Potential examples of allelic variation in maize. A hypothetical small chromosomal region is diagrammed for B73 and Mo17. The genes (red) are separated by clusters of transposons (black) and several different classes of retrotransposons (various shades of green). There are likely to be numerous SNPs and small indels within this region. The composition of repetitive sequences also shows significant variation between the two inbreds. The specific location of a causative change that has resulted in functional allelic variation is indicated by the yellow lightening bolts. Gene A is an example of a variant in which the proteins are different. Gene B is a nonshared sequence that is only present in B73 at this locus. Gene C is more highly expressed in Mo17 than in B73 because of differences in the repetitive elements surrounding this gene in B73 and Mo17. Gene D is expressed only in B73 and not in Mo17 because of altered sequence in nearby regulatory regions. Gene E shows no functional variation in B73 relative to Mo17.
