCOs than expected, negative interference is present
           c. If no DCOs are present, complete interference is present
       4) Coefficient of Coincidence (C) = observed DCO/expected DCO
           a. Showing how interference is calculated using data from this cross
       5) Interference (I) = 1 - coefficient of coincidence
       6) Non-addetivity of genetic distances
           a. Due to undetected double-crossovers that occur between two genes
           b. Tetrads and additivity
               (1) If there are only non-recombinant and single exchange tetrads, all crossover chromatids are recombinant
               (2) If two exchanges occur between a pair of genetic loci, some crossover chromatids are non-recombinant
   D. Mapping relationships
   E. Types of multiple exchanges (2-strand, 3-strand, and 4-strand double crossovers)
   F. Three-point testcross #2 (with maize): Pr V Bm
   G. Three-point testcross #3 (with Drosophila): sc, ec, vg (sc and ec are linked, vg is unlinked)
   
   
6. Cytological proof of crossing over
   A. Creighton and McClintock with Zea mays (1931)
   B. Stern with Drosophila melanogaster (1931)
   C. Both studies used chromosomes that were marked genetically and cytologically
   D. Both studies found that when genetic recombination occurs, there is actual exchange of chromosome segments
   
   
7. Mitotic recombination (recombination in somatic cells between mitotic chromosomes)
   A. Stern's 1936 study
   
   
8. Sister chromatid exchanges (SCEs) = exchanges between sister chromatids of the same chromosome
   
   
9. Genetic analysis with tetrad organisms
   A. Full ordered tetrad analysis in Neurospora crassa (bread mold)
       1) Life cycle of Neurospora crassa
       2) Demonstration that recombination occurs at the 4-strand stage and involves 2 of the 4 chromatids (Lindegren 1932)
       3) Description of first vs. second division segregation asci
       4) Determining the distance between a gene and the centromere in Neurospora crassa (Lindegren 1932)
           a. The distance (in map units) between a gene and the centromere is 1/2 the frequency of second division asci
   B. Unordered tetrad analysis (Chlamydomonas, yeast)
       1) Parental ditypes (P), non-parental ditypes (NP), and tetratypes
       2) Expectations for two genes that are not linked (P = NP)
       3) Expectations for two genes that are linked (P > NP)
       4) Determining the exchange frequency between two linked loci
           a. (NP + 1/2 T)/total x 100
   
   
10. Somatic cell hybridization between mouse and human cells
    A. Human cells (with 46 chromosomes) and mouse cells (with 40 chromosomes) are fused to produce cells with 86 chromosomes
    B. The human chromosomes are lost as these cells divide in tissue culture,
         so eventually cell lines are produced that contain all of the mouse chromosomes and 1 or a few human chromosomes
    C. These cell lines are analyzed for the presence of proteins that are present in human but not mouse cells.
    D. If a specific human protein is present in a particular cell line, the human chromosome which has the gene
         that produces that protein is present in the cell line
    E. Using this approach, large numbers of human genes have been assigned to specific human chromosomes

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Updated 9/15/00