Genetic linkage, and the joint inheritance of traits

So far we have talked about genes whose alleles are inherited independently from one generation to the next. However, if two loci are close on a chromosome, their alleles tend to be inherited together. If they are not extremely close, these alleles will be separated at least some of the time when gametes are formed by ``crossovers'' in the process of meiosis. The end result is called recombination because, while the genes on the chromosome are the same, the specific alleles are not.

For example, let's say that in the pea plant the height and flower-color genes are on the same chromosome. and that red (R) is dominant to white (r), and tall (T) is dominant to short (t). A tall red plant that is that is the F1 hybrid of a cross between a "pure" tall red line (plants RR, TT) and a short white line (plants rr, tt) is heterozygous for flower-color (Rr) and for height (Tt) and has has the following two chromosomal arrangements of these genes:

If no recombination occurs between these two genetic loci, the plant will pass on either the combination RT or the combination rt to an offspring. These non-recombinant types are sometimes know as parental types, since the combination one of the ones received by the plant from its parents.
If recombination occurs, then in the gamete copied to the next generation, the arrangement on the transmitted chromosome would be:
R---------t    or r---------T
A recombination occurs if there are an odd number of crossover events (usually just one) between the two loci. An even number of crossovers (usually 0, maybe 2) would return these genes to their original chromosomal arrangement.

Recombination between two genes on a chromosome happens in meiosis with some probability that is known as the recombination frequency. If the genes are close together on the chromosome, the recombination frequency is very small. If the genes are far apart on a chromosome, or on different chromosomes, the recombination frequency is 50%. In this case, inheritance of alleles at the two loci are independent. If the recombination frequency is less than 50% we say the two loci are linked. Under most models of meiosis, recombination frequencies cannot be larger than 50%.

You can tell if the genes are linked by looking at the offspring. For example, let's say that we breed our above parent with genotype RT/rt to a parent who is rt/rt. If the offspring are white and short, you know the first parent contributed rt. If they are tall and red, you know the first parent contributed RT. If they are red and short, you know the first parent contributed Rt. If they are white and tall, you know the first parent contributed rT.

Suppose, these two plants have 100 offspring, and that 5 are red and short, 10 are white and tall, 40 are red and tall, and 45 are white and short. The red short and white tall plants exist because the first parent's chromosomes underwent recombination. Remember the original forms were RT and rt. 15 of the offspring have phenotypes that could have only resulted from recombination.

Next, you calculate the recombination frequency. This is the proportion of offspring that have genotypes, assuming you can determine them, which exist because of recombination. In this example, the recombination frequency in the sample of 100 offspring is 15/100 = 0.15.