Linkage Mapping

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Linkage groups: genes on the same chromosome are part of the same linkage group.

Linkage: genes in the same linkage group may or may not show linkage.

If genes in the same linkage group are close together they will show linkage

If genes in the same linkage group are far apart they will no show linkage.

The distance between two genes is directly proportional to the chance of recombination (crossing over) between them.

Crossovers produce genetic diversity and can be complex

Linkage mapping

As the distance between two genes is proportional to the chance of crossing over between them:

the frequency of crossing over between two genes is directly proportional to the distance between them

the frequency of offspring with non-parental (recombinant) combinations of alleles at two genes is equal to the frequency between them and therefore the distance between them.

Map distance = (number of recombinant offspring/ total number of offspring) x 100

The units are %, map units (mu) or centiMorgans (cM)

Calculating intergenic distances

Look at the recombination in a single parent to simplify. Perform a testcross with a heterozygote parent and corresponding homozygous recessive. Recombination during meiosis can only generate variation in the heterozygous parent.

Non-recombinant progency are always the most abundant phenotype, recombinant progeny have unexpected phenotypes and are present at lower frequency.

Not much information can be gained from looking at two loci, investigate at least 3 genes in a single cross.

Recombinants from double crossovers are the rarest.

% recombinace and map distances don't add up as above 50% recombination frequency genes behave as unlinked.

As the distance between genes increases the probability of mulitple crossovers increases. An even number of crossovers between genes maintains the genes on the same chromosome therefore the number of recombinants observed is always lower as distance increases

20%-50% recombinants the number of recombinant is significantly less than the number of crossovers

50% recombinants, the number of crossovers is not determinable

Interferance

This is when a single crossever event affects the probability of a second crossover occuring in that vicinity. Quantified by calculating coincidence (C):

C= observed number of double crossovers/expected number of double crossovers

Interferance (I) is expressed as:

I=1-C

it gives the percentage of crossovers that didn't occur. Positive interferance gives a positive value, negative interferance gives a negative value is when a crossover enhances the probability of a second crossover occuring nearby.

Other chromosomes mapping methods

Cytogenic mapping: physical location

Molecular location: based on DNA sequence numbering. Human genome project. Gene position can be defined exactly in term of base pairs allows detailed knowledge of the relationship between genes

Traditional genetic markers

Modern genetic markers