Helitrons contribute to the lack of gene colinearity observed in modern maize inbreds

Until recently, it was assumed that the order of gene sequences within modern maize would be virtually invariant. Recent discoveries have shown that gene colinearity is not always the case. Several laboratories (1-3) have found DNA regions rich in gene sequences that are present in some maize inbred lines but absent at homologous sites in other lines. This variation, termed “intraspecific violation of genetic colinearity” or “plus/minus genetic polymorphism,” was shown by Lai et al. (4) in a recent issue of PNAS to be caused by a newly described transposable element family termed Helitrons.

Lai et al. (4) revisited the 110-kb region of chromosome 9, which contains a number of genes, most notably the well characterized bronze-1 locus. Earlier work by this group (1) showed that whereas the inbred McC (for McClintock) contained sequences of 10 genes in this region, only 6 of these genes were present in this region in B73, the model inbred chosen for complete DNA sequencing. In addition, hybridization experiments showed that other lines exhibited plus/minus polymorphisms for these four gene sequences that were different from McC or B73.

Lai et al. (4) showed that the presence of two Helitrons in McC and their absence in B73 totally accounts for the plus/minus variation of these four gene sequences. One Helitron, termed HelA, is 5.9 kb and contains three of the four polymorphic gene sequences described earlier (1). A second Helitron, HelB, is 2.7 kb and contains the fourth gene sequence distinguishing McC and B73. Sites of insertion of the two elements are separated by only 900 bp. A second, virtually identical copy of HelA was also found in the genome, albeit on a different chromosome. This second …