5.1 - Linkage

Gametic phase or phase

Phase represents the allele combinations that were inherited from each parent

Phased does not mean

linked

Linkage leads to more ___ phases in offspring

parental

Parental/non-recombinant/coupled/in phase

The phase in the gamete matches the phase in the parent

Non-parental/recombinant/in repulsion/ uncoupled/ out of phase

The phase in the gamete is different than the phases in the parent

Thomas Hunt Morgan

• Linkage in fruit flies

• Observed that sometimes inheritance of separate traits wasn’t always random and that there were “non-parental” gametes, and suggested that chromosomes may be recombining

Who were the unsung heroes?

• Harriet Creighton and Barbara McClintock

• Discoverers of Recombination, 1932

Linkage analysis

test cross for linkage

When are you going to deploy a linkage analysis?

To understand when two different genes are linked to one another

Chi-squared test for independence

• Asks if two variables/ variance is independent of one another

• “You want to know if gene X and gene Y show evidence of linkage; what test is appropriate?”

• Will typically be in questions focused on linkage and will use “evidence of linkage” or “are inherited independently” or “show evidence of independent assortment”

Chi-squared test for goodness of fit

• Asks if a single categorical variable matches an expected distribution

• “You expect 25% of each type of offspring, you observe 108,123, 99,111. How would you determine if this fits expectations”

• Will typically be embedded in larger question

If multiple expected or observed values are <5 then assumptions are…

not met and test invalid

Mapping multiple genes with recombination frequency creates…

chromosome maps

Why does the recombination frequencies not add up?

• If double cross-over occurs between two genes, recombination (of those two genes) will not occur

• This leads to underestimates of genetic distance if the genes are relatively far apart

• More genes will allow us to more accurately measure distance

Two strand double crossover has…

0% detectable recombinants

What does more genetic markers increase?

Accuracy of genetic distance measures

Three factor crosses allow…

the ORDER of genes on a chromosome and map distances to be determined

Reciprocal classes

• Recombination happened in the same region

• Should have similar number of offspring since they are created by crossing over in the same area and have the same probability

How to calculate map distances in a three factor cross?

1. Write genes in the correct order

2. Group reciprocal classes

3. Add and divide by total

4. Make a map

Cytogenetic Map

shows positions on chromosomes based on cytological features

Genetic Map

shows relative positions of genes (or SNPs) based on how frequently recombination between them occurs

Physical Map

based on DNA sequences

Genetic and Physical maps can be…

different