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Genetics: Gene Linkage
We know come back to the topic of Mendel's assumption regarding genes: That they are not linked together in any way. It turns out that many genes in fact are linked together. Independent assortment may not always be the case.
Linkage
Linked genes can be separated by "crossing over"
- Cytologically - To form chiasmata
- Genetically - To form recombinants
Much of our analysis will be to determine how linked together certain genes are and thus how likely it is for them to crossed/swapped/separated. What if the observed is so different from the expected, that the Chi-Squared analysis does not work? (seeGenetics: Mendelian Genetics) This is probably the result of gene linkage. We can determine the degree of how much certain genes want to stay linked together. For these analyses, it can be assumed that linked genes are on the same stick of DNA.
When crosses happen with linked genes, less than 50% of the offspring are recombinants. Most of the genotypes observed contains the same unaltered chromosomes from one of the parents. These are referred to as parental. A low frequency of recombinant offspring suggests gene linkage.
For 2 linked genes the frequency is:
\begin{equation*} Frequency = \frac{Recombinants}{Total} \end{equation*}This yields the frequency in units of Morgans. If the frequency was 0.18 Morgans, that means the genes will be separated 18% of the time.
Use notation such as $AB/ab$ to denote genes linked on DNA. When offspring receive these chromosomes it is refered to as coupling. When offspring receive separated/recombinant chromosomes, $Ab/aB$, it is referred to as repulsive.
Three Linked Genes
There are now 8 chromosomal possibilities with 3 linked genes. If sex-linked, and father has recessive, that is the only chromosome he can give. Most of the offspring will receive chromosomes from the mother as is. Two biggest observed numbers are the parental classes. The rarest event is a double crossover in the gene. Sometimes, it is important to note, that none of the offspring have this genotype.
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Determine the order of the genes on the DNA since gene order is often not certain.
- Can be found by comparing the double crosses with the parental chromosomes. The only different gene when comparing them is the gene that come in the middle. The order is then found.
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Calculate distances between genes in Morgans
- Only look at two genes at a time. Ignore the other one.
- Add up numbers of observed genotypes where the two observed genes are the same as they are on the parental chromosome. Divide by the total to find the Morgans.
- To find total distance, add up all values from preceeding step.
- Find theoretical rate of double crosses by multiplying the two rates together for each single cross (from step 2)
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Find the actual rate of double crosses. Do this by:
\begin{equation*} Actual\;Rate = \frac{double\;crosses}{total} \end{equation*}You will find that the actual rate is always less than the theoretical rate. This is because of interference.
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Find interference by the following formula:
\begin{equation*} Interference = 1 - \frac{actual\;rate}{theoretical\;rate} \end{equation*}
Thus concludes the topic of gene linkage. I hope you can see how Mendel was revolutionary and successful in his hypotheses, yet did not account for certain cases in which certain genes are very close to each other on a given segment of DNA.