Exceptional haplotype variation in maize

Comparative mapping of plant genomes has shown extensive conservation of gene content and gene order along the chromosomes, especially among the grasses, including maize, rice, sorghum, and wheat (1). This overall genomic colinearity at the recombinational map level has indicated that a few major chromosomal rearrangements have differentiated individual lineages of grasses. The comparative maps have assisted in the identification of truly orthologous loci, that is, those that are directly derived from the same ancestral gene in the last common ancestor of the investigated species. However, the first comparative sequence analyses of these orthologous regions in sorghum versus rice (2), maize versus sorghum (3), barley versus rice (4), or wheat versus barley (5, 6) have shown many small chromosomal rearrangements that involve genes, including inversions, duplications, and deletions. Hence, it appears that small rearrangements have outnumbered events that could be detected by recombinational mapping by more than 1,000-fold (7). The mechanisms, rates, and biological significance of these microrearrangements have not yet been investigated in any comparison, partly because the compared species have not been more closely related than wheat and barley, whose ancestors diverged 10–15 million years ago. In the first sequence-based investigation of the same genomic region in two different maize inbreds, Fu and Dooner (8) report in this issue of PNAS that much of the variation observed between species can also be found within the maize germplasm itself. Moreover, their results force us to rethink our general assumptions about the nature of intraspecies allelic variation.

For many years, the Dooner laboratory has used the bronze1 (bz1) locus of maize as a site for very basic studies of transposable element function and meiotic recombination (9, 10) (Fig. 1). In all of these experiments, the observed genetic phenomena could not be interpreted relative to local genome structure, because …