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Biology 212 General Genetics Lectures 11 and 12: Linkage Mapping II and III Spring 2007 Reading Chapter 4 pp. 132-139 Lecture Outline: 1. Double crossovers 2. Three factor linkage example 1 (Table 4.1) 3. interference 4. Three factor mapping in Drosophila example 2 (Solved problem) Lecture: 1. Double crossovers When genes lie far apart on the chromosome, more than one crossover may occur between them. Probability of multiple crossovers increases as map distance between two genes increases. Double crossovers may not be detected, thus recombination frequencies (and therefore genetic map distances) may be underestimated. Use of a marker between two distant genes makes it easier to detect double crossover types. See Fig. 4.13 prior to double crossovers: a a + + c c + + b b + + after double crossovers: a a + + c + c + b b b + Ability to identify double crossovers types is important to construction of three factor linkage maps. 2. Three factor linkage (=three point linkage) Maps of three genes (factors) Break down problem to series of two-factor linkage problems 1 Use double crossovers to help determine gene order Example 1: Three linked corn plant traits trait 1 lz=lazy (growth habit) Lz=wild type growth trait 2 gl=glossy leaf Gl=normal leaf Trait 3 su=sugary endosperm (seed kernel) Su=normal endosperm Carry out a testcross of a heterozygote corn parent: Lz Gl Su lz gl su x lz gl su lz gl su Produce the progeny shown in Table 4.1 Phenotype of testcross progeny Wildtype Lazy Glossy Sugary Lazy, glossy Lazy, sugary Glossy, sugary Lazy, glossy, sugary Genotype of gamete from hybrid parent Lz Gl Su lz Gl Su Lz gl Su Lz Gl su lz gl Su lz Gl su Lz gl su lz gl su Number of progeny 286 33 59 4 2 44 40 272 Interpretation of results and construction of a linkage map: The two most frequent class identify the non-recombinant (parental) gametes. The two rarest classes identify the double crossover gametes. The remaining classes are single crossover gametes. a. What is the order of the three genes? Compare the genotype of the most frequent class to the least frequent class and determine which marker changes places. 2 Lz Gl Su lz gl su parental types Lz Gl su lz gl Su double recombinant types The Su/su alleles have exchanged places on the chromosomes in the double recombinants. Therefore the su gene is between the lz and gl genes: lz su gl b. What are the distances between the three genes? break up into a series of two-factor linkage problems compare the arrangement in the parental classes to the other classes o if the same then they are non-recombinant o if they are different, then they are recombinant and are used to compute the recombination frequency i) lz to su Lz lz Su su parental types Lz lz su Su recombinant types calculate the recombination frequency between lz and su: 40 + 33 + 4 + 2/740 x 100 = 10.7% recombination 10.7 map units separate lz and su ii) su to gl Su su Gl gl parental types Su su gl Gl recombinant types calculate the recombination frequency between su and gl: 59 + 44 + 4 + 2/740 = 14.7% recombination 3 14.7 map units separate su and gl lz su 10.7 m.u. gl 14.7 m.u. 3. Interference interference = when crossing over in one region interferes with crossing over in a neighboring region can use probabilities to determine the expected numbers of double crossovers coefficient of coincidence = observed number of double crossovers/expected number; gives a quantitative measure of interference; Interference = 1 - (coefficient of coincidence) Interference and graphs of mapping functions (Fig. 4.17) can be used to compute the actual map distances from the recombination frequencies. For short distances the recombination frequency = map distance. For long distances, need to know the extent of interference to correctly estimate map distance. In this course, we will use the additive distance of close markers to estimate the distance of more distal markers. 4. Three factor mapping in Drosophila example 2 (Solved problem--handout) 4 5