Review two point and three-point mapping:

• Imagine the testcross aabb x AaBb gives the following results:
• A-B- 70
• A-bb 20
• aaB- 25
• aabb 85
• Total = 200

Are these genes linked? If so, How far apart are they?

You should be able to do this one easily. Make sure you know:

• Why is a test cross needed?
• What is the genotype of the heterozygous parent? (i.e. which alleles are on the same chromosome in the parent?)
• The offsping represent those from gametes that are either parental or recombinant-which ones are which?

If that is giving you trouble, try drawing the chromosomes of the two parents, and figure out what kinds of gametes can be produced, with and without recombination. Then combine the gametes to produce offspring, and figure out which phenotype they will have.

Three point crosses let you find gene order and distance

Here is a test cross between a triple heterozygote and a triple recessive tester, AaBbCc x aabbcc

What offspring phenotypes do you expect if the loci are unlinked?

Remember these steps:

1. Find the pairs of reciprocal types
2. • each crossover event produces a pair of gametes with complementary alleles, e.g. dnA and DNa; draw that out for youself if that is not obvious
3. Figure out which are the parentals, single recombinants, and double recombinants
4. There should be 8 classes for 3 genes (2ⁿ; some classes may be missing, especially if they are rare)
5. Use the double recombinants to find the middle gene
6. • it is the one that changes place when you compare the double recombinant to the parental types).
7. Estimate the recombination fraction between pairs of loci (= % single + double crossovers)
8. • If it is hard to figure out which single crossovers corresond to which pair of genes, re-label these data with the correct gene orders, then draw out the chromosomes with a single crossover and figure out which kinds of gametes are produced.
   • Remember that you have to include the double crossovers too, because they, too, have a crossover in that interval.
9. Draw the linkage map

Here are the example data that we used in class: (remember that these are offspring phenotypic classes)

d a n	293
d a +	21
d + n	131
d + +	55
+ + +	302
+ + n	24
+ a +	124
+ a n	50
Total = 1000

We spent a fair amount of time on this one in class. Make sure you understand it.

Interference

• You can predict the frequecy of double crossovers: it should be the product of the two single crossovers
• • R(abc) = R(ab) * R(bc)
• Often the observed number is less than expected due to interference.
• • The presence of one crossover makes it less likely to have a second one nearby.
• Coincidence coefficient (CC)= observed double crossover / expected double crossovers
• • Interference is 1-CC
• In Drosophila, there is complete interference (no double crossovers) to about 10 cM; in yeast, only partial interference at even short disantces (eg 50% At 3 cM)
• There is essentially no interference beyond 20 or 30 cm in most organisms

Predicting phenotypes in crosses with linked genes

• In maize, the genes gl and r1 are 20 cM apart on Chromosome 10. What are the expected phenotypic classes in the cross:
• • gl r1//gl r1 X gl r1 // + +
• You can also use the mapping concept 'in reverse' to predict the phenotypes of offspring when genes are linked. To get started, first figure out what happens if the loci are independent (as we have done before) and then again if there is zero crossing over. Finally, figure out the proportion of each gamete type (and thus offspring phenotypes) when there is crossing over.

• What would you expect if the map distance was zero?
• What would you expect if they were unlinked?

Meiosis, once again . . .

To make sure you are comfortable with this, draw the cells and chromosomes in meiosis I and II, for each scenario

• What are the gametes produced by the heterozygous parent (gl r1/+ +)?
• Do it with and without crossing over
• What do those chromosomes look like after meiosis I and meiosis II?

Maximum recombination frequency is 50%

• For well-separated genes (far enough that at least two crossovers occur) there will be on average 50% recombination.
• We skipped this because there wasn't enough time, but you book makes it pretty clear. In short, there are various types of double crossovers that are all equally likely to occur, but they average out to 50% recombination. See figure 13.8 in your book.
• Types of double crossover:
• • 2 chromatid: 0 apparent recombinants
  • 3 chromatid: 50% apparent recombinants
  • 4 chromatid: 100% apparent recombinants
  • Average is 50%

Various types of maps

• Genetic vs Physical maps
• There may only loose correlation between the two distances
• Recombination is not exactly equal along the chromosome
• • Heterochromatin (e.g. near the centromere) has much lower recombination
  • We looked at a diagram of a Drosophila chromosome where the middle third is heterochromatin. Maximum recombination within either end is about 50%, but there is only 3% recombination within the centromere heterochromatic region. Therefore two genes on opposite sides of the heterochromatic region would appear tightly linked even though they are physically far apart.

How does recombination actually happen?

Holliday model:

• Single strand break
• One strand invades the other helix to form a heteroduplex
• The junction migrates along the chromosome
• Eventually snipped apart
• May be cut "horizontally" or "vertically" to yield different types of recombinant chromosomes
• See Box. 13.1 Model of branch migration

The critical take home message of this model is that recombination is a well-coordinated event. Specialized enzymes cut the strands and direct the branch migration, etc.

Mitotic recombination

It happens occasionally, but it is very rare. . . .

See p.364-8 in your book.

Back to Mendel

• Why didn't any of Mendel's genes show linkage? Linkage would have messed up his principle of independent assortment.
• Peas have only 7 chromosomes
• He published data on 7 traits . . .
• we now know that two were on Chr 1 and three were on Chr 4
• Fortunately, most are far enough apart to appear unlinked
• One pair (smooth pod vs tall plants) is closely linked, but he didn't publish those data!