Chapter 5 Basics of Linkage and Gene mapping 45 Chapter 5 Basics of Linkage and Gene Mapping Julius van der Werf Basics of Linkage and Gene Mapping ......................................................................45 Linkage ....................................................................................................................45 Linkage disequilibrium ............................................................................................47 Mapping functions ...................................................................................................48 Mapping of genetic markers .....................................................................................50 Estimation of the recombination fraction ..............................................................50 Maximum likelihood estimation of linkage (recombination fraction).....................51 Testing for linkage: LOD scores ...............................................................................52 Design of mapping ...................................................................................................54 References............................................................................................................54 Linkage Two genes are said to be linked if they are located on the same chromosome. We assume that different chromosomes segregate independently during meiosis. Therefore, for two genes located at different chromosomes, we may assume that their alleles also segregate independently. The chance that an allele at one locus co-inherits with an allele at another locus of the same parental origin is then 0.5 and such genes are unlinked. parent 1 AABB x aabb parent 2 F1 AaBb (100%) F1-gametes AB Ab aB ab A and B are unlinked: frequency (%) 25 25 25 25 A and B linked: e.g. frequency (%) 35 15 15 35 A and B tightly linked e.g. frequency (%) 48 2 2 48 The chance that A/B or a/b co-inherit to the offspring is 0.5 in case the genes are unlinked. This chance increases if the genes are linked. We can observe a degree of linkage. The reason is that even if genes are located on the same chromosome, they have a chance of not inheriting as in the parental state. This is due to recombination. During meiosis, the chromosome often breaks and the rejoins with the homologue chromosome, such that new chromosomal combinations appear (indicated as crossover). In the example, the combination aB and Ab did not appear in the parental