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Lecture 5: "Linkage, Recombination & Mapping"

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Biology 2581B
Jim Karagiannis

Genetics Lecture No. 5: Linkage, Recombination & Mapping Wednesday January 23 , 2013 Recombination, Genetic Linkage, & The Chi Square Test: -Recombination is the sorting of alleles into new combinations and is within the realm of Mendelian genetics as it occurs during Independent Assortment. Four combinations results from recombination: 2 are parental (same arrangement of alleles as parents) and 2 are recombinant (carry a novel combination). Genetic linkage is a violation of Mendel’s Law of Independent Assortment as the resultant gametes deviate from the expected 1:1:1:1 ratio (more parental genotypes observed than recombinant). -We can use the chi square test to determine if the deviations from the expected 1:1:1:1 phenotypic ratio are due to sampling error, or if an underlying biological phenomenon is the cause. With the degrees of freedom being 3 (4 classes – 1), we conclude that the observed differences from the expected 1:1:1:1 ratio are not due to sampling error (we reject the null hypothesis), but some biological/genetic phenomenon is present. However a second trial with phenotypically identical parents gives converse phenotypic ratios in the progeny. What genotypic difference could account for these results and what is the underlying cause for the deviation from the expected ratio? Crossing Over, Synapsis & Reciprocal Changes: -In addition to the independent assortment of homologous chromosomes during meiosis, crossing over between two nearby loci on the same chromosome provides an alternate mechanism of deriving recombinants. Crossing over is thus the physical exchange of the arms of the chromosomes that results in the flipping of alleles (two hybrid chromatids). This process occurs during prophase meiosis subsequent to synapsis (homologous chromosomes become aligned and “zipped” together). The synaptonemal complex is a structure that helps align homologous chromosomes during prophase of meiosis I by literally zipping them together. Structures called recombination nodules are the site of exchange of parts between non-sister chromatids. Structure and function of recombination nodules are not very well understood, but the number and location of recombination nodules correlates with the number and location of crossover events. -Curt Stern demonstrated in experiments that recombination events can result from reciprocal changes between homologous chromosomes. He did this by isolating genes at two loci in Drosophila: car (mutant carnation of wild type red eye colour) and bar (mutant bar shape of circular shape eye). Whenever there was a crossover it correlated with the genetics and proved that crossing over definitely had something to do with genetics. Genetic Crosses & Linkage Notation: -Assuming two loci are on the same chromosome (linked genes) and that the arrangement of alleles is st different, we can describe our genetic crosses in linkage notation. The 1 trial cross is a cis dihybrid (AB__ab), while the 2 trial cross is a trans dihybrid (Ab__aB). In a cis dihybrid cross, parental genotypes are overrepresented and the recombination frequency is not that high (deficit of recombinant genotypes). In a trans dihybrid cross, parental genotypes are underrepresented and the recombinant frequency is high. So, in response to the two earlier que
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