complex genomes. It is possible that most genes in most plant genomes reside in duplicated chromosomal regions.
Repetitive DNA constitutes a high proportion of plant genomes. This fact has been confirmed experimentally by reassociation (or C0t) kinetics. For example, Flavell et al. (1974) found that repetitive DNA (defined, in this case, as DNA with more than 100 copies per genome) constitutes ≈80% of genomes with a haploid DNA content >5 pg. In contrast, small genomes of <5 pg contain 62% repetitive DNA on average. Maize falls into this range; reassociation experiments indicate that the genome contains from 60% to 80% repetitive DNA (Flavell et al., 1974; Hake and Walbot, 1980). The repetitive DNA of maize can be categorized further as 20% highly repetitive (over 800,000 copies per genome) and 40% middle repetitive (over 1,000 copies per genome; Hake and Walbot, 1980).
It is obvious that repetitive DNA is a large component of the maize genome, and thus the proliferation of repeat sequences has had important evolutionary implications. However, reassociation studies alone cannot answer two important questions about repetitive DNA in maize: what is the repetitive DNA, and when did it arise?
To date, the most complete answers to these two questions come from studies of the maize Adh1 region by Bennetzen and coworkers (SanMiguel et al., 1996, 1998; Springer et al., 1994; Tikhonov et al., 1999). They isolated a 280-kilobase yeast artificial chromosome clone of the Adh1 region and characterized the composition of the repetitive intergenic DNA. Retrotransposons comprise roughly 62% of the 240 kilobases analyzed, with an additional 6% of the clone consisting of miniature inverted-repeat transposable elements, remnants of DNA transposons, and other low-copy repeats. In total, the region contained 23 retrotransposons representing 10 distinct families. Of the 23 retroelements, 10 inserted within another element, resulting in a nested or “layered” structure of intergenic DNA within maize (Fig. 3). The architecture of this region suggests that retrotransposons preferentially target other retroelements for insertion.
Perhaps the most interesting feature of the Adh1 region is that it seems to be a representative region of the maize genome. Three observations support this contention. First, Southern blot and other analyses suggest that the retrotransposon families in the Adh1 region comprise at least 50% of the maize genome; altogether, just three of the retroelement families found in the Adh1 region constitute a full 25% of the genome (SanMiguel et al., 1996). Second, 85% of repetitive DNAs from other regions were also