Biology 212 General Genetics Spring 2007Lectures 11 and 12: Linkage Mapping II and IIIReading Chapter 4 pp. 132-139Lecture Outline:1. Double crossovers2. Three factor linkageexample 1 (Table 4.1)3. interference4. Three factor mapping in Drosophilaexample 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. 4.13prior to double crossovers:a c ba c b+ + ++ + +after double crossovers:a c ba + b+ c 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 problems1- Use double crossovers to help determine gene orderExample 1: Three linked corn plant traitstrait 1lz=lazy (growth habit)Lz=wild type growthtrait 2gl=glossy leafGl=normal leafTrait 3su=sugary endosperm (seed kernel)Su=normal endospermCarry out a testcross of a heterozygote corn parent:Lz Gl Su x lz gl sulz gl su lz gl suProduce the progeny shown in Table 4.1Phenotype of testcross progenyGenotype of gamete from hybrid parentNumber of progenyWildtype Lz Gl Su 286Lazy lz Gl Su 33Glossy Lz gl Su 59Sugary Lz Gl su 4Lazy, glossy lz gl Su 2Lazy, sugary lz Gl su 44Glossy, sugary Lz gl su 40Lazy, glossy, sugary lz gl su 272Interpretation 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 determinewhich marker changes places.2Lz Gl Su Lz Gl sulz gl su lz gl Suparental types 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 glb. 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 classeso if the same then they are non-recombinanto if they are different, then they are recombinant and are used to compute the recombination frequencyi) lz to suLz Su parental typeslz suLz su recombinant typeslz Sucalculate the recombination frequency between lz and su:40 + 33 + 4 + 2/740 x 100 = 10.7% recombination10.7 map units separate lz and suii) su to glSu Gl parental typessu glSu gl recombinant typessu Glcalculate the recombination frequency between su and gl:59 + 44 + 4 + 2/740 = 14.7% recombination14.7 map units separate su and gl3lz su gl 10.7 m.u. 14.7 m.u.3. Interferenceinterference = when crossing over in one region interferes with crossing over in a neighboring regioncan use probabilities to determine the expected numbers of double crossoverscoefficient 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 Drosophilaexample 2 (Solved