But what happens to genes that are on the same chromosome? These genes are physically close to one another – they are physically linked, so they kind of have to go together into the same gamete. They are not inherited independently of one another like genes on different chromosomes, so as well as being physically linked they are also said to be genetically linked. In a way, it's a lot like taking a school trip to the museum. You are part of your class and you are "linked" to your classmates. If your class goes first to the dinosaur exhibit, you go with them. Then you go again, as a group, to the watch the 3D show on mammals. At the end of the day, you obviously get on the bus assigned to your class, not the one assigned to the grade above you. That would not be a fun ride - they are not your buddies!
If groups of genes are linked and tend to be inherited together, so are the alleles for these different genes. Let's look at a simple, real life example. In the pea plant, the locus for flower color and the locus for pollen shape are on the same chromosome; they are linked. For flower color, purple (symbolized by P) is dominant to red (symbolized by p). For pollen shape, long pollen (symbolized by L) is dominant to round pollen (symbolized by l) (Russell, 1998). If we cross a true-breeding plant with purple flowers and long pollen (and thus with a PPLL genotype, and producing only "PL" gametes), to a true-breeding plant with red flowers and round pollen (and thus with a ppll genotype and producing only "pl" gametes), we get F1 with purple flowers and long pollen (as both purple flower color and long pollen are dominant). All the F1 have a PpLl genotype.
Now, what would an F2 look like? Let's take a step back for a moment: what if these two characters were located on non-homologous chromosomes (that is, different chromosomes) and the genes for flower color and pollen shape were not linked? What gametes would the F1 generation produce? Just like we did before, let's think of it as a bag of marbles for each locus: a bag for flower color with equal numbers of "P" and "p" marbles, and a bag for pollen shape with equal numbers of "L" and "l" marbles. For each gamete, you blindly draw a marble from each bag. You would expect to see equal number of gametes with "PL", "Pl", "pL", and "pl" genotypes and you would also expect to see the 9:3:3:1 phenotypic ratio we learned about in the Mendelian Genetics section.
So far, so good, but what happens if they ARE linked (i.e. on the same chromosome)? Well, in that case, there's simply a single bag of marbles to deal with. Our bag is now for both flower color AND pollen shape, and each marble has two letters on it. In our bag, we have "PL" and "pl" marbles, so the gametes an F1 produces are only of two kinds: "PL" and "pl", the exact same gametes that the parental strains produced, because in each parental the alleles were linked. So in the F2 we find only 3 possible genotypes and 2 phenotypes:
OK, so that was the basic theory. But you know how it goes, there's always a catch. As it turns out, sometimes -inked alleles can become unlinked –they part ways and get into different gametes. So if we go back to our school trip comparison, you went everywhere with your class as expected, but then you decided your group was getting kind of boring so you rode back on a different bus with a different class. You're not actually physically linked to your classmates, no matter what we said earlier (that would be a bit weird!), so you can easily decide to do your own thing.
But how does a gene, part of a chromosome, go its own way? During meiosis, the process of gamete formation, homologous chromosomes sometimes swap pieces: "I give you my right arm if you give me your right arm" kind of thing. Exchanging of identical fragments between homologous chromosomes is called recombination. This process generates new combinations of previously "linked" alleles. The larger the distance between genes on the same chromosome, the more chance there is that recombination will take place between them.
Let's go back to our pea plants and their linked genes for flower color and pollen shape. Picture a plant heterozygous for both loci, where one chromosome carries a P allele for flower color and an L allele for pollen shape, and the second chromosome carries a p allele for flower color and an l allele for pollen shape. Without recombination, this plant produces only two kinds of alleles: 50% PL and 50% pl, just like we discussed before. If self-fertilized, 75% of the next (F2) generation should have purple flowers and elongated pollen (either PPLL or PpLl) and 25% of them should have red flowers and round pollen (ppll). Now, in reality, because during gamete formation the chromosome pair bearing these genes will sometimes swap pieces, we will also get a small number of plants that combine the different phenotypes in a new way: purple flowers with round pollen, and red flowers with elongated pollen. This is because the recombination that took place during meiosis leads to gametes with new allele combinations (either "Pl", or "pL").
- Did you know that you can use recombination frequency to work out where genes are on a chromosome? By looking at the numbers of recombinant phenotypes compared to the ones you were expecting, you can work out where the genes are in relationship to each other. The unit of measurement for these chromosomal gene maps is called the centiMorgan (cM), named after the geneticist Thomas Hunt Morgan, who worked on linkage using the fruit fly Drosophila melanogaster
- Fruit flies are very important in genetic research, but they are a bit pongy, thanks to the fact that they live on rotting fruit! For more on how Drosophila is used to study heredity, have a look at this article from Catalyst magazine