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Classic Mendelian Traits:

- Single locus
- Two alleles
- Generally two phenotypic classes (or three classes in the case of partial dominance)


Quantitative/complex traits:

- Polygenic or many 'quantitative trait loci: QTLs'
- Trait value often partially influence by environment
- Continuum of phenotypic classes ('continuous variation')
- Often exhibit a normal distribution


Quantitative traits are important in:

- Complex disease (risk factors, genetics, environment, genetics)
- Agricultural traits (production and yield characters and their trade-offs)
- Evolution (what maintains variation?)


QTL mapping experiments utilise:

- Genetic/linkage mapping and molecular markers
- Without recombination, relying on independent assortment


In an experiment using drosophila bristles on the sternopleural and abdominal body segment pre-molecular markers were used because..

- limited to model organisms/phenotypic markers
- Model traits
- Balancer chromosomes/No recombination in Drosophila males


In order to map polygenes to a chromosome two fly strains were used. They were

- Low score (with a phenotypic marker, unrelated to the trait but still attached)
- High score (selected for)
- Perform a backcross with F1 to the selected stain (assuming bristle related genes are recessive).
- Take sons of F2 and determine which chromosomes contain genes contributing to this trait.


Phenotype score:

- A tally of the number of offspring that contain a particular genotype..
- ABC, AB+, A+C, A++, +BC, +B+, ++C, +++


How do you tell which flies have bristle loci?

- Look at which genotype shows no difference when graphed on phenotype score.
- There is no bristle loci on the chromosome that has no effect on the bristle number.


Can also calculate the effect (in addition to the position):

- The effect of substituting c with + is __
- The effect of substituting b with + is __
- The effect of substituting a with + is __
- We must also make sure this is statistically significant


Students t-test

- Compares two populations with
- Assumes variation in both populations are normally distributed
- Ho: the means of the two populations are the same
- P=0.05, means that the probability that the null hypothesis is true and you get this result is 1/20. This is sufficiently rare that we reject the null hypothesis.


To map within a chromosome we need:

- Recombination
- Markers
- Maps


Physical map:

- Composed of nucleotide sequences (eg. restriction sites, contigs of clones, nucleotide sequences) where distance is measured in base pairs


Cytological map:

- Composed of chromosomal features (eg. puffs, bands), an example if the polytene chromosomes of Drospohila which are divided into 'divisions' and 'bands'.


Linkage/genetic map:

- Composed of polymorphic markers where distance is measured from recombination fractions (cM)


Recombination frequencies are not additive:

- We only 'see' recombination if there has been an odd number of recombination events between the markers we are looking at.
- To see recombination between A and C you can have either recombination between A and B, or B and C.
- rAC = rAB(1-rBC)+(1-rAB)rBC


Haldanes mapping function:

- Accounts for double crossovers
- Let c be the actually recombination distance between markers
- We estimate c from the observed recombination fraction (r)
- c+-1/2In(1-2r)