Crossing Over and Recombinants: Videos & Practice Problems

Understanding gamete formation is crucial for grasping genetic mapping. Mendel's Law of Independent Assortment states that alleles of two genes assort independently, leading to distinct gamete genotypes. However, when genes are linked on the same chromosome, they are inherited together unless crossing over occurs, resulting in recombinant gametes. Key experiments by McClintock and Morgan demonstrated crossing over, revealing the significance of recombination frequency in determining gene distances on chromosomes, which is essential for genetic mapping and understanding inheritance patterns.

Gamete Genotypes

We're first going to focus on gamete formation. And this is super important, because people get really confused with mapping and gametes, and what the genotypes of the gametes are. And it's crucial, because if you don't understand the genotypes of the gametes, you're not going to understand anything about mapping. So we're going to go through this very slowly in the beginning. So first, we're going to talk about independent assortment. Now, we've talked about this and you've actually seen this before in a different chapter when we talked about independent assortment. But I want to refresh it here, so that when we go on and talk about crossing over and mapping, you understand how it's different. So Mendel's Law of Independent Assortment says the alleles of 2 genes assort independently. So what that looks like is here. We're looking at these 2 genes, a and b. There's 2 alleles for each of them, and they create certain phenotypes. So if I were to ask you what are the genotypes of the gametes, you hopefully can fill this out. Because this is normal Mendelian inheritance. So take a second, fill out what are the genotypes of the gametes, and then you can come back, press play again, and see if your answers are correct. They should be, hopefully.

So, if we're determining the genotypes of the gametes, you're going to take one of each allele, so a big A, a little a, and you need to repeat it because there are 4. Then you make the other combinations with the b. You do big B, little b, little b, big B. And this gets you 4 gametes and these are the genotypes. Right? And eventually, when they create an organism, they'll combine with other gametes, and then be dihybrid again. But for now, they're haploid, because they contain one allele for each gene, a and b. Now, this is independent assortment. So we're saying that these genes assort independently, so they are not on the same chromosome. But what happens if these 2 a and b genes are on the same chromosome? They're physically linked and but they still have to be sorted in the gamete. So what do you get? Well, first, you can see this looks different. Right? So each one of these lines is representing a chromosome. Remember, they come in pairs. So here you have your dominant allele and recessive allele on the different chromosomes, and your dominant for b. Now you're never gonna see this like this. Why? Why is this wrong? You know? Right. The reason is that this is not heterozygous. These are if you write it like this, you're saying that these are 2 different genes. Instead, the other allele must be written over here because this is on its homologous pair. This is not. This is a separate gene location on the same chromosome. Homologous pairs are written on different chromosomes. So here, we have it written like this, a and b. Now, you'll notice that, before, remember an independent assortment, we wrote it like this. Well, when we know that things are linked, we write it differently. Right? So this is a a−b and a−b, and this is representing different homologous chromosomes. The dash. So, it's a little different notation, but you do need to understand this notation. And then it's something you cannot just blow off because if you get asked a question, and you need to know if it's written like this or like this, because this represents 2 different things. This represents independent assortment and this represents linkage. But the question is now, what are the genotypes of the gametes?

Okay. So now we're talking about dividing the chromosome. So what we get is we get the 1st chromosome, and it has a and b. And we get the 2nd chromosome, and it has a and b. Now, because these are linked they're physically linked what are the other 2 gametes? Now, they would be a and b a and b. This is if no crossing over is occurring. We'll get the crossing over in the next example. Right? So these are very different gametes than what you saw above. Right? Because the genotypes are these, is this. You have 2 genotypes and they're just repeated again for the other 2. So this is if 2 genes are on the same chromosome. And the reason that it's like this, right, is because the full chromosome goes into the daughter cell. They don't split and cut up the genes. The entire chromosome has to go. So these two alleles are linked together. They have to be sorted into these gametes this way. But we know that crossing over occurs, and crossing over results in different gametes. And the reason is that homologous chromosomes break and rejoin. So notice here, that the genotype and the notation is written exactly the same as above. The only thing that's different is I made this one red, and this one blue. So let's follow what happens now if there's crossing over. So crossing over can occur here. Right? And switch these around. So what happens is you get 2 genotypes which are normal. You get the a, b, and the a, b, which is what you're expecting. Right? Actually, it's, let me write this correctly. You're not gonna care, but I don't wanna lead you astray. So, it's written like that. Right? It suggests there are 2 separate chromosomes. But crossing over can occur and what you get is you get a connected to b and you get a connected with b. And so now you have 4 genotypes. You have the a b, you have the uppercase a and little b, and the lowercase a and big b. Now this looks similar to independent assortment. Right? I mean, it looks exactly the same as independent assortment. Right? The genotypes are exactly the same. But what's different here is the independent assortment, these are 2 chromosomes. Clearly, 2 different chromosomes where this is the result of crossing over. Now, you may ask yourself, okay, if I'm just given the gametes, I know the genotypes, but I know nothing else about the problem, How do I tell if it's crossing over or independent assortment? Well, I'm going to explain it, but how you know is by your ratios. And I'm going to go through the ratios. So normal independent assortment with 2 genes is going to have an f two ratio of 9 to 3 to 3 to 1. But you're gonna see is that if it's crossing over, it's not going to be this ratio. It's going to be very different. So, with that, let's now move on.

Discovery of Crossing Over

Okay. So now let's talk about the discovery of crossing over. I can very easily, you know, explain crossing over to you, because there are textbooks on this. We know and have known for a while that this concept exists. But if we go back way back when, they had no idea that this existed. So, I want to go through two important experiments that really confirmed to the scientific community that crossing over was a thing that happened. And because it's kind of weird. Right? You don't expect chromosomes to just kind of break off a piece of themselves and be like, hey, you can have this part of me, and I'll take your part, and we'll be all good. It's kind of an unusual thing. So it's actually brilliant how these scientists figured out that this happened. So the first study I want to talk about is between McClintock and Creighton, and they studied corn. And so what they did is they had a corn, and it was heterozygous for color, which here you can see, and starch. And the starch is dominant, so this is the allele for this. So the chromosomes for this plant were this. You have one chromosome here, you have the second one here. You can see that you have heterozygous for color and heterozygous for starch, but you can see that the dominant alleles are on different chromosomes. The c allele is here, and the starchy dominant allele is on a different chromosome. Now the reason that they did this is in order to be able to look at crossing over. So if they didn't do this, they would not be able to look at crossing over at all, because it would just look exactly; you wouldn't be able to tell. So they did this so that you could easily tell crossing over. Now, they also added a very interesting component onto these chromosomes. So on chromosome number 1, it had two special markers. It had this thing they call the knob, which I'm representing with this circle. And they had a piece of foreign chromosome, which they had translocated, meaning that they had just, like, broken it off and attached it from another chromosome, on the other end. And they used these markers to be able to follow crossing over. Right? Because if this segment crosses to this end, it's going to take the knob with it. Whereas if this segment crosses over, it's going to take this foreign chromosome with it and they can actually visualize it under a microscope. So what they did is they mated their chromosomes, or their organisms, this one here, with a colorless starchy plant, which is here. So what they found is that the offspring, some of them looked parental. So what do I mean by that? Well, it looked like this. It was heterozygous or it was dominant for color and starch. But some of them were recombinant, which means that it wasn't heterozygous dominant. It was heterozygous dominant for color, but homozygous recessive for starch. And that was very odd. Not necessarily how it's supposed to be. And so recombinants mean that it's a mixing between the two parents. And you can talk about recombinant genotypes and you can talk about recombinant phenotypes. But essentially, if you have a red tall plant and you mate it with a red short plant, then it's going to be recombinant if you mix those two together if you get short and red. So those are recombinant genotypes or phenotypes. Now, chromosomal markers were able to identify the recombinants because when they had crossed over, either the knob or the foreign chromosome came with them. So let's look at this. So here, this is what we started with. Right? This is the cross that we did, here we have our knob and our chromosome, and here's our mate. And so this is the offspring down here. And what you can see is that crossing over occurred because now you have a chromosome that has the foreign piece but no knob, and you have a chromosome that has the knob but no foreign piece. And they are also recombinant. Right? They don't neither one of these look like the parents. So here you have the here you have a colorless waxy, and this one was colored starchy. And here you have colored, colorless starchy, which actually did look like this. But this one didn't have the knob and this one did. So it actually looked different from the parenteral. So these are the recombinant types here. So this is a really important study, and you probably will be asked about this study in some way. But the important parts of this study are using these chromosomal markers, the knob and the foreign chromosome piece, in order to be able to identify that the chromosomes crossed over, they switched out parts of each other at some point during the development of these gametes. So with that, let's now turn the page.

Morgan's Studies of Crossing Over

Okay. The second major study that I identified crossing over and linked chromosomes was done by Thomas Hunt Morgan and his student, Alfred. Now, this is a super important study. You'll all be asked questions about this, so make sure you understand how they set up this experiment. They studied fruit flies, Drosophila, and these fruit flies had two traits, eye color and wing length. The eye color was red if it had the wild type marker, represented as p⁺, and it was purple if it was the mutant, represented as pp (without the plus sign). For wings, it was long if it had the vestigial plus sign (vg⁺), but short if it was vg (without the plus sign). This is short for vestigial, and it just means short wings, essentially. So they did crosses. The parental types were homozygous wild type for both eye color and wing for one. And they were homozygous mutant for both eye color and wing for the other. This was wild type and this was completely mutant.

Now, when talking about gametes from this cross, parent number 1 provides a wild type p and a wild type vg. On the other hand, parent number 2 can only provide the mutant versions. When these two mate, they produce the F₁ generation, which is heterozygous for both traits.

Next, they conducted a test cross with the F₁ generation crossed through a tester that is homozygous recessive for the mutant traits. From this test cross, Thomas Hunt Morgan and his student Alfred, following Mendel's laws, used Punnett squares and the branch method to predict expected ratios. They expected an outcome where half the offspring would show one phenotype, and the other half would show another, resulting in a 1:1:1:1 ratio of different phenotypic combinations according to the Punnett square results. However, they encountered unexpected results: 1339, 1195, 151, 154. These numbers were nowhere near a 1:1:1:1 ratio, prompting a deeper analysis.

They classified the outcomes into parental and recombinant types. Parental types resembled either parent entirely, while recombinant types were a mixture of traits from both parents. Surprisingly, the recombinant types appeared less frequently than expected, with a calculated frequency of 10.7%, significantly lower than the expected 50%. This led to the conclusion that the two genes were located on the same chromosome, which reduced the frequency of recombinant types due to fewer crossing over events. This discovery was crucial as it suggested that genes linked on the same chromosome do not assort independently and gave rise to the concept of recombination frequency as a measure for the distance between genes, quantified here as 10.7 map units on the chromosome.

This study was pivotal not only in confirming the occurrence of crossing over but in introducing the method of using recombination frequencies to estimate distances for gene mapping, which has significant implications in genetic studies. More experiments and detailed analyses in future projects are needed to refine the understanding and use of recombination frequencies in genetic mapping. Now, let's turn the page.

Crossing Over Terminology

Okay. So now let's talk about crossing over terminology. This is super important because when you're reading these word problems or you have questions on tests or whatever, they're going to be using special terminology to talk about, you know, which chromosomes and how things are interacting and crossing over. And you have to be able to understand the terminology to understand what's actually happening. So, you're going to have to memorize these words. But, hopefully, you know some of them already from previous classes, but crossing over occurs between two chromatids. Do you remember what a chromatid is? Well, chromatid, so tin, is going to be DNA plus protein. Chromatids are essentially just a single copy of one of the chromosomes. Okay? So, like I said, it occurs between two chromatids. Now you have sister chromatids and non-sister chromatids. And the difference is that sister chromatids are two copies of the same chromosome. Non-sister copies are copies, but they're not of the same chromosome; they're of the homologous pair. Right? So if we have two chromosomes, here they are. During meiosis, what happens is that they get replicated. Actually, let me draw these different colors and go back. So we have this chromosome and this chromosome, and these are called what? Homologous, I'm not going to write it out, but they're homologous pairs. Now, during meiosis, they get replicated. Sister chromatids of these, you can tell because they're the same color, whereas non-sister chromatids are going to be these. They're from the same original homologous pair, and they're both copies, but the non-sister chromatids are of the different homologous pairs, while the sister chromatids are of the same homologous pair of the same chromosome. So this is important. Now crossing over typically occurs in these non-sister chromatids because they're different chromosomes, you know, they're from the same pair but essentially different, but it can happen in sister chromatids as well. But generally when we're talking about crossing over, we're talking about non-sister chromatids. Now during meiosis, longest pairs line up and undergo crossing over. Now when I talk about lining up of chromosomes, what I'm talking about is actually the full four chromosomes that I showed before. So the replicated versions, they line up like this in the middle. So if I have another pair here, they're lined up in the middle of the cell during metaphase. Remember? Sort of refreshing your memory on meiosis, mitosis? Yeah. It'll come back. So, there are different terms to describe this. So these four here are called a tetrad. Dyads are pairs of two chromosomes or two chromatids. So that could be these two, could be a pair of sister or it could be a pair of non-sister. These are dyads. Generally, it'll work for is it a non-sister dyad or a sister dyad? Bivalent refers to the pair of homologous chromosomes. Right? So remember that these are two copies. So here we have, here we have the homologous pair. Bivalent refers to the pair. So here, this whole thing, when it pairs chiasmata. And thing. And then, chiasmata, and this is a structure that forms between two dyads, remember pair two chromosomes, or chromatids, are crossing over. Usually between non-sister, but can also happen between sister. So although I'm pretty sure this is a different language, chiasmata are here. So they are written here. So you can see that this, is a point where crossing over is occurring and here's another one, crossing over. So that's chiasmata. Now this is super important, here's another example of crossing over, you start with these chromosomes, crossing over happens, and you get the mixture that shows up. But, knowing these terms is super super super super super important. Now linked genes, remember genes on the same chromosome, also have certain terminologies. There's the cis conformation, and that means the dominant alleles of two genes are on the same chromosome. So if we're writing it like this, it would look like this. If we're writing it with the chromosomes, it's going to look like this, because the dominant alleles are on the same chromosome. The trans conformation, you can imagine, is exactly opposite. It means two different alleles or two genes are on the same chromosome. So you can write it like this, or if I'm writing this, it's going to look like this. So here you have a dominant and a recessive. And these are two different alleles, but they're on the same chromosome. This is cis, and this is trans. And again, I've mentioned this before, but linked genes are written differently. You can see it here. So instead of writing it like this, b, you write it like this. And this is because the alleles on the same homologue have no punctuation between them. And so, you can see this here, ab instead of, back up, ab. The slash is going to separate homologs, so it's going to look like this, ab, to represent this one up here, or if I wanted to do this one, it would be ab. That's ab, because this slash represents that they're on different chromosomes. And if linkage is unknown, which some of your questions will be, right, like, they're going to ask you they'll give you a bunch of information and ask, are these genes linked? They're not going to write it like this because that'll tell you for sure that they're linked. So what you're going to see is you're going to see a lot of this and especially this dot. This dot is used a lot to differentiate different genotypes if it's unknown if they're linked. So if you're answering a question saying, are these genes linked? Oftentimes, you're going to see it written like this with this dot. So understand the different ways to write things because you're going to be getting a lot of questions asked, you know, is it linked? Is it not? Is it independent assortment? Is it not? You know, is it all these different things or not? And each one of them is written differently. And so that can not only impact how you do the problem and understanding, you know, what you're starting with, but it also can impact your answer choice. Right? Because if you have an answer choice and one of them is written with linkage and one of them is written without, if you know for a fact is linkage, then that can help you figure out that problem. So, with that, let's now move on.

Which of the following gametes can be formed from the genotype AaBb if AB and ab are linked?

• A. AB, ab
• B. Ab, aB
• C. Aa, Bb

Answer: (A)

An experiment that was performed found the recombination frequency between two genes was 12.5%. What is the distance (in mapping units) between two genes?

• A. 25
• B. 6.25
• C. 12.5
• D. 10

Answer: (C)

Which of the following terms describes two copies of the same chromosome?

• A. Non-sister chromatids
• B. Sister-chromatids
• C. Bivalent
• D. Dyads

Answer: (B)

Here’s what students ask on this topic:

What is the significance of crossing over in genetic mapping?

Crossing over is crucial in genetic mapping because it allows for the exchange of genetic material between homologous chromosomes, leading to recombinant gametes. This process helps determine the distance between genes on a chromosome. The frequency of recombination events between two genes is directly proportional to the distance separating them. By analyzing recombination frequencies, geneticists can create linkage maps that show the relative positions of genes on a chromosome. This information is essential for understanding inheritance patterns and for identifying the genetic basis of traits and diseases.

How do you calculate recombination frequency?

Recombination frequency is calculated by dividing the number of recombinant offspring by the total number of offspring and then multiplying by 100 to get a percentage. The formula is:

$\frac{\mathrm{Number\; of\; Recombinants}}{\mathrm{Total\; Number\; of\; Offspring}}\times 100$

This percentage represents the recombination frequency, which can be used to estimate the distance between two genes on a chromosome. One map unit (or centimorgan) corresponds to a 1% recombination frequency.

What are the differences between independent assortment and crossing over?

Independent assortment and crossing over are both mechanisms that increase genetic diversity, but they operate differently. Independent assortment occurs during metaphase I of meiosis, where homologous chromosome pairs align randomly, leading to the independent segregation of alleles. This results in a 9:3:3:1 phenotypic ratio in a dihybrid cross. Crossing over, on the other hand, involves the physical exchange of chromosome segments between non-sister chromatids during prophase I of meiosis. This creates recombinant chromosomes with new allele combinations, which can be identified by deviations from the expected 9:3:3:1 ratio.

What was the contribution of McClintock and Creighton to the understanding of crossing over?

McClintock and Creighton conducted pioneering experiments on corn that provided direct evidence for crossing over. They used chromosomal markers, such as a knob and a translocated segment, to track the exchange of genetic material between homologous chromosomes. By analyzing the offspring, they observed recombinant phenotypes that differed from the parental types, confirming that crossing over had occurred. Their work demonstrated that chromosomes physically break and rejoin, exchanging genetic material, which was a significant advancement in understanding genetic recombination and inheritance.

How did Thomas Hunt Morgan's experiments with fruit flies contribute to genetic mapping?

Thomas Hunt Morgan's experiments with fruit flies (Drosophila melanogaster) were pivotal in establishing the concept of genetic linkage and mapping. By crossing flies with different traits for eye color and wing length, Morgan observed that certain traits did not assort independently, as predicted by Mendel's laws. Instead, they were inherited together, indicating that the genes were linked on the same chromosome. Morgan and his student Alfred Sturtevant used recombination frequencies to calculate the distances between genes, creating the first genetic linkage maps. This work laid the foundation for modern genetic mapping techniques.