We have already used the term "linked" to refer to genes located on the sex chromosome. These genes are called "sex-linked." We saw at the beginning of this chapter that, given the large number of genes in an individual and given the limited number of chromosomes present in that individual's cells, each chromosome must carry a large number of genes. When genes are located on the same chromosome, they are said to be linked. In the example above, which uses sickle-cell anemia and galactosemia as a pair of contrasting traits, the genes are on different chromosomes and are thus unlinked.

Gene linkage was elucidated in the laboratory of Thomas Hunt Morgan at Columbia University. As we explained before, Morgan generated many types of mutant fruit flies and crossed them. One cross involved flies with mutant wings, symbolized by r (the normal wing is represented by R), and black body indicated as b (B indicates again the dominant, normal body-color gene). Since mutant wings and black bodies are both recessive, these flies must be homozygous for the trait, and their genotype is thus rrbb. They were crossed with normal flies of genotype RRBB. Remember that normal is dominant over mutant. All the offspring of this cross are double heterozygotes, RrBb, and thus are phenotypically normal. Then, Morgan crossed these double heterozygous offspring. This cross, written RrBb x RrBb, involves two different pairs of traits, equivalent to the example with sickle-cell anemia and galactosemia in humans that we saw above.

Thus, in the offspring of his cross, Morgan should have observed four phenotypic classes: normal wings and body color, normal wings and black bodies, mutant wings with normal body color, and mutant wings with black bodies. Furthermore, these four categories should be produced in 9:3:3:1 proportions (56 percent, 19 percent, 19 percent, 6 percent) following the rule of independent assortment. Morgan did observe four categories, but the numbers of flies in each category were completely off! He observed 74 percent normal, only 1.5 percent each of just mutant wings or just black body, and 22 percent that had both mutant wings and black body. That is, he observed many more totally normal flies as well as flies with mutant wings and black body (rrbb) than expected. Further, he observed extremely low numbers of flies that had normal wings with a black body, or mutant wings with normal body color.

What can account for this gross deviation from the expected proportions of different phenotypes that we expect from the rules of independent assortment? Morgan correctly interpreted these results: he hypothesized that the R and B genes were on the same chromosome from one of the original parents. Similarly, the r and b genes were also located on the same chromosome, this time the one from the other original parent (figure 9.2). It is because the genes Morgan studied were not assorting independently (i.e., were not on different chromosomes) that a 9:3:3:1 ratio was not observed. Genes that do not assort independently must be on the same chromosome; they are linked.

If the two genes are on the same chromosome, figure 9.2 predicts that we should have gotten 75 percent flies with normal body color and normal wings (RRBB or RrBb), and 25 percent flies with mutant wings and black body (rrbb). We should not have gotten any flies that had just black bodies or mutant wings. So, how can we account for the small but significant numbers of flies that had just black bodies or mutant wings? The reason is that chromosomes can break and rejoin and, in the process, shuffle genes. This process is called "recombination."

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