McClintock worked with what is known as the Ac/Ds system in maize, which she discovered by conducting standard genetic breeding experiments with an unusual phenotype. Through these experiments, McClintock recognized that breakage occurred at specific sites on maize chromosomes. Indeed, the first transposable element she discovered was a site of chromosome breakage, aptly named "dissociation" (Ds). Although McClintock eventually found that some TEs can "jump" autonomously, she initially noted that the movements of Ds are regulated by an autonomous element called "activator" (Ac), which can also promote its own transposition.

Of course, these discoveries were preceded by extensive breeding experimentation. It was known at the time from previous work by Rollins A. Emerson, another American maize geneticist and the "rediscoverer" of Mendel's laws of inheritance, that maize had genes encoding variegated, or multicolored, kernels; these kernels were described as colorless (although they were actually white or yellow), except for spots or streaks of purple or brown (Figure 2). Emerson had proposed that the variegated streaking was due to an "unstable mutation," or a mutation for the colorless phenotype that would sometimes revert back to its wild-type variant and result in an area of color. However, he couldn't explain why or how this occurred. As McClintock discovered, the unstable mutation Emerson puzzled over was actually a four-gene system, as outlined in Table 1.

Table 1: Maize Genes Studied by Barbara McClintock

Gene Description C' Dominant allele on the short arm of chromosome 9 that prevents color from being expressed in the aleurone layer of the maize kernel, causing a so-called "colorless" phenotype (which is actually white or yellow in color). This is also known as the inhibitor allele. C Recessive allele on the short arm of chromosome 9 that leads to color development. Bz Dominant allele on the short arm of chromosome 9 that leads to a purple phenotype. bz Recessive allele on the short arm of chromosome 9 that leads to a dark brown phenotype. Ds Genetic location on the short arm of chromosome 9 at which chromosomal breakage occurs. As A factor of unknown location (at least when McClintock was conducting her research) that impacts the expression of Ds.

Adapted from McClean, 1997

In her experiments, McClintock bred females that were homozygous for C and bz and that lacked Ds (denoted CCbzbz--, where the dashes indicate the absence of Ds alleles) with males that were homozygous for C', Bz, and Ds (denoted C'C'BzBzDsDs) to yield heterozygotes with an aleurone layer that had the genotype C'CCBzbzbz--Ds. (Remember, in double fertilization, the sperm provides one set of alleles, and the egg provides two.) Because of the presence of the dominant inhibitor allele C', the offspring kernels were expected to be colorless, no matter what their genetic makeup at the Bz/bz locus. In fact, upon crossbreeding, many of these kernels were indeed colorless. However, McClintock also observed many kernels with colorless backgrounds and varying amounts of dark brown spots or streaks, and she concluded that individual cells in those kernels had lost their C' and Bz alleles because of a chromosomal break at the Ds locus. Without either the C' allele (to prevent color expression) or the Bz (purple) allele, the cells that had experienced a breakage at the Ds locus ended up with some brown coloring.

Within the affected seeds, the amount of colored streaking or spotting depended upon when during seed development the somatic cell mutation at Ds occurred. If this mutation occurred early in development, then, as the one mutant cell continued to divide, more cells in the mature kernel would have the brownish phenotype, and the spot or streak of color on the kernel would be larger. On the other hand, if the mutation occurred later in development, the spotting would be smaller, because the kernel would undergo less cell division prior to maturity.