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(tip: for practice to use the molecular notation, determine the segregation pattern in question 3.2 and 3.3)
Genetic linkage map
The SNP data in the segregating populations (also called mapping populations) can be used to make a genetic linkage map. A linkage map shows the position of known genes and/or genetic markers relative to each other on the different chromosomes. The distance between the genes/markers is given in terms of recombination frequencies, also denoted as centimorgans. These recombination frequencies are a result from crossovers between genetically linked genes/markers on homologous chromosomes during meiosis.
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First count the recombinants between two markers and calculate the recombination frequency per marker combination. Do this for each marker combination possible. Finally draw a molecular linkage map based on the recombination frequencies.
From recombination frequency to cM (centimorgans)
In publications the distance between the genes/markers is give in in centimorgans (cM). This unit of genetic linkage is named after Thomas Hunt Morgan. A distance of 1cM between two markers means that the recombination frequence was 1%.
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4.13 How many basepairs would that be on average? (for info see next page)
Comparison between genetic and physical maps
The chance for a crossover and thereby related estimate of the recombination frequency is not equal over the whole chromosome. In the lower figure on page 16 you see next to the genetic map (given in centimorgan) a physical map of the same chromosome given in basepairs), In the middle part of a chromosome (the centromere) there is hardly any recombination. Also, the frequency is much higher in the distal regions. This difference in recombination frequency is the reason that a genetic linkage map (based on recombination frequency) is different from a physical map (based on the number of bases between two recombination events).
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