Why is it possible for two genes on the same chromosome to behave independently as if they are not linked?

Gregor Mendel's law of independent assortment states that when genes are inherited, they are inherited independent of each other. Linked genes are exceptions to the law of independent assortment because two genes are located on the same chromosome, but this is generally mitigated when chromosomes cross over.

One of the basic principles of inheritance or genetics is the law of independent assortment otherwise known as Mendel's second law. And this is the idea that the inheritance of one trait does not influence the ihnheritance of another. i.e. they are sort to the gametes independent of each other. Now this is caused by the way that the genes get shuffled and your chromosomes randomly assort themselves during the process known as meiosis which is the creation of gametes. Now I'm going to be talking about a couple of different alleles or genes in this context. One of them that I'll refer to is the ability to roll your tongue or the inability to roll your tongue. Tongue rolling is a dominant allele, non-rolling is a recessive allele. There's another gene for earlobe shape. The dominant version or allele is the free or detached earlobe shape while the recessive allele creates a not attached earlobe. So if we're talking about somebody who is homozygous sorry, heterozygous for both traits, they're big e little e and they cross with somebody who's also big e little e and big r little r. Let me put that little r in there, good. What you do is instead of using the smaller punnett square that you're familiar with, you wind up using the larger punnett square that has 16 boxes. Now this person I'm going to put their gametes on the left hand side. The second person I'll put across the top.So this person can give every gamete one of their two r alleles. So they'll give him the big r and they'll give them the big e. Similarly they could give the exact same big r only in combination with the little e. The big e and little sorry, the big r and the big e do not have to travel together. They can be separate. You can have the little r go with the big e or you can have the little r go with the little e. This person, with the identical genotype can also produce a big r and a big e. Big r little e, a little r big e or a little r little e. With me so far? Great.So now that I have my gametes on the outside, I start creating my offspring on the inside. So this sperm swims to meet that egg and I get a big r big r, and I get a big e big e. So, that's how I'd fill this out. Now, I can spend a lot of time filling out all 16 of these but let's just skip to the end and see what it would look like.So here we have a completed punnett square demonstrating the effects of Mendel's second law, the law of independent assortment. And we can see we get this broad array of different kinds of offspring. Now I've color coded them to make them easier to figure out what their phenotypes are. You'll notice all these guys here are red. That represents individuals or offspring who are dominant for both traits. And if we count it up we'll see that the rollers with the detached earlobe shape, people who look like myself would be nine out of these 16 offspring. Those who are rollers they can roll their tongue they've got the attached earlobe shape, they would be three of our 16 offspring. We'd have an identical amount of non-rollers but with detached earlobes and we'd have one out of our 16 offspring would be non-roller attached earlobe shapes. So that's how the law of independent assortment plays out when you're talking about punnett squares and what effects you get with inheritance but a lot of times teachers like to ask you to not just to know how to use it but they want you to know why it works. And that goes back again to the process of meiosis where you have one cell create 4 possible gametes. Now I could go through this and talk about homologous chromosomes but I found that a lot of times it's just simpler to use shoes because much like the homologous chromosomes, they too come in pairs. So I'm going to use these black men's dress shoes to represent the chromosome pair the homologous chromosome pair that carries the big e allele and the little e allele. I'm going to use the white sneakers to represent the big r and little r carrying chromosomes. So these are homologous shoes very similar, not identical. This is a right, this is a left and these are homologous shoes. Not identical. One's a left, one's a right and they carry different versions of the same gene. This one keeps trying to go for a chromosomal mutation, a deletion of the little e allele. So, when you undergo meiosis metaphase 1 of meiosis, let me raise these up, we could have these two line up on the same side, these two line up on the other side. And when they separate from their gametes, I've lined up with one gamete that has the combination little e and big r and I'll have another one that has the combination little r big e. But how these shoes line up has no influence on how those shoes line up. So I could have done it like this. Let me swap this over. And now, here we go.

Here, when I wind up creating this gamete I get the big r big e together in one gamete. Here I get the little r and little e in one gamete. Each outcome is equally probable. So there's no influence that the black shoes have on the white shoes. They're independent of each other. That's the law of independent assortment.

When two genes are located on the same chromosome they are called linked genes because they tend to be inherited together. They are an exception to Mendel's law of Segregation because these genes are not inherited independently. When chromosomes cross over, two different chromosomes trade pieces of genetic information during prophase I of meiosis. If the linked genes are far apart on the chromosome, it is more likely that crossing over will separate them.

When my students start trying to study linked genes initially they get kind of confused but when you first after you get past that first confusion and you start to learn what it really is it's actually pretty simple concept. The Human Genome Project has determined that humans have somewhere in the range of about 25,000 genes now if we only have 23 different kinds of chromosomes that tells you could do the same simple Math that we have roughly a 1000 genes plus or minus a bit on average per chromosomes so linked genes is simply the idea that if you have two genes on the same chromosomes, when that chromosome goes into a sperm or an egg those two genes travel together and windup being inherited together so they are "linked." This would violate Mendel's second law, the law of independent Assortment, but luckily there's this process during meiosis during the first step called prophase I that does this process called crossing over where physically a chromosome will break and exchange parts with its homologous pair so that even though two genes were right next to each other, maybe they get swapped over so your mum's version of a particular allele will get swapped over to the DNA that originally came from your dad and vice versa so that all of your children don't look the same.Now, one thing about this is that genes that are far apart on the chromosome they tend to get crossed over very easily because they have lots of room for those breaks and exchanges to occur but if they're right smacked up next to each other it's very unlikely that you'll get the crossing over even between them so they tend to be inherited together. A lot of genetic test where they test your DNA to see if you have a particular disease or a chance for a particular disease, they're not actually testing for that gene they're actually testing for a linked gene that they found tends to be passed on along with the disease because they are still trying to figure out where exactly the disease gene is, so let's take a look at this and see how it works. Now, here is a standard Mendelian example here we have somebody's homozygote recessive for two genes the r gene and the e gene I don't really care in this context what they stand for and this person is having a crossing event with somebody who is big R little r big E little e heterozygotes for both traits. Now this person can only create one possible kind of gamete, a gamete sperm or egg, that has little r and little e in it, this person on the other hand through the process of meiosis can create four possible gametes for example here is their chromosomes with the big R's and the larger I'm sorry the r gene is on the larger chromosomes the e gene is on the smaller chromosomes and if they are aligned this way when these separate we windup getting our r's and our e's like this. Now that was with the big r's and big e's together on one side. What if they work the other way? What if the big e happens to be on that side? On the opposite side from the big r what that means happens is that when they separate I windup creating a different possible combination than with the earlier combo, so what I'm going to do is I'm going to create for you here the four possible gametes that this one individual could create so they could make the big r little e that we see right here, they could see the big r big e version that's right here we could create a little r little e right here and our last one our little r big e right there and so when we do this cross when we have these two individuals have their offspring we would expect 25% would be this way 25, 25 and 25 so we'd have equal distributions of our genotypes and phenotypes make sense?Alright, let's take a look at what happens when they're not on different chromosomes when instead the r and the e are on the same chromosome so here I have again same individuals same genotype but now the little r and little e are on physically the same piece of paper or DNA molecule similarly over here we have them together on the same DNA molecule so now when they pair up yes the red one could be on my left or on the right or can swap around it doesn't matter however they windup only creating two kinds of gametes what we see here alright? So we have only our big r big e gametes being formed these guys here absolutely none of the big r little e, fail, we have some little r's little e's right here but none of our little r big e's so 50% of our offspring will be this way 50% that way.Now what's their crossing over stuff well let's put them back you recall meiosis during prophase I, the homologous chromosomes come together and then randomly they get broken by enzymes and then other enzymes specifically the enzyme used in your cells is an enzyme called ligase in this case I call it the enzyme tape and so they cross over like that and we windup getting this being formed and this being formed and this being formed, and our tape is running out too bad so sad, this being formed but wait even though these two chromosomes are now different from those the crossing over didn't occur between my r's and my e's so my eventual outcome winds-up being the same and that's because these guys are so close to each other. What if they were further apart? Let's take a look at that, here I have again two chromosomes again the r's and the e's are together on the same chromosome but now there's much further distance between them which gives, if I make the break at roughly the same spot there's a greater chance that the crossing over can occur so now I make the break at roughly the spot and now when I separate them I wind up going back to having something approaching a quarter or a quarter or a quarter so now I do start to see these sets of offspring when I do the breeding now it may not be 25, 25, 25, 25 percent it maybe 15% and 15% of this and then hmm let's see of 40 oh sorry, let me do my Math, 35 and 35% there but again we've de-linked them because of this crossing over event so that's linked genes.