Table of Contents

• Prequiz...
• When linked genes stay linked...
• 1: Punnett Square Redux
• 2: Here's Smiley
• 3: Smiley's First Punnett Square
• 4: But what if the genes are linked?
• 5: Some notation
• 6: Since the linked genes don't separate...
• 7: Here's another one to try
• 7a: Here's another one to try
• ...And when they don't
• 8: But life is not so easy
• 9: Here's how the Punnett Square gets more complicated...
• 10: An easy Question
• 11: How about a general rule?
• The math of crossing over
• 12: But how often does cross-over occur?
• 13: Fun with map units...
• 14: The farther apart the genes are, the more they act like they're unlinked
• Getting an earful
• 15: Putting it all together
• 16: Spock's Ears
• 17: Yoda's Ears
• 18: Recomb - Review

But life is not so easy

Life would be relatively easy if linked alleles would just stay put -- this is, if alleles on the same chromosome stayed on the same chromosome. If that was true, then each parent could only have 2 rather than 4 variations on their gametes, and the Punnett squares would be easy to figure out.

However, just because two alleles start out on the same chromosome does not mean they stay there! Chromosomes can and do break apart and exchange sections with each other. Once that happens, other possibilities for gametes also exist. This process is called crossover. (As opposed to the smiley face on the right, which is cross-stitch).

The key question is, how does crossover affect the proportions of offspring?

Let's use the Smileys as an example.

Here are the parental genotypes:	And here is the Punnett Square, assuming no crossover:
Mrs. Smiley ET/et Mr. Smiley ET/et	ET et ET ET/ET et/ET et ET/et et/et Phenotypic ratio 3:1

But what if crossover affected these two alleles in 1 out of 10 cases (or more formally, if the recombination frequency is 10%)?

First step: 1 out of 10 chromosomes are now cobbled together out of two pieces. These cobbled together chromosomes will form non-standard gametes. So 10% of gametes will be non-standard. Moreover, there will be 2 kinds of nonstandard gametes. So 5% of gametes will be the first non-standard type, and 5% of gametes second non-standard type.

On the other hand, 90% of chromosomes are 'standard', and these will split evenly into two kinds of standard gametes.

Disclaimer: The movie does NOT depict the process of meiosis, which is more complicated. To be more specific, the replicated chromosomes, shown here, could not have all 4 alleles at the same time. The movie is just a way to rationalize the proportions of different kinds of gametes that result from recombination.

This means the Punnett Square gets considerably more complicated again...