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Table: Molecular marker segregation patterns in different segregating populations
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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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In summary, a genetic linkage map represents the distance between a lot of genes/markers along the chromosomes of an organism.
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A segregating F2 population was made and the segregation pattern of in total 589 SNP markers were determined. Markers that were difficult to score of had identical segregation patterns were removed. From this dataset a genetic linkage map with molecular markers was calculated using JoinMap 4.1. Markers that were difficult to score were removed from the dataset and markers that showed an identical segregating pattern were considered as derived from the same place (locus) on the chromosome and only one was taken. Finally, 589 markers could be used to construct a genetic or molecular linkage map. An example of a linkage map of chromosome 6 of potato is given below.
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linkage map of potato chromosome 6 is according to van Os et al. (2006). Click to enlarge
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4.8 Can you determine the order of the following genes, L, R, S, based on their recombination frequencies?
R-S: 29,4 %
R-L: 35 %
S-L: 7,8 %
4.9 What is the order and distance of the genes A, B, C, D and E based on the recombination frequencies?
A,B 50 %
A,C 15 %
A,D 38 %
A,E 8 %
B,C 50 %
B,D 13 %
B,E 50 %
C,D 50 %
C,E 7 %
D,E 45 %
Note: If the recombination frequency is 50% it means that the markers/genes are unlinked. This means they are located on different chromosomes or very far apart from each other on the same chromosome.
4.10 A genetic map consists usually of several chromosomes. How many chromosomes can you find in this dataset? What is the order and distance of the makers on these chromosomes.
A,B 50 %
A,C 17 %
A,D 50 %
A,E 50 %
A,F 12 %
A,G 3 %
B,C 50 %
B,D 2 %
B,E 5 %
B,F 50 %
B,G 50 %
C,D 50 %
C,E 50 %
C,F 7 %
C,G 19 %
D,E 7 %
D,F 50 %
D,G 50 %
E,F 50 %
E,G 50 %
F,G 15 %
4.11 Now calculate the recombination frequency yourselves and construct a linkage map based on the data from the molecular dataset on the next page.
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4.14 In the picture below the difference is shown between the genetic map (x-axis in cM) and the physical map (y-axis in Mb – Megabases). Can you calculate (estimate) the number of bases per cM for the first 50 cM, in the centromeric region and in the last 80 cM. How large is the region in cM and Mb where there is hardly any recombination? Many markers have been determined in this region but in the picture we see only one. It appears that there is only one marker because all identical segregating markers minus one have been removed from the data set.
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