Advanced Linkage Problems - Ordered Tetrad Analysis

Why was the mushroom the life of the party?

He was a fun guy. 💀

Idea creds @Delphinidin 

Joke creds @Danixx 

Advanced linkage problems are very hard to understand, and they’re a lot of fun. Let’s go over one kind: ordered tetrad analysis. Investigating this involves the use of a really cool organism, bread mold (Neurospora crassa). This organism is special because during meiosis and recombination, its chromosomes stay in order, so we can see the patterns of crossover. This can make for some fun problems.

Let’s first go over Neurospora’s life cycle. Ascospores of two mating types germinate, and the resultant cells fuse. Then, the nuclei combine in a process called karyogamy. This results in the formation of an ascus, which is a sac containing a cell with one complete nucleus with DNA from each mating type in it. The cell inside the ascus undergoes meiosis, which is comprised of two divisions (meiosis I and II), yielding four cells within the ascus. Following meiosis is a postmeiotic mitosis step, which basically splits each of those resultant cells into two via mitosis. Now, we have 8 cells in an ascus. Ascospores form by ordered grouping of these 8 cells into two-cell ascospores. Here’s a few visuals:

Don’t get confused by the meiosis I color split: remember that in meiosis I, homologous chromosomes randomly choose a side so it doesn’t matter what the image shows for that. What is important to remember is that Neurospora has ordered tetrads, so all the chromosomes stay in order when being grouped into ascospores. That’s the main concept.

This concept can be extended to recombination events, which occur during pachytene of meiosis I. Below is a comparison of normal ascospore formation, versus what the situation would look like after crossover:

satish petkar’s 1500 genetics problems🐐

Notice the 4:4 vs 2:2:2:2 ratio. This was due to the crossover in meiosis I, and the maintained order. The brackets to the left of the final 8-cell ascus reflect how the cells will be packaged into ascospores. Also consider: if the crossover was between the 1st and 3rd segment, or 2nd and 4th, then we’d have a 2:4:2 ratio because the adjacent 2’s in the center would be the same, so they’d be added in order.

For problem-solving, at the most thorough level, you’ll get something like this, which shows the pattern of cells in the ascus, and the frequency of each pattern:

You’ll be asked to find the recombination frequency. Notice that we’re only investigating one gene in ordered tetrad analysis. In unordered tetrad analysis, there’s 2 genes. For ordered tetrad analysis, we are essentially finding the distance between the gene and the centromere. The last 4 groups are recombinant, and the first 2 are normal. So RF is (5+3+4+2)/(40+46+5+3+4+2)x100%=14%. 

HOWEVER, we need to divide this by 2 to yield 7% because the RF calculated above is for both chromatids involved in recombination, so it’s the combined distance from both centromeres. Dividing this by 2 would yield the distance from centromere to gene on one chromatid.

Here’s a past USABO question on this:

2018 semis

The genes are on different chromosomes, so the RF is 50%. This means independent assortment occurs normally, and each combo occurs at a 25% rate. Each nucleus that would be produced is as follows, and like nuclei are in the same ascospore: AB, AB, ab, ab, Ab, Ab, aB, aB. So, one ascus is dark, and the rest are light; the answer is C. (key says E; lmk if that’s right but I think it’s scuffed).

EDIT! Creds @Delphinidin for helping me understand why the answer is indeed E and not C!

So basically, since A and B are on different chromosomes, the RF is 50%. This means that half of the asci will have a normal combo of 4 ascospores composed of 2 cells each (AB/AB, AB/AB, ab/ab, ab/ab) and half the asci will have the recombinant combo of 4 ascospores (Ab/Ab, Ab/Ab, aB/aB, aB/aB). In the first case, the first two ascospores are dark, and the last two are light. In the second case, all are light. This matches with E.

The error with my previous solution was that I thought each meiotic combo was one cell, and they were grouped into ascospores into one big ascus, while each group was actually separate asci.

So yeah! That’s ordered tetrad analysis.

Watch this: https://www.youtube.com/watch?v=iz8669bleoM