Levels of synteny between rice and maize

Tarchini et al. completely sequenced a 340 kb region surrounding the rice Adh1 and Adh2 loci as the starting point for their analysis of colinearity between rice and maize. The Adh1 region is a logical starting point because it has been the subject of detailed analysis in other crop species. The authors discovered 33 putative genes in the region, including Adh1 and Adh2. Twelve of the genes show similarity to genes of known function, most related to disease resistance. Frequent gene duplications were seen, closely spaced and mostly in the same orientation. Similar duplications have been found in Arabidopsis and suggest that gene duplication events are a common occurrence in plant genome evolution. Almost 30% of the region comprises repetitive elements, including retrotransposons, transposons, miniature inverted-repeat transposable elements, and simple-sequence repeats. Thirteen of the loci in the region were tested for their ability to cross-hybridize with maize genomic DNA. Only five genes hybridized well, and only three of those showed useful polymorphisms in the maize mapping populations tested. The authors' results indicate microcolinearity between the Adh1-Adh2 region on rice chromosome 11 and the Adh2 region on maize chromosome 4. Data from other labs have shown that the maize Adh1 gene is on maize chromosome 1, indicating that at some point after the duplication event that created Adh1 and Adh2, a translocation occurred in maize (and sorghum), placing the two Adh genes in these species on different chromosomes. The limited success of Tarchini et al. with cross-hybridization of rice genes with maize genomic DNA, as well as gene duplications, divergent selection and micro- and macro-translocation events in the grasses generally, suggest that there will be complications in using rice to facilitate map-based cloning in maize. There appear to be blocks of microcolinearity, interspersed with unrelated genes and repetitive elements. These results agree with those of